Multiple sequence alignment - TraesCS7A01G178000

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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 TraesCS7A01G178000 chr7A 100.000 4177 0 0 1 4177 131836178 131832002 0.000000e+00 7714
1 TraesCS7A01G178000 chr7D 91.638 3480 150 55 690 4110 133227135 133223738 0.000000e+00 4684
2 TraesCS7A01G178000 chr7D 93.495 661 20 11 1 660 133227772 133227134 0.000000e+00 961
3 TraesCS7A01G178000 chr7B 89.815 1787 73 33 2379 4110 94310239 94308507 0.000000e+00 2191
4 TraesCS7A01G178000 chr7B 92.237 1520 80 11 1 1515 94312535 94311049 0.000000e+00 2119
5 TraesCS7A01G178000 chr7B 89.867 829 46 17 1508 2336 94311027 94310237 0.000000e+00 1031
6 TraesCS7A01G178000 chr6A 78.138 709 120 20 2495 3177 552832981 552832282 6.460000e-113 418
7 TraesCS7A01G178000 chr6A 77.333 300 55 10 1025 1316 552833334 552833040 9.290000e-37 165
8 TraesCS7A01G178000 chr6D 78.114 297 58 6 1025 1316 407208866 407208572 9.220000e-42 182
9 TraesCS7A01G178000 chr6D 82.209 163 29 0 1025 1187 406345708 406345546 1.570000e-29 141
10 TraesCS7A01G178000 chr6B 77.778 297 59 7 1025 1316 611349223 611348929 4.290000e-40 176


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 TraesCS7A01G178000 chr7A 131832002 131836178 4176 True 7714.000000 7714 100.000000 1 4177 1 chr7A.!!$R1 4176
1 TraesCS7A01G178000 chr7D 133223738 133227772 4034 True 2822.500000 4684 92.566500 1 4110 2 chr7D.!!$R1 4109
2 TraesCS7A01G178000 chr7B 94308507 94312535 4028 True 1780.333333 2191 90.639667 1 4110 3 chr7B.!!$R1 4109
3 TraesCS7A01G178000 chr6A 552832282 552833334 1052 True 291.500000 418 77.735500 1025 3177 2 chr6A.!!$R1 2152

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
579 584 0.614979 TGTTTCCTCCTCCTCTCCCG 60.615 60.0 0.0 0.0 0.00 5.14 F
1506 1515 0.459237 ATGAGAGCTTTCGTGCGGAG 60.459 55.0 0.0 0.0 38.13 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1700 1739 0.096454 CTTACGGCAGGCGCTAAAAC 59.904 55.0 17.72 0.0 38.6 2.43 R
3378 3452 0.792640 GCTCACTCACACAACATCCG 59.207 55.0 0.00 0.0 0.0 4.18 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
50 51 7.971722 GGTCTCTATCTTATTCTTATTCGCCTC 59.028 40.741 0.00 0.00 0.00 4.70
128 131 2.456000 GCGTTCTTTCTCGCCATCA 58.544 52.632 0.00 0.00 45.54 3.07
171 174 3.655810 GAGACCGGAGCAGCCTGTG 62.656 68.421 9.46 0.00 33.84 3.66
195 198 8.263640 GTGGAGACCGGAGTAGTATATAGATTA 58.736 40.741 9.46 0.00 0.00 1.75
280 285 1.218230 GAGGCGCCGCTTTAGATCTG 61.218 60.000 24.06 0.00 0.00 2.90
281 286 2.628657 GCGCCGCTTTAGATCTGC 59.371 61.111 5.18 0.00 0.00 4.26
310 315 1.104577 CCTCTCTCCTGGTACTCGCC 61.105 65.000 0.00 0.00 0.00 5.54
321 326 3.857038 ACTCGCCGGTTGGTGTGT 61.857 61.111 1.90 0.00 46.30 3.72
322 327 3.345808 CTCGCCGGTTGGTGTGTG 61.346 66.667 1.90 0.00 46.30 3.82
397 402 1.137614 CATCTTGCTGCTGCTGCTG 59.862 57.895 27.67 20.66 40.48 4.41
512 517 4.436998 GCGTGCGGTGCTCTAGGT 62.437 66.667 0.00 0.00 0.00 3.08
546 551 2.045536 CCAGCCTCTTGGACTGGC 60.046 66.667 10.77 0.00 44.44 4.85
579 584 0.614979 TGTTTCCTCCTCCTCTCCCG 60.615 60.000 0.00 0.00 0.00 5.14
641 646 1.261619 CAGCGTGCGACTTCTTTCTTT 59.738 47.619 0.00 0.00 0.00 2.52
646 651 1.002468 TGCGACTTCTTTCTTTGCAGC 60.002 47.619 0.00 0.00 0.00 5.25
688 693 5.934935 AAATGTAATCGTCTCGGTGTTTT 57.065 34.783 0.00 0.00 0.00 2.43
722 727 0.806868 TTTATCGTCCTCGTCGCTGT 59.193 50.000 0.00 0.00 38.33 4.40
734 740 5.466058 TCCTCGTCGCTGTGTTTTATTTTTA 59.534 36.000 0.00 0.00 0.00 1.52
758 764 1.271597 ACCTTGGTAGCTGCTCCTTTG 60.272 52.381 4.91 3.24 0.00 2.77
787 793 6.374333 TGGTCTTGAAATACTGGCAACTTATC 59.626 38.462 0.00 0.00 37.61 1.75
802 808 9.554395 TGGCAACTTATCATCTCGAAATAAATA 57.446 29.630 0.00 0.00 37.61 1.40
853 859 3.326747 AGGAAAGCACATTCGTACTGTC 58.673 45.455 0.00 0.00 0.00 3.51
863 869 6.036083 GCACATTCGTACTGTCAATATGAGTT 59.964 38.462 0.00 0.00 0.00 3.01
893 899 7.587629 TGAAATTCTGAATGTGCTACTTCAAG 58.412 34.615 3.22 0.00 31.40 3.02
900 906 3.207265 TGTGCTACTTCAAGCCTTCAA 57.793 42.857 0.00 0.00 42.05 2.69
909 915 2.564771 TCAAGCCTTCAACTGTGTGAG 58.435 47.619 0.00 0.00 0.00 3.51
917 923 3.667497 TCAACTGTGTGAGCTAAGGAG 57.333 47.619 0.00 0.00 0.00 3.69
926 932 5.012664 TGTGTGAGCTAAGGAGATTTTACCA 59.987 40.000 0.00 0.00 0.00 3.25
927 933 5.938125 GTGTGAGCTAAGGAGATTTTACCAA 59.062 40.000 0.00 0.00 0.00 3.67
1080 1086 1.219393 CTTCCGCAACCTCTCCCTC 59.781 63.158 0.00 0.00 0.00 4.30
1212 1221 3.314331 CCTGACCAGCTCACCCGT 61.314 66.667 0.00 0.00 0.00 5.28
1320 1329 3.192001 TCATCGCGAACCAGTAAGTAGTT 59.808 43.478 15.24 0.00 0.00 2.24
1330 1339 8.179615 CGAACCAGTAAGTAGTTTTCTTTTGTT 58.820 33.333 0.00 0.00 0.00 2.83
1396 1405 5.842328 TGATAACCTAGATGGGAACGGTATT 59.158 40.000 0.00 0.00 41.11 1.89
1397 1406 4.684484 AACCTAGATGGGAACGGTATTC 57.316 45.455 0.00 0.00 41.11 1.75
1402 1411 6.384886 ACCTAGATGGGAACGGTATTCTTTTA 59.615 38.462 0.00 0.00 41.11 1.52
1406 1415 8.904099 AGATGGGAACGGTATTCTTTTATTAG 57.096 34.615 0.00 0.00 0.00 1.73
1506 1515 0.459237 ATGAGAGCTTTCGTGCGGAG 60.459 55.000 0.00 0.00 38.13 4.63
1515 1553 1.434555 TTCGTGCGGAGTATGGTTTG 58.565 50.000 0.00 0.00 0.00 2.93
1516 1554 1.017177 TCGTGCGGAGTATGGTTTGC 61.017 55.000 0.00 0.00 0.00 3.68
1582 1620 5.709164 GTGATTGCATTATAGGAGCTGGATT 59.291 40.000 0.00 0.00 0.00 3.01
1586 1624 7.553504 TTGCATTATAGGAGCTGGATTACTA 57.446 36.000 0.00 0.00 0.00 1.82
1675 1714 1.669760 CGGTAGACAAAAGGGCGCA 60.670 57.895 10.83 0.00 0.00 6.09
1692 1731 1.070786 CAAGCGGTGTGTGTAGGGT 59.929 57.895 0.00 0.00 0.00 4.34
1693 1732 1.070786 AAGCGGTGTGTGTAGGGTG 59.929 57.895 0.00 0.00 0.00 4.61
1694 1733 1.692173 AAGCGGTGTGTGTAGGGTGT 61.692 55.000 0.00 0.00 0.00 4.16
1695 1734 1.959226 GCGGTGTGTGTAGGGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
1696 1735 1.444250 CGGTGTGTGTAGGGTGTGT 59.556 57.895 0.00 0.00 0.00 3.72
1697 1736 0.675083 CGGTGTGTGTAGGGTGTGTA 59.325 55.000 0.00 0.00 0.00 2.90
1698 1737 1.336517 CGGTGTGTGTAGGGTGTGTAG 60.337 57.143 0.00 0.00 0.00 2.74
1699 1738 1.001633 GGTGTGTGTAGGGTGTGTAGG 59.998 57.143 0.00 0.00 0.00 3.18
1700 1739 1.001633 GTGTGTGTAGGGTGTGTAGGG 59.998 57.143 0.00 0.00 0.00 3.53
1788 1827 3.624777 GGCCCAAATCTCTGAGAAATGA 58.375 45.455 12.00 0.00 0.00 2.57
1905 1944 3.238597 TCCAAATTTACCTGCCTTGCTT 58.761 40.909 0.00 0.00 0.00 3.91
1933 1972 9.562408 TGTATTTGTCTTTACACAATAAGGTCA 57.438 29.630 0.00 0.00 36.16 4.02
1942 1981 8.492673 TTTACACAATAAGGTCAGCTCTATTG 57.507 34.615 13.06 13.06 0.00 1.90
2086 2125 9.461312 GCATCAATCCATAAATACAGGGTTATA 57.539 33.333 0.00 0.00 0.00 0.98
2091 2130 8.751215 ATCCATAAATACAGGGTTATAGGTGA 57.249 34.615 0.00 0.00 0.00 4.02
2096 2135 7.941053 AAATACAGGGTTATAGGTGATGGTA 57.059 36.000 0.00 0.00 0.00 3.25
2160 2199 8.394971 TGTTTTCTGATAGTGATGAATGTTGT 57.605 30.769 0.00 0.00 0.00 3.32
2288 2327 6.381133 TGGCTCTGATCTATTTTCTGACTGTA 59.619 38.462 0.00 0.00 0.00 2.74
2320 2359 0.530744 AACTCAGTTCATAGCCGCGA 59.469 50.000 8.23 0.00 0.00 5.87
2500 2546 1.416243 ACTGACCCTACCGTGTTTGA 58.584 50.000 0.00 0.00 0.00 2.69
2540 2586 0.178891 TCAAGACCCTGGAGCTTCCT 60.179 55.000 0.00 0.00 37.46 3.36
3178 3248 0.982852 TGGCCGGAGTCTCCATGAAT 60.983 55.000 19.15 0.00 35.91 2.57
3179 3249 0.533755 GGCCGGAGTCTCCATGAATG 60.534 60.000 19.15 1.11 35.91 2.67
3180 3250 0.465705 GCCGGAGTCTCCATGAATGA 59.534 55.000 19.15 0.00 35.91 2.57
3181 3251 1.134401 GCCGGAGTCTCCATGAATGAA 60.134 52.381 19.15 0.00 35.91 2.57
3186 3256 4.335416 GGAGTCTCCATGAATGAACCAAA 58.665 43.478 14.46 0.00 36.28 3.28
3195 3265 4.177537 TGAATGAACCAAACCTTCCTCA 57.822 40.909 0.00 0.00 0.00 3.86
3208 3278 4.723309 ACCTTCCTCATCATCAATAAGCC 58.277 43.478 0.00 0.00 0.00 4.35
3229 3299 3.243569 CCGTCAAGAGAAGTGAAGTCTGT 60.244 47.826 0.00 0.00 0.00 3.41
3244 3318 0.604780 TCTGTCTGCCTGCTTGCTTC 60.605 55.000 0.00 0.00 0.00 3.86
3259 3333 1.449956 CTTCCTCCTGCTGCTGCTC 60.450 63.158 17.00 0.00 40.48 4.26
3260 3334 2.872931 CTTCCTCCTGCTGCTGCTCC 62.873 65.000 17.00 0.00 40.48 4.70
3261 3335 3.400928 CCTCCTGCTGCTGCTCCT 61.401 66.667 17.00 0.00 40.48 3.69
3262 3336 2.125065 CTCCTGCTGCTGCTCCTG 60.125 66.667 17.00 4.62 40.48 3.86
3263 3337 4.405671 TCCTGCTGCTGCTCCTGC 62.406 66.667 17.00 1.02 40.48 4.85
3264 3338 4.411981 CCTGCTGCTGCTCCTGCT 62.412 66.667 17.00 0.00 40.48 4.24
3265 3339 3.128188 CTGCTGCTGCTCCTGCTG 61.128 66.667 17.00 1.17 40.48 4.41
3271 3345 3.128188 CTGCTCCTGCTGCTGCTG 61.128 66.667 17.00 15.58 40.48 4.41
3272 3346 3.903616 CTGCTCCTGCTGCTGCTGT 62.904 63.158 17.00 0.00 40.48 4.40
3273 3347 3.126225 GCTCCTGCTGCTGCTGTC 61.126 66.667 17.00 4.39 40.48 3.51
3274 3348 2.663796 CTCCTGCTGCTGCTGTCT 59.336 61.111 17.00 0.00 40.48 3.41
3275 3349 1.003597 CTCCTGCTGCTGCTGTCTT 60.004 57.895 17.00 0.00 40.48 3.01
3276 3350 0.605860 CTCCTGCTGCTGCTGTCTTT 60.606 55.000 17.00 0.00 40.48 2.52
3277 3351 0.686789 TCCTGCTGCTGCTGTCTTTA 59.313 50.000 17.00 0.00 40.48 1.85
3296 3370 7.172190 TGTCTTTATTATAGCATGCTTCAGCTC 59.828 37.037 28.02 7.78 42.05 4.09
3378 3452 0.672342 CTGCTTGCAGATATTGGCCC 59.328 55.000 16.78 0.00 0.00 5.80
3387 3461 1.494721 AGATATTGGCCCGGATGTTGT 59.505 47.619 0.73 0.00 0.00 3.32
3436 3511 4.037923 AGAACCTGTGGTGCTTAAAACATG 59.962 41.667 0.00 0.00 38.75 3.21
3483 3558 3.250744 GTTGAGAATACTGCTGCGTGTA 58.749 45.455 7.56 7.56 0.00 2.90
3504 3594 8.960075 CGTGTAGTAATTTTTCGTTTTTGGATT 58.040 29.630 0.00 0.00 0.00 3.01
3514 3604 2.413634 CGTTTTTGGATTACGAGTGGCC 60.414 50.000 0.00 0.00 37.47 5.36
3519 3609 1.883084 GATTACGAGTGGCCGGCTG 60.883 63.158 28.56 13.59 0.00 4.85
3664 3760 3.636231 CAACGCCCAGACCCCAGA 61.636 66.667 0.00 0.00 0.00 3.86
3665 3761 3.322466 AACGCCCAGACCCCAGAG 61.322 66.667 0.00 0.00 0.00 3.35
3681 3777 2.596631 AGCCAGCCAACAGTGCAG 60.597 61.111 0.00 0.00 0.00 4.41
3801 3912 3.134458 GGCAGATCCTAGATTTTGTCCG 58.866 50.000 0.00 0.00 0.00 4.79
4084 4216 0.249238 GATACCAGCTCTGAGCACCG 60.249 60.000 29.49 18.24 45.56 4.94
4097 4229 3.353836 CACCGGGCACACCTTTCG 61.354 66.667 6.32 0.00 36.97 3.46
4110 4242 3.746492 ACACCTTTCGATGCTCTTGTTAC 59.254 43.478 0.00 0.00 0.00 2.50
4111 4243 3.997021 CACCTTTCGATGCTCTTGTTACT 59.003 43.478 0.00 0.00 0.00 2.24
4112 4244 3.997021 ACCTTTCGATGCTCTTGTTACTG 59.003 43.478 0.00 0.00 0.00 2.74
4113 4245 3.997021 CCTTTCGATGCTCTTGTTACTGT 59.003 43.478 0.00 0.00 0.00 3.55
4114 4246 5.168569 CCTTTCGATGCTCTTGTTACTGTA 58.831 41.667 0.00 0.00 0.00 2.74
4115 4247 5.812642 CCTTTCGATGCTCTTGTTACTGTAT 59.187 40.000 0.00 0.00 0.00 2.29
4116 4248 6.019479 CCTTTCGATGCTCTTGTTACTGTATC 60.019 42.308 0.00 0.00 0.00 2.24
4117 4249 4.933330 TCGATGCTCTTGTTACTGTATCC 58.067 43.478 0.00 0.00 0.00 2.59
4118 4250 4.645136 TCGATGCTCTTGTTACTGTATCCT 59.355 41.667 0.00 0.00 0.00 3.24
4119 4251 4.742167 CGATGCTCTTGTTACTGTATCCTG 59.258 45.833 0.00 0.00 0.00 3.86
4120 4252 3.861840 TGCTCTTGTTACTGTATCCTGC 58.138 45.455 0.00 0.00 0.00 4.85
4121 4253 3.515502 TGCTCTTGTTACTGTATCCTGCT 59.484 43.478 0.00 0.00 0.00 4.24
4122 4254 4.116238 GCTCTTGTTACTGTATCCTGCTC 58.884 47.826 0.00 0.00 0.00 4.26
4123 4255 4.688021 CTCTTGTTACTGTATCCTGCTCC 58.312 47.826 0.00 0.00 0.00 4.70
4124 4256 4.093743 TCTTGTTACTGTATCCTGCTCCA 58.906 43.478 0.00 0.00 0.00 3.86
4125 4257 4.716784 TCTTGTTACTGTATCCTGCTCCAT 59.283 41.667 0.00 0.00 0.00 3.41
4126 4258 5.897250 TCTTGTTACTGTATCCTGCTCCATA 59.103 40.000 0.00 0.00 0.00 2.74
4127 4259 5.531122 TGTTACTGTATCCTGCTCCATAC 57.469 43.478 0.00 0.00 0.00 2.39
4128 4260 5.208890 TGTTACTGTATCCTGCTCCATACT 58.791 41.667 0.00 0.00 0.00 2.12
4129 4261 5.302059 TGTTACTGTATCCTGCTCCATACTC 59.698 44.000 0.00 0.00 0.00 2.59
4130 4262 3.235200 ACTGTATCCTGCTCCATACTCC 58.765 50.000 0.00 0.00 0.00 3.85
4131 4263 2.230025 CTGTATCCTGCTCCATACTCCG 59.770 54.545 0.00 0.00 0.00 4.63
4132 4264 2.240279 GTATCCTGCTCCATACTCCGT 58.760 52.381 0.00 0.00 0.00 4.69
4133 4265 1.333177 ATCCTGCTCCATACTCCGTC 58.667 55.000 0.00 0.00 0.00 4.79
4134 4266 1.101635 TCCTGCTCCATACTCCGTCG 61.102 60.000 0.00 0.00 0.00 5.12
4135 4267 1.299468 CTGCTCCATACTCCGTCGC 60.299 63.158 0.00 0.00 0.00 5.19
4136 4268 1.729470 CTGCTCCATACTCCGTCGCT 61.729 60.000 0.00 0.00 0.00 4.93
4137 4269 1.008309 GCTCCATACTCCGTCGCTC 60.008 63.158 0.00 0.00 0.00 5.03
4138 4270 1.655329 CTCCATACTCCGTCGCTCC 59.345 63.158 0.00 0.00 0.00 4.70
4139 4271 0.820074 CTCCATACTCCGTCGCTCCT 60.820 60.000 0.00 0.00 0.00 3.69
4140 4272 0.471191 TCCATACTCCGTCGCTCCTA 59.529 55.000 0.00 0.00 0.00 2.94
4141 4273 1.134007 TCCATACTCCGTCGCTCCTAA 60.134 52.381 0.00 0.00 0.00 2.69
4142 4274 1.679680 CCATACTCCGTCGCTCCTAAA 59.320 52.381 0.00 0.00 0.00 1.85
4143 4275 2.100252 CCATACTCCGTCGCTCCTAAAA 59.900 50.000 0.00 0.00 0.00 1.52
4144 4276 3.429822 CCATACTCCGTCGCTCCTAAAAA 60.430 47.826 0.00 0.00 0.00 1.94
4145 4277 2.365408 ACTCCGTCGCTCCTAAAAAG 57.635 50.000 0.00 0.00 0.00 2.27
4146 4278 1.000145 CTCCGTCGCTCCTAAAAAGC 59.000 55.000 0.00 0.00 36.38 3.51
4147 4279 0.606604 TCCGTCGCTCCTAAAAAGCT 59.393 50.000 0.00 0.00 37.62 3.74
4148 4280 1.001633 TCCGTCGCTCCTAAAAAGCTT 59.998 47.619 0.00 0.00 37.62 3.74
4149 4281 1.128692 CCGTCGCTCCTAAAAAGCTTG 59.871 52.381 0.00 0.00 37.62 4.01
4150 4282 1.798813 CGTCGCTCCTAAAAAGCTTGT 59.201 47.619 0.00 0.00 37.62 3.16
4151 4283 2.159827 CGTCGCTCCTAAAAAGCTTGTC 60.160 50.000 0.00 0.00 37.62 3.18
4152 4284 3.067833 GTCGCTCCTAAAAAGCTTGTCT 58.932 45.455 0.00 0.00 37.62 3.41
4153 4285 3.498777 GTCGCTCCTAAAAAGCTTGTCTT 59.501 43.478 0.00 0.00 37.62 3.01
4154 4286 4.689345 GTCGCTCCTAAAAAGCTTGTCTTA 59.311 41.667 0.00 0.00 37.62 2.10
4155 4287 4.929808 TCGCTCCTAAAAAGCTTGTCTTAG 59.070 41.667 0.00 7.87 37.62 2.18
4156 4288 4.929808 CGCTCCTAAAAAGCTTGTCTTAGA 59.070 41.667 18.21 5.42 37.62 2.10
4157 4289 5.582665 CGCTCCTAAAAAGCTTGTCTTAGAT 59.417 40.000 18.21 0.00 37.62 1.98
4158 4290 6.092807 CGCTCCTAAAAAGCTTGTCTTAGATT 59.907 38.462 18.21 0.00 37.62 2.40
4159 4291 7.361286 CGCTCCTAAAAAGCTTGTCTTAGATTT 60.361 37.037 18.21 8.56 37.62 2.17
4160 4292 8.947115 GCTCCTAAAAAGCTTGTCTTAGATTTA 58.053 33.333 18.21 9.11 32.98 1.40
4162 4294 9.787435 TCCTAAAAAGCTTGTCTTAGATTTACA 57.213 29.630 18.21 0.00 32.98 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.321298 TTTCGCGAAAGGAGAAGGGG 60.321 55.000 29.22 0.00 35.80 4.79
102 105 2.565005 CGAGAAAGAACGCAAAAGCTC 58.435 47.619 0.00 0.00 0.00 4.09
171 174 7.442062 GCTAATCTATATACTACTCCGGTCTCC 59.558 44.444 0.00 0.00 0.00 3.71
281 286 4.244802 GAGAGAGGAGGACGCGCG 62.245 72.222 30.96 30.96 0.00 6.86
282 287 3.894947 GGAGAGAGGAGGACGCGC 61.895 72.222 5.73 0.00 0.00 6.86
283 288 2.124487 AGGAGAGAGGAGGACGCG 60.124 66.667 3.53 3.53 0.00 6.01
310 315 1.436195 CCTCACACACACACCAACCG 61.436 60.000 0.00 0.00 0.00 4.44
321 326 5.650266 ACTTTGTTAAACATCACCTCACACA 59.350 36.000 0.00 0.00 0.00 3.72
322 327 6.131544 ACTTTGTTAAACATCACCTCACAC 57.868 37.500 0.00 0.00 0.00 3.82
398 403 0.242825 TCCAAGAACCAGACGCGTAG 59.757 55.000 13.97 8.16 0.00 3.51
399 404 0.892755 ATCCAAGAACCAGACGCGTA 59.107 50.000 13.97 0.00 0.00 4.42
400 405 0.892755 TATCCAAGAACCAGACGCGT 59.107 50.000 13.85 13.85 0.00 6.01
512 517 1.720781 TGGCTAGATATGGCAGAGCA 58.279 50.000 0.00 0.00 35.04 4.26
546 551 6.809869 AGGAGGAAACATGAACTTTCTTTTG 58.190 36.000 0.00 0.00 0.00 2.44
631 636 2.228343 CCCTGAGCTGCAAAGAAAGAAG 59.772 50.000 1.02 0.00 0.00 2.85
646 651 1.331214 TTTTGCAAGCTTCCCCTGAG 58.669 50.000 0.00 0.00 0.00 3.35
734 740 1.486726 GGAGCAGCTACCAAGGTACAT 59.513 52.381 0.00 0.00 0.00 2.29
758 764 2.488153 GCCAGTATTTCAAGACCACCAC 59.512 50.000 0.00 0.00 0.00 4.16
816 822 9.290988 TGTGCTTTCCTATACTATGAAACAAAA 57.709 29.630 0.00 0.00 0.00 2.44
820 826 8.276325 CGAATGTGCTTTCCTATACTATGAAAC 58.724 37.037 0.00 0.00 0.00 2.78
829 835 6.127563 TGACAGTACGAATGTGCTTTCCTATA 60.128 38.462 0.00 0.00 39.18 1.31
863 869 7.112122 AGTAGCACATTCAGAATTTCATGGTA 58.888 34.615 0.00 0.00 0.00 3.25
893 899 2.169832 TAGCTCACACAGTTGAAGGC 57.830 50.000 0.00 0.00 0.00 4.35
900 906 4.899352 AAATCTCCTTAGCTCACACAGT 57.101 40.909 0.00 0.00 0.00 3.55
909 915 6.879458 TCACTCTTTGGTAAAATCTCCTTAGC 59.121 38.462 0.00 0.00 0.00 3.09
926 932 7.397221 TCAGGAACAATGATACATCACTCTTT 58.603 34.615 0.00 0.00 40.03 2.52
927 933 6.950842 TCAGGAACAATGATACATCACTCTT 58.049 36.000 0.00 0.00 40.03 2.85
1080 1086 1.153489 CACGGTGAGCATCTCCTGG 60.153 63.158 0.74 0.00 46.27 4.45
1212 1221 3.527533 GGTGACAAGCGTATGAACCATA 58.472 45.455 11.29 0.00 33.57 2.74
1343 1352 6.115446 TCATCAGGAAAGTATCATCCAACAC 58.885 40.000 0.00 0.00 38.23 3.32
1355 1364 7.637511 AGGTTATCAAATCTCATCAGGAAAGT 58.362 34.615 0.00 0.00 0.00 2.66
1402 1411 6.349300 CAGCTAATGGTCCACAACTACTAAT 58.651 40.000 0.00 0.00 0.00 1.73
1406 1415 3.270877 CCAGCTAATGGTCCACAACTAC 58.729 50.000 0.00 0.00 44.91 2.73
1423 1432 0.604578 ACATGCACATTTCCACCAGC 59.395 50.000 0.00 0.00 0.00 4.85
1506 1515 3.296628 CTTGTCACAACGCAAACCATAC 58.703 45.455 0.00 0.00 0.00 2.39
1515 1553 1.260561 CACTACACCTTGTCACAACGC 59.739 52.381 0.00 0.00 0.00 4.84
1516 1554 1.864711 CCACTACACCTTGTCACAACG 59.135 52.381 0.00 0.00 0.00 4.10
1582 1620 2.423947 CCTCCCTCTAACCGCCTTAGTA 60.424 54.545 0.00 0.00 34.43 1.82
1586 1624 0.688087 CTCCTCCCTCTAACCGCCTT 60.688 60.000 0.00 0.00 0.00 4.35
1611 1649 3.997400 CTCCTCTCCGTCGCCCTCA 62.997 68.421 0.00 0.00 0.00 3.86
1623 1662 2.364448 GCTTCCCGACCCTCCTCT 60.364 66.667 0.00 0.00 0.00 3.69
1632 1671 0.832135 ACCACTCTCTTGCTTCCCGA 60.832 55.000 0.00 0.00 0.00 5.14
1675 1714 1.070786 CACCCTACACACACCGCTT 59.929 57.895 0.00 0.00 0.00 4.68
1678 1717 0.675083 TACACACCCTACACACACCG 59.325 55.000 0.00 0.00 0.00 4.94
1692 1731 0.688487 AGGCGCTAAAACCCTACACA 59.312 50.000 7.64 0.00 0.00 3.72
1693 1732 1.084289 CAGGCGCTAAAACCCTACAC 58.916 55.000 7.64 0.00 0.00 2.90
1694 1733 0.675522 GCAGGCGCTAAAACCCTACA 60.676 55.000 7.64 0.00 34.30 2.74
1695 1734 1.374343 GGCAGGCGCTAAAACCCTAC 61.374 60.000 7.64 0.00 38.60 3.18
1696 1735 1.078001 GGCAGGCGCTAAAACCCTA 60.078 57.895 7.64 0.00 38.60 3.53
1697 1736 2.361230 GGCAGGCGCTAAAACCCT 60.361 61.111 7.64 0.00 38.60 4.34
1698 1737 3.810896 CGGCAGGCGCTAAAACCC 61.811 66.667 7.64 0.00 38.60 4.11
1699 1738 1.300266 TTACGGCAGGCGCTAAAACC 61.300 55.000 17.72 1.06 38.60 3.27
1700 1739 0.096454 CTTACGGCAGGCGCTAAAAC 59.904 55.000 17.72 0.00 38.60 2.43
1764 1803 2.568546 TCTCAGAGATTTGGGCCCTA 57.431 50.000 25.70 14.07 0.00 3.53
1788 1827 0.173935 CATTCATGCCCATGTTGCGT 59.826 50.000 8.02 0.00 39.72 5.24
1890 1929 2.656947 ACAGAAGCAAGGCAGGTAAA 57.343 45.000 0.00 0.00 0.00 2.01
1895 1934 3.755378 AGACAAATACAGAAGCAAGGCAG 59.245 43.478 0.00 0.00 0.00 4.85
1897 1936 4.773323 AAGACAAATACAGAAGCAAGGC 57.227 40.909 0.00 0.00 0.00 4.35
1905 1944 9.787435 ACCTTATTGTGTAAAGACAAATACAGA 57.213 29.630 0.00 0.00 39.25 3.41
1933 1972 4.128925 TGAATTCAGCGACAATAGAGCT 57.871 40.909 3.38 0.00 42.64 4.09
1942 1981 9.502145 TGTTTATAAATGATTGAATTCAGCGAC 57.498 29.630 8.41 2.81 0.00 5.19
1998 2037 8.193250 TGAATCAATAGTTTACGAGCCTTTAC 57.807 34.615 0.00 0.00 0.00 2.01
2040 2079 3.068165 TGCACTGGAATGATACTACTCCG 59.932 47.826 0.00 0.00 0.00 4.63
2048 2087 5.051409 TGGATTGATGCACTGGAATGATA 57.949 39.130 0.00 0.00 0.00 2.15
2086 2125 4.684485 GCTAGCAACTTGATACCATCACCT 60.684 45.833 10.63 0.00 39.39 4.00
2091 2130 4.220693 TGTGCTAGCAACTTGATACCAT 57.779 40.909 21.29 0.00 0.00 3.55
2096 2135 7.227512 GGAGTATTATTGTGCTAGCAACTTGAT 59.772 37.037 21.29 13.32 0.00 2.57
2160 2199 2.934887 CAGGATATGGCACCATGTTCA 58.065 47.619 12.54 0.00 37.82 3.18
2288 2327 9.877178 CTATGAACTGAGTTCCTAACATTTAGT 57.123 33.333 21.45 0.00 41.35 2.24
2320 2359 7.986085 ACCTGCTCGATTAAATGCTATTAAT 57.014 32.000 6.92 6.92 38.00 1.40
2448 2490 9.739276 GAACCAAATATTATGGATAGGATCACA 57.261 33.333 18.02 0.00 40.56 3.58
2500 2546 1.523095 GAGATCGCGCGCTTAGAAAAT 59.477 47.619 30.48 10.95 0.00 1.82
2540 2586 2.513897 TCGCTGATCTCGCTCCGA 60.514 61.111 0.00 0.00 0.00 4.55
2813 2865 2.202756 GACGCGATCTCCACCACC 60.203 66.667 15.93 0.00 0.00 4.61
3050 3117 2.815298 CTCCTCGTCCTCGTCGCTC 61.815 68.421 0.00 0.00 38.33 5.03
3059 3126 3.775654 CACAGGGCCTCCTCGTCC 61.776 72.222 0.95 0.00 42.67 4.79
3178 3248 3.874383 TGATGAGGAAGGTTTGGTTCA 57.126 42.857 0.00 0.00 0.00 3.18
3179 3249 4.335416 TGATGATGAGGAAGGTTTGGTTC 58.665 43.478 0.00 0.00 0.00 3.62
3180 3250 4.387026 TGATGATGAGGAAGGTTTGGTT 57.613 40.909 0.00 0.00 0.00 3.67
3181 3251 4.387026 TTGATGATGAGGAAGGTTTGGT 57.613 40.909 0.00 0.00 0.00 3.67
3186 3256 4.723309 GGCTTATTGATGATGAGGAAGGT 58.277 43.478 0.00 0.00 0.00 3.50
3195 3265 5.282055 TCTCTTGACGGCTTATTGATGAT 57.718 39.130 0.00 0.00 0.00 2.45
3208 3278 3.971150 ACAGACTTCACTTCTCTTGACG 58.029 45.455 0.00 0.00 0.00 4.35
3229 3299 1.002868 GAGGAAGCAAGCAGGCAGA 60.003 57.895 2.37 0.00 35.83 4.26
3244 3318 3.400928 AGGAGCAGCAGCAGGAGG 61.401 66.667 3.17 0.00 45.49 4.30
3259 3333 1.747709 ATAAAGACAGCAGCAGCAGG 58.252 50.000 3.17 0.00 45.49 4.85
3260 3334 5.333952 GCTATAATAAAGACAGCAGCAGCAG 60.334 44.000 3.17 0.00 45.49 4.24
3261 3335 4.512944 GCTATAATAAAGACAGCAGCAGCA 59.487 41.667 3.17 0.00 45.49 4.41
3262 3336 4.512944 TGCTATAATAAAGACAGCAGCAGC 59.487 41.667 0.00 0.00 37.32 5.25
3263 3337 6.600350 CATGCTATAATAAAGACAGCAGCAG 58.400 40.000 0.00 0.00 44.73 4.24
3264 3338 5.049198 GCATGCTATAATAAAGACAGCAGCA 60.049 40.000 11.37 0.00 44.73 4.41
3265 3339 5.180868 AGCATGCTATAATAAAGACAGCAGC 59.819 40.000 21.21 0.00 44.73 5.25
3266 3340 6.798315 AGCATGCTATAATAAAGACAGCAG 57.202 37.500 21.21 0.00 44.73 4.24
3267 3341 6.767423 TGAAGCATGCTATAATAAAGACAGCA 59.233 34.615 23.00 0.00 45.51 4.41
3268 3342 7.194607 TGAAGCATGCTATAATAAAGACAGC 57.805 36.000 23.00 0.00 0.00 4.40
3269 3343 7.172875 AGCTGAAGCATGCTATAATAAAGACAG 59.827 37.037 23.00 16.10 45.16 3.51
3270 3344 6.994496 AGCTGAAGCATGCTATAATAAAGACA 59.006 34.615 23.00 7.56 45.16 3.41
3271 3345 7.387397 AGAGCTGAAGCATGCTATAATAAAGAC 59.613 37.037 23.00 6.12 45.16 3.01
3272 3346 7.387122 CAGAGCTGAAGCATGCTATAATAAAGA 59.613 37.037 23.00 0.00 45.16 2.52
3273 3347 7.387122 TCAGAGCTGAAGCATGCTATAATAAAG 59.613 37.037 23.00 11.48 45.16 1.85
3274 3348 7.219322 TCAGAGCTGAAGCATGCTATAATAAA 58.781 34.615 23.00 0.00 45.16 1.40
3275 3349 6.762333 TCAGAGCTGAAGCATGCTATAATAA 58.238 36.000 23.00 0.00 45.16 1.40
3276 3350 6.350629 TCAGAGCTGAAGCATGCTATAATA 57.649 37.500 23.00 4.92 45.16 0.98
3277 3351 5.224821 TCAGAGCTGAAGCATGCTATAAT 57.775 39.130 23.00 4.63 45.16 1.28
3296 3370 2.693069 ACACGGAAGAAGATGCTTCAG 58.307 47.619 9.56 1.34 44.71 3.02
3350 3424 6.016860 CCAATATCTGCAAGCAGCTAAACATA 60.017 38.462 16.89 8.87 45.94 2.29
3351 3425 5.221185 CCAATATCTGCAAGCAGCTAAACAT 60.221 40.000 16.89 6.99 45.94 2.71
3353 3427 4.604976 CCAATATCTGCAAGCAGCTAAAC 58.395 43.478 16.89 0.00 45.94 2.01
3378 3452 0.792640 GCTCACTCACACAACATCCG 59.207 55.000 0.00 0.00 0.00 4.18
3387 3461 1.413118 TCCAGACAAGCTCACTCACA 58.587 50.000 0.00 0.00 0.00 3.58
3436 3511 7.434307 CAGTTCATATTGATGATTTGTTGCTCC 59.566 37.037 0.00 0.00 41.77 4.70
3483 3558 9.389570 CTCGTAATCCAAAAACGAAAAATTACT 57.610 29.630 0.00 0.00 44.20 2.24
3544 3634 2.432628 CACGTCTTCTCCACGGCC 60.433 66.667 0.00 0.00 41.73 6.13
3546 3636 1.080705 GGTCACGTCTTCTCCACGG 60.081 63.158 0.00 0.00 41.73 4.94
3600 3696 2.106683 CCAGAGCCTTTTACCGCCG 61.107 63.158 0.00 0.00 0.00 6.46
3657 3753 3.971702 GTTGGCTGGCTCTGGGGT 61.972 66.667 2.00 0.00 0.00 4.95
3658 3754 3.933048 CTGTTGGCTGGCTCTGGGG 62.933 68.421 2.00 0.00 0.00 4.96
3659 3755 2.360852 CTGTTGGCTGGCTCTGGG 60.361 66.667 2.00 0.00 0.00 4.45
3660 3756 1.970114 CACTGTTGGCTGGCTCTGG 60.970 63.158 2.00 0.00 0.00 3.86
3661 3757 2.623915 GCACTGTTGGCTGGCTCTG 61.624 63.158 2.00 3.02 0.00 3.35
3662 3758 2.282040 GCACTGTTGGCTGGCTCT 60.282 61.111 2.00 0.00 0.00 4.09
3663 3759 2.595463 TGCACTGTTGGCTGGCTC 60.595 61.111 2.00 0.00 0.00 4.70
3664 3760 2.596631 CTGCACTGTTGGCTGGCT 60.597 61.111 2.00 0.00 0.00 4.75
3665 3761 3.677648 CCTGCACTGTTGGCTGGC 61.678 66.667 3.68 0.00 42.26 4.85
3666 3762 2.987547 CCCTGCACTGTTGGCTGG 60.988 66.667 8.49 8.49 46.40 4.85
3667 3763 3.677648 GCCCTGCACTGTTGGCTG 61.678 66.667 0.00 0.00 40.77 4.85
3696 3792 2.048316 AAAAAGCGCATTGGCCGG 60.048 55.556 11.47 0.00 36.38 6.13
3801 3912 0.179134 CCGTCCGTCACAAGATCTCC 60.179 60.000 0.00 0.00 0.00 3.71
3868 3979 2.726691 CTTGCCAAGTACGCGACGG 61.727 63.158 15.93 6.38 0.00 4.79
4056 4188 0.811616 GAGCTGGTATCCTGGCAACG 60.812 60.000 0.00 0.00 42.51 4.10
4068 4200 3.699894 CCGGTGCTCAGAGCTGGT 61.700 66.667 23.15 0.00 42.97 4.00
4084 4216 1.648467 GAGCATCGAAAGGTGTGCCC 61.648 60.000 2.92 0.00 46.24 5.36
4092 4224 6.019479 GGATACAGTAACAAGAGCATCGAAAG 60.019 42.308 0.00 0.00 42.67 2.62
4097 4229 4.509600 GCAGGATACAGTAACAAGAGCATC 59.490 45.833 0.00 0.00 41.41 3.91
4110 4242 2.230025 CGGAGTATGGAGCAGGATACAG 59.770 54.545 0.00 0.00 41.41 2.74
4111 4243 2.239400 CGGAGTATGGAGCAGGATACA 58.761 52.381 0.00 0.00 41.41 2.29
4112 4244 2.240279 ACGGAGTATGGAGCAGGATAC 58.760 52.381 0.00 0.00 41.94 2.24
4113 4245 2.677542 ACGGAGTATGGAGCAGGATA 57.322 50.000 0.00 0.00 41.94 2.59
4114 4246 3.541224 ACGGAGTATGGAGCAGGAT 57.459 52.632 0.00 0.00 41.94 3.24
4123 4255 7.900069 AGCTTTTTAGGAGCGACGGAGTATG 62.900 48.000 0.00 0.00 44.71 2.39
4124 4256 5.945599 AGCTTTTTAGGAGCGACGGAGTAT 61.946 45.833 0.00 0.00 44.71 2.12
4125 4257 4.681276 AGCTTTTTAGGAGCGACGGAGTA 61.681 47.826 0.00 0.00 44.71 2.59
4126 4258 3.983932 AGCTTTTTAGGAGCGACGGAGT 61.984 50.000 0.00 0.00 44.71 3.85
4127 4259 1.000145 GCTTTTTAGGAGCGACGGAG 59.000 55.000 0.00 0.00 0.00 4.63
4128 4260 0.606604 AGCTTTTTAGGAGCGACGGA 59.393 50.000 0.00 0.00 44.71 4.69
4129 4261 1.128692 CAAGCTTTTTAGGAGCGACGG 59.871 52.381 0.00 0.00 44.71 4.79
4130 4262 1.798813 ACAAGCTTTTTAGGAGCGACG 59.201 47.619 0.00 0.00 44.71 5.12
4131 4263 3.067833 AGACAAGCTTTTTAGGAGCGAC 58.932 45.455 0.00 0.00 44.71 5.19
4132 4264 3.402628 AGACAAGCTTTTTAGGAGCGA 57.597 42.857 0.00 0.00 44.71 4.93
4133 4265 4.929808 TCTAAGACAAGCTTTTTAGGAGCG 59.070 41.667 16.32 0.00 44.71 5.03
4134 4266 6.993786 ATCTAAGACAAGCTTTTTAGGAGC 57.006 37.500 16.32 0.00 38.05 4.70
4136 4268 9.787435 TGTAAATCTAAGACAAGCTTTTTAGGA 57.213 29.630 16.32 5.30 38.05 2.94


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

AutoCloner maintained by Alex Coulton.