Multiple sequence alignment - TraesCS2D01G282000

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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 TraesCS2D01G282000 chr2D 100.000 6711 0 0 1 6711 354956004 354962714 0.000000e+00 12393.0
1 TraesCS2D01G282000 chr2A 96.857 3436 76 12 741 4175 474785442 474788846 0.000000e+00 5718.0
2 TraesCS2D01G282000 chr2A 96.441 2529 74 7 4188 6711 474788829 474791346 0.000000e+00 4157.0
3 TraesCS2D01G282000 chr2A 88.308 325 30 7 434 755 474784538 474784857 3.800000e-102 383.0
4 TraesCS2D01G282000 chr2A 89.051 137 15 0 655 791 72965212 72965348 3.220000e-38 171.0
5 TraesCS2D01G282000 chr2A 100.000 30 0 0 6 35 661705640 661705669 1.000000e-03 56.5
6 TraesCS2D01G282000 chr2B 96.884 2471 61 9 1709 4175 422500960 422503418 0.000000e+00 4122.0
7 TraesCS2D01G282000 chr2B 96.855 1526 42 5 4186 5707 422503399 422504922 0.000000e+00 2547.0
8 TraesCS2D01G282000 chr2B 90.476 1218 69 24 462 1662 422499763 422500950 0.000000e+00 1563.0
9 TraesCS2D01G282000 chr2B 82.143 476 48 16 1 461 422499256 422499709 2.290000e-99 374.0
10 TraesCS2D01G282000 chr2B 89.051 137 15 0 655 791 233169112 233169248 3.220000e-38 171.0
11 TraesCS2D01G282000 chr2B 89.051 137 15 0 655 791 281965944 281965808 3.220000e-38 171.0
12 TraesCS2D01G282000 chr7B 89.051 137 15 0 655 791 103952789 103952925 3.220000e-38 171.0
13 TraesCS2D01G282000 chr7B 89.051 137 15 0 655 791 619127561 619127425 3.220000e-38 171.0
14 TraesCS2D01G282000 chr6B 89.051 137 15 0 655 791 633042584 633042448 3.220000e-38 171.0
15 TraesCS2D01G282000 chr6A 89.051 137 15 0 655 791 562521815 562521679 3.220000e-38 171.0
16 TraesCS2D01G282000 chr1B 89.051 137 15 0 655 791 385302145 385302281 3.220000e-38 171.0
17 TraesCS2D01G282000 chr5B 94.872 39 1 1 1 38 605830552 605830514 7.270000e-05 60.2
18 TraesCS2D01G282000 chr3A 97.059 34 0 1 6 38 562575062 562575095 1.000000e-03 56.5
19 TraesCS2D01G282000 chr1D 100.000 28 0 0 7 34 193498614 193498641 1.200000e-02 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 TraesCS2D01G282000 chr2D 354956004 354962714 6710 False 12393.000000 12393 100.000000 1 6711 1 chr2D.!!$F1 6710
1 TraesCS2D01G282000 chr2A 474784538 474791346 6808 False 3419.333333 5718 93.868667 434 6711 3 chr2A.!!$F3 6277
2 TraesCS2D01G282000 chr2B 422499256 422504922 5666 False 2151.500000 4122 91.589500 1 5707 4 chr2B.!!$F2 5706

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
184 187 0.108804 AGATTACTGGCGGTCACACG 60.109 55.000 0.06 0.0 0.00 4.49 F
1052 1733 0.027586 GAGAGAGAGAGCGAACGAGC 59.972 60.000 0.00 0.0 37.41 5.03 F
2481 3164 0.031994 GCCAAGTTGCACGTTCCATT 59.968 50.000 0.00 0.0 0.00 3.16 F
2822 3508 3.463944 AGTACTTCAACCTTTGTCACCG 58.536 45.455 0.00 0.0 0.00 4.94 F
4180 4867 0.108041 CCGTGTTAATGTACCGGGCT 60.108 55.000 6.32 0.0 35.11 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 2067 0.034616 CATCCGAGATCCCCTTCAGC 59.965 60.0 0.0 0.0 0.00 4.26 R
2708 3392 0.904649 TGGTCCAGCCACTGTATCAG 59.095 55.0 0.0 0.0 43.61 2.90 R
4178 4865 0.804989 AACACGGCATAAAGAGCAGC 59.195 50.0 0.0 0.0 0.00 5.25 R
4742 5430 2.478370 GCAACCATGATGATCACCAACG 60.478 50.0 0.0 0.0 0.00 4.10 R
6171 6865 0.326264 ATGAGACAGCCCTCCACAAC 59.674 55.0 0.0 0.0 32.32 3.32 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
48 50 7.615757 AGATTCCCAAAACGGATTCTTTAGAAT 59.384 33.333 4.71 4.71 46.54 2.40
62 64 1.474330 TAGAATGCACCTCTCGCTGA 58.526 50.000 3.45 0.00 0.00 4.26
95 98 3.452627 AGTCCCATCTTAGTTGATTCGCT 59.547 43.478 0.00 0.00 0.00 4.93
100 103 2.798680 TCTTAGTTGATTCGCTCGCTC 58.201 47.619 0.00 0.00 0.00 5.03
116 119 3.656243 CTCGCGGTGTGCATTGCAG 62.656 63.158 12.53 1.06 46.97 4.41
120 123 2.336088 GGTGTGCATTGCAGCGTT 59.664 55.556 12.53 0.00 40.08 4.84
129 132 2.350772 GCATTGCAGCGTTAGTTTGTCT 60.351 45.455 3.15 0.00 0.00 3.41
130 133 3.482786 CATTGCAGCGTTAGTTTGTCTC 58.517 45.455 0.00 0.00 0.00 3.36
140 143 1.258676 AGTTTGTCTCGAGACCTCCC 58.741 55.000 36.01 22.92 44.15 4.30
142 145 1.550976 GTTTGTCTCGAGACCTCCCAT 59.449 52.381 36.01 0.00 44.15 4.00
143 146 1.186200 TTGTCTCGAGACCTCCCATG 58.814 55.000 36.01 0.00 44.15 3.66
149 152 1.326213 CGAGACCTCCCATGCAGAGT 61.326 60.000 9.40 0.00 0.00 3.24
156 159 2.749621 CCTCCCATGCAGAGTTTACAAC 59.250 50.000 9.40 0.00 0.00 3.32
158 161 1.135689 CCCATGCAGAGTTTACAACGC 60.136 52.381 0.00 0.00 36.23 4.84
159 162 1.135689 CCATGCAGAGTTTACAACGCC 60.136 52.381 0.00 0.00 36.23 5.68
160 163 1.135689 CATGCAGAGTTTACAACGCCC 60.136 52.381 0.00 0.00 36.23 6.13
161 164 0.179043 TGCAGAGTTTACAACGCCCA 60.179 50.000 0.00 0.00 36.23 5.36
162 165 1.165270 GCAGAGTTTACAACGCCCAT 58.835 50.000 0.00 0.00 36.23 4.00
163 166 1.539827 GCAGAGTTTACAACGCCCATT 59.460 47.619 0.00 0.00 36.23 3.16
164 167 2.745281 GCAGAGTTTACAACGCCCATTA 59.255 45.455 0.00 0.00 36.23 1.90
165 168 3.189702 GCAGAGTTTACAACGCCCATTAA 59.810 43.478 0.00 0.00 36.23 1.40
166 169 4.671766 GCAGAGTTTACAACGCCCATTAAG 60.672 45.833 0.00 0.00 36.23 1.85
167 170 4.693566 CAGAGTTTACAACGCCCATTAAGA 59.306 41.667 0.00 0.00 36.23 2.10
168 171 5.354234 CAGAGTTTACAACGCCCATTAAGAT 59.646 40.000 0.00 0.00 36.23 2.40
169 172 5.944007 AGAGTTTACAACGCCCATTAAGATT 59.056 36.000 0.00 0.00 36.23 2.40
170 173 7.065324 CAGAGTTTACAACGCCCATTAAGATTA 59.935 37.037 0.00 0.00 36.23 1.75
171 174 7.065443 AGAGTTTACAACGCCCATTAAGATTAC 59.935 37.037 0.00 0.00 36.23 1.89
172 175 6.882678 AGTTTACAACGCCCATTAAGATTACT 59.117 34.615 0.00 0.00 36.23 2.24
173 176 6.671614 TTACAACGCCCATTAAGATTACTG 57.328 37.500 0.00 0.00 0.00 2.74
174 177 3.945285 ACAACGCCCATTAAGATTACTGG 59.055 43.478 2.75 2.75 34.33 4.00
175 178 2.572290 ACGCCCATTAAGATTACTGGC 58.428 47.619 3.97 0.00 33.49 4.85
176 179 1.531149 CGCCCATTAAGATTACTGGCG 59.469 52.381 5.58 5.58 33.49 5.69
177 180 1.880027 GCCCATTAAGATTACTGGCGG 59.120 52.381 3.97 0.00 33.49 6.13
184 187 0.108804 AGATTACTGGCGGTCACACG 60.109 55.000 0.06 0.00 0.00 4.49
185 188 0.389426 GATTACTGGCGGTCACACGT 60.389 55.000 0.06 0.00 35.98 4.49
193 196 1.284715 CGGTCACACGTGCTAGACA 59.715 57.895 26.91 2.57 32.79 3.41
204 207 4.368756 CTAGACAGCACGCGACTC 57.631 61.111 15.93 0.14 0.00 3.36
209 212 1.409227 GACAGCACGCGACTCATGAG 61.409 60.000 21.37 21.37 0.00 2.90
218 221 2.621338 GCGACTCATGAGACCATTTGA 58.379 47.619 29.27 0.00 0.00 2.69
223 229 4.927049 ACTCATGAGACCATTTGACCAAT 58.073 39.130 29.27 0.00 0.00 3.16
230 236 5.774184 TGAGACCATTTGACCAATCATTGAA 59.226 36.000 0.00 0.00 33.85 2.69
235 241 8.326680 ACCATTTGACCAATCATTGAATTTTC 57.673 30.769 0.00 0.00 33.85 2.29
352 368 7.572759 TCGCTAATTTGAAACAAGTTCACTAG 58.427 34.615 0.00 0.00 46.09 2.57
362 378 8.519526 TGAAACAAGTTCACTAGTTTGAATGTT 58.480 29.630 11.14 9.53 41.47 2.71
363 379 8.911247 AAACAAGTTCACTAGTTTGAATGTTC 57.089 30.769 11.14 0.00 37.57 3.18
389 405 9.626045 CTTTTATGAATTTGTAAAGTCCACTCC 57.374 33.333 2.81 0.00 32.42 3.85
390 406 8.698973 TTTATGAATTTGTAAAGTCCACTCCA 57.301 30.769 2.81 0.00 32.42 3.86
557 630 4.546224 AACCTTCTAGGGTTCCCAAAAA 57.454 40.909 10.73 0.46 45.38 1.94
571 644 0.845768 CAAAAACGGTGCAGCGAAAG 59.154 50.000 41.29 22.16 0.00 2.62
586 659 3.055094 AGCGAAAGATGACAGTATGGGTT 60.055 43.478 0.00 0.00 43.62 4.11
687 761 4.869297 TGTTGGTTCAGTGCAATTTTCAAG 59.131 37.500 0.00 0.00 0.00 3.02
693 767 2.727798 CAGTGCAATTTTCAAGCTTCGG 59.272 45.455 0.00 0.00 0.00 4.30
901 1582 6.314400 TGCCTAAATGTATACGGAGTTGAAAC 59.686 38.462 0.00 0.00 37.78 2.78
992 1673 3.763897 ACTCGGAAGAAAAATCCCCAATG 59.236 43.478 0.00 0.00 41.32 2.82
999 1680 2.647846 AAAATCCCCAATGCCCTTCT 57.352 45.000 0.00 0.00 0.00 2.85
1004 1685 0.475906 CCCCAATGCCCTTCTCCTAG 59.524 60.000 0.00 0.00 0.00 3.02
1044 1725 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
1046 1727 2.362397 GAGAGAGAGAGAGAGAGAGCGA 59.638 54.545 0.00 0.00 0.00 4.93
1047 1728 2.766263 AGAGAGAGAGAGAGAGAGCGAA 59.234 50.000 0.00 0.00 0.00 4.70
1048 1729 2.866762 GAGAGAGAGAGAGAGAGCGAAC 59.133 54.545 0.00 0.00 0.00 3.95
1050 1731 1.206132 AGAGAGAGAGAGAGCGAACGA 59.794 52.381 0.00 0.00 0.00 3.85
1051 1732 1.593006 GAGAGAGAGAGAGCGAACGAG 59.407 57.143 0.00 0.00 0.00 4.18
1052 1733 0.027586 GAGAGAGAGAGCGAACGAGC 59.972 60.000 0.00 0.00 37.41 5.03
1053 1734 1.297304 GAGAGAGAGCGAACGAGCG 60.297 63.158 0.00 0.00 43.00 5.03
1054 1735 1.697772 GAGAGAGAGCGAACGAGCGA 61.698 60.000 5.91 0.00 43.00 4.93
1055 1736 1.297304 GAGAGAGCGAACGAGCGAG 60.297 63.158 5.91 0.00 43.00 5.03
1056 1737 2.947109 GAGAGCGAACGAGCGAGC 60.947 66.667 5.91 0.00 43.00 5.03
1066 1747 2.881266 CGAGCGAGCGAGAGAGAGG 61.881 68.421 0.00 0.00 0.00 3.69
1312 1993 2.741612 CAATTTTTGGTTCGCTCTGCA 58.258 42.857 0.00 0.00 0.00 4.41
1333 2014 1.134670 GCGCACCTCTTTAGATCTGGT 60.135 52.381 5.18 0.00 0.00 4.00
1334 2015 2.678190 GCGCACCTCTTTAGATCTGGTT 60.678 50.000 5.18 0.00 0.00 3.67
1335 2016 3.430374 GCGCACCTCTTTAGATCTGGTTA 60.430 47.826 5.18 0.00 0.00 2.85
1386 2067 2.560504 TCTGTGCTGTGTTGGTTAGTG 58.439 47.619 0.00 0.00 0.00 2.74
1456 2137 1.271543 TGGAGAAACTGGTGAGCCATG 60.272 52.381 0.00 0.00 45.05 3.66
1662 2345 2.631160 TGTCCACACGATGTTCCTTT 57.369 45.000 0.00 0.00 0.00 3.11
2223 2906 4.394300 CACAGGTGGCTTCTTCTCTATTTG 59.606 45.833 0.00 0.00 0.00 2.32
2239 2922 9.778741 TTCTCTATTTGTCATGTAACTGAACTT 57.221 29.630 0.00 0.00 0.00 2.66
2427 3110 7.761704 TGATGCTTCAGAGTAATGTAACTTCTC 59.238 37.037 0.00 0.00 0.00 2.87
2481 3164 0.031994 GCCAAGTTGCACGTTCCATT 59.968 50.000 0.00 0.00 0.00 3.16
2523 3206 3.882888 TGGAACACTCTTTGCTGGTTTAG 59.117 43.478 0.00 0.00 0.00 1.85
2707 3391 7.823665 TGAAATCACGACTAGTTATGTACTGT 58.176 34.615 0.00 0.00 37.73 3.55
2708 3392 7.966753 TGAAATCACGACTAGTTATGTACTGTC 59.033 37.037 0.00 0.00 37.73 3.51
2709 3393 7.627298 AATCACGACTAGTTATGTACTGTCT 57.373 36.000 0.00 0.00 37.73 3.41
2710 3394 6.418585 TCACGACTAGTTATGTACTGTCTG 57.581 41.667 0.00 0.00 37.73 3.51
2822 3508 3.463944 AGTACTTCAACCTTTGTCACCG 58.536 45.455 0.00 0.00 0.00 4.94
2834 3520 4.420168 CTTTGTCACCGTTTGTCAATTGT 58.580 39.130 5.13 0.00 33.91 2.71
2858 3544 8.342634 TGTTCTTTATGCTGTTCAAGTAGAAAC 58.657 33.333 0.00 0.00 38.13 2.78
2876 3562 6.325919 AGAAACGTTCTTATTGGCATTTGA 57.674 33.333 0.00 0.00 36.36 2.69
2965 3651 7.549488 GGTATGTGCACAGTCTATCTTAGTTTT 59.451 37.037 25.84 4.68 0.00 2.43
3494 4181 6.875948 TGTAGTTGTTTGCATGATTACACT 57.124 33.333 0.00 0.00 0.00 3.55
3500 4187 5.211454 TGTTTGCATGATTACACTGTTTCG 58.789 37.500 0.00 0.00 0.00 3.46
3644 4331 6.151144 CGACCATTAAGGAACAAGAAAAGGAT 59.849 38.462 0.00 0.00 41.22 3.24
3995 4682 7.120579 CAGGCACCTTAAAAGTTATGTACATGA 59.879 37.037 18.81 7.50 0.00 3.07
4107 4794 5.579904 GGTCTTTTCCTCAAGGTAATACGAC 59.420 44.000 0.00 1.54 36.34 4.34
4138 4825 7.928307 AAGCTGAATCTTAGTTTCATAAGCA 57.072 32.000 14.06 0.00 32.94 3.91
4175 4862 9.738832 ATTTTATTTATGCCGTGTTAATGTACC 57.261 29.630 0.00 0.00 0.00 3.34
4176 4863 4.861389 TTTATGCCGTGTTAATGTACCG 57.139 40.909 0.00 0.00 0.00 4.02
4177 4864 1.658994 ATGCCGTGTTAATGTACCGG 58.341 50.000 0.00 0.00 41.50 5.28
4178 4865 0.391395 TGCCGTGTTAATGTACCGGG 60.391 55.000 6.32 0.00 39.05 5.73
4179 4866 1.708193 GCCGTGTTAATGTACCGGGC 61.708 60.000 6.32 0.00 39.05 6.13
4180 4867 0.108041 CCGTGTTAATGTACCGGGCT 60.108 55.000 6.32 0.00 35.11 5.19
4181 4868 1.003851 CGTGTTAATGTACCGGGCTG 58.996 55.000 6.32 0.00 0.00 4.85
4182 4869 0.730840 GTGTTAATGTACCGGGCTGC 59.269 55.000 6.32 0.00 0.00 5.25
4183 4870 0.616371 TGTTAATGTACCGGGCTGCT 59.384 50.000 6.32 0.00 0.00 4.24
4184 4871 1.296727 GTTAATGTACCGGGCTGCTC 58.703 55.000 6.32 0.00 0.00 4.26
4185 4872 1.134491 GTTAATGTACCGGGCTGCTCT 60.134 52.381 6.32 0.00 0.00 4.09
4186 4873 1.200519 TAATGTACCGGGCTGCTCTT 58.799 50.000 6.32 0.00 0.00 2.85
4187 4874 0.328258 AATGTACCGGGCTGCTCTTT 59.672 50.000 6.32 0.00 0.00 2.52
4188 4875 1.200519 ATGTACCGGGCTGCTCTTTA 58.799 50.000 6.32 0.00 0.00 1.85
4189 4876 1.200519 TGTACCGGGCTGCTCTTTAT 58.799 50.000 6.32 0.00 0.00 1.40
4190 4877 1.134521 TGTACCGGGCTGCTCTTTATG 60.135 52.381 6.32 0.00 0.00 1.90
4191 4878 0.179056 TACCGGGCTGCTCTTTATGC 60.179 55.000 6.32 0.00 0.00 3.14
4192 4879 2.189499 CCGGGCTGCTCTTTATGCC 61.189 63.158 0.00 0.00 44.22 4.40
4193 4880 2.537560 CGGGCTGCTCTTTATGCCG 61.538 63.158 0.00 0.00 45.75 5.69
4194 4881 1.452108 GGGCTGCTCTTTATGCCGT 60.452 57.895 0.00 0.00 45.75 5.68
4195 4882 1.718757 GGGCTGCTCTTTATGCCGTG 61.719 60.000 0.00 0.00 45.75 4.94
4196 4883 1.026718 GGCTGCTCTTTATGCCGTGT 61.027 55.000 0.00 0.00 35.79 4.49
4197 4884 0.804989 GCTGCTCTTTATGCCGTGTT 59.195 50.000 0.00 0.00 0.00 3.32
4198 4885 2.006888 GCTGCTCTTTATGCCGTGTTA 58.993 47.619 0.00 0.00 0.00 2.41
4199 4886 2.418628 GCTGCTCTTTATGCCGTGTTAA 59.581 45.455 0.00 0.00 0.00 2.01
4200 4887 3.065371 GCTGCTCTTTATGCCGTGTTAAT 59.935 43.478 0.00 0.00 0.00 1.40
4201 4888 4.591202 CTGCTCTTTATGCCGTGTTAATG 58.409 43.478 0.00 0.00 0.00 1.90
4202 4889 4.006989 TGCTCTTTATGCCGTGTTAATGT 58.993 39.130 0.00 0.00 0.00 2.71
4203 4890 5.179533 TGCTCTTTATGCCGTGTTAATGTA 58.820 37.500 0.00 0.00 0.00 2.29
4204 4891 5.064198 TGCTCTTTATGCCGTGTTAATGTAC 59.936 40.000 0.00 0.00 0.00 2.90
4368 5055 7.798982 GTCCGAGAAAACTTTTATTGTTGAGAG 59.201 37.037 0.00 0.00 0.00 3.20
4742 5430 1.227380 CATCTCCGCTACACCTGGC 60.227 63.158 0.00 0.00 0.00 4.85
4795 5483 9.184523 TCGACATTTTGGGTATTATTCTCATTT 57.815 29.630 0.00 0.00 0.00 2.32
5033 5724 1.783979 TGTTCCATGTGTTTACCCCCT 59.216 47.619 0.00 0.00 0.00 4.79
5152 5843 4.227300 TGAAGAACAGGCATTACCAGGTAT 59.773 41.667 0.00 0.00 43.14 2.73
5250 5941 3.190118 AGCTAGCTTGCACAATGACTTTC 59.810 43.478 22.05 0.00 34.99 2.62
5368 6059 9.614792 GTTAGATAGTTGATTACCCATGAAACT 57.385 33.333 0.00 0.00 0.00 2.66
5790 6484 2.269940 AGCAGGAGTGATTTAGTGGGT 58.730 47.619 0.00 0.00 0.00 4.51
5801 6495 6.899114 GTGATTTAGTGGGTCACTGTTTTAG 58.101 40.000 10.46 0.00 45.01 1.85
5829 6523 4.344968 CCAAGACCAAAGAAACCCTCAATT 59.655 41.667 0.00 0.00 0.00 2.32
5859 6553 5.818678 AGTCTACACCCAAATGTCTGTAA 57.181 39.130 0.00 0.00 33.85 2.41
5909 6603 1.227118 GCTAGAGAAGCCACCTCGC 60.227 63.158 0.00 0.00 46.25 5.03
5916 6610 2.885774 GAAGCCACCTCGCGGTAGTC 62.886 65.000 6.13 0.00 43.24 2.59
5926 6620 2.296471 CTCGCGGTAGTCCATCCTAATT 59.704 50.000 6.13 0.00 0.00 1.40
5927 6621 3.489355 TCGCGGTAGTCCATCCTAATTA 58.511 45.455 6.13 0.00 0.00 1.40
6071 6765 3.655777 ACAATGTAGTCCCTTCCCTCAAA 59.344 43.478 0.00 0.00 0.00 2.69
6146 6840 5.634859 CCACTGTTTATCAAATTGCCAACTC 59.365 40.000 0.00 0.00 0.00 3.01
6183 6877 1.985159 TGAATACAGTTGTGGAGGGCT 59.015 47.619 0.00 0.00 0.00 5.19
6196 6890 1.919600 GAGGGCTGTCTCATGGGCTT 61.920 60.000 0.00 0.00 34.13 4.35
6255 6949 2.014335 CGCAAGGACATCTGATGTGA 57.986 50.000 26.71 0.00 45.03 3.58
6256 6950 2.558378 CGCAAGGACATCTGATGTGAT 58.442 47.619 26.71 12.49 45.03 3.06
6262 6956 2.479275 GGACATCTGATGTGATGATGCG 59.521 50.000 26.71 0.00 45.03 4.73
6293 6987 0.967887 TCGGGCAGGAGAAGAGTCTG 60.968 60.000 0.00 0.00 32.80 3.51
6296 6990 1.809209 GCAGGAGAAGAGTCTGCGC 60.809 63.158 0.00 0.00 46.35 6.09
6300 6994 2.094494 CAGGAGAAGAGTCTGCGCTTTA 60.094 50.000 9.73 0.00 46.35 1.85
6420 7114 3.764434 ACAACATCATAGAGACACGACCT 59.236 43.478 0.00 0.00 0.00 3.85
6464 7158 2.812358 AACCGCCAAACCAAGAATTC 57.188 45.000 0.00 0.00 0.00 2.17
6473 7167 1.523758 ACCAAGAATTCACGGTCTGC 58.476 50.000 8.44 0.00 0.00 4.26
6534 7228 6.915544 ATAGTGCTGTGTATGACATGAAAG 57.084 37.500 0.00 0.00 32.74 2.62
6638 7332 0.385029 GCACAAGCAACACATGGACA 59.615 50.000 0.00 0.00 41.58 4.02
6692 7386 1.269723 CTTGAGCATAGGCATGGCATG 59.730 52.381 22.99 22.99 44.61 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 86 0.866061 GCGAGCGAGCGAATCAACTA 60.866 55.000 1.41 0.00 0.00 2.24
84 87 2.161486 GCGAGCGAGCGAATCAACT 61.161 57.895 1.41 0.00 0.00 3.16
104 107 0.238289 ACTAACGCTGCAATGCACAC 59.762 50.000 2.72 0.00 33.79 3.82
116 119 1.984297 GGTCTCGAGACAAACTAACGC 59.016 52.381 38.52 19.39 46.47 4.84
117 120 3.490399 GAGGTCTCGAGACAAACTAACG 58.510 50.000 38.52 0.56 46.47 3.18
120 123 2.224942 TGGGAGGTCTCGAGACAAACTA 60.225 50.000 38.52 24.93 46.47 2.24
129 132 1.000359 TCTGCATGGGAGGTCTCGA 60.000 57.895 0.00 0.00 0.00 4.04
130 133 1.326213 ACTCTGCATGGGAGGTCTCG 61.326 60.000 6.43 0.00 35.34 4.04
140 143 1.135689 GGGCGTTGTAAACTCTGCATG 60.136 52.381 0.00 0.00 46.99 4.06
142 145 0.179043 TGGGCGTTGTAAACTCTGCA 60.179 50.000 0.00 0.00 46.99 4.41
143 146 1.165270 ATGGGCGTTGTAAACTCTGC 58.835 50.000 0.00 0.00 46.99 4.26
149 152 6.094325 CCAGTAATCTTAATGGGCGTTGTAAA 59.906 38.462 8.25 0.00 43.25 2.01
156 159 1.531149 CGCCAGTAATCTTAATGGGCG 59.469 52.381 15.86 14.87 46.11 6.13
158 161 3.139077 GACCGCCAGTAATCTTAATGGG 58.861 50.000 15.86 7.80 46.11 4.00
160 163 4.034048 GTGTGACCGCCAGTAATCTTAATG 59.966 45.833 0.00 0.00 0.00 1.90
161 164 4.189231 GTGTGACCGCCAGTAATCTTAAT 58.811 43.478 0.00 0.00 0.00 1.40
162 165 3.592059 GTGTGACCGCCAGTAATCTTAA 58.408 45.455 0.00 0.00 0.00 1.85
163 166 2.416296 CGTGTGACCGCCAGTAATCTTA 60.416 50.000 0.00 0.00 0.00 2.10
164 167 1.671850 CGTGTGACCGCCAGTAATCTT 60.672 52.381 0.00 0.00 0.00 2.40
165 168 0.108804 CGTGTGACCGCCAGTAATCT 60.109 55.000 0.00 0.00 0.00 2.40
166 169 0.389426 ACGTGTGACCGCCAGTAATC 60.389 55.000 0.00 0.00 0.00 1.75
167 170 0.669318 CACGTGTGACCGCCAGTAAT 60.669 55.000 7.58 0.00 0.00 1.89
168 171 1.300311 CACGTGTGACCGCCAGTAA 60.300 57.895 7.58 0.00 0.00 2.24
169 172 2.337170 CACGTGTGACCGCCAGTA 59.663 61.111 7.58 0.00 0.00 2.74
171 174 3.567478 TAGCACGTGTGACCGCCAG 62.567 63.158 18.38 0.00 0.00 4.85
172 175 3.567478 CTAGCACGTGTGACCGCCA 62.567 63.158 18.38 0.00 0.00 5.69
173 176 2.809601 CTAGCACGTGTGACCGCC 60.810 66.667 18.38 0.00 0.00 6.13
174 177 2.087009 GTCTAGCACGTGTGACCGC 61.087 63.158 18.38 0.54 0.00 5.68
175 178 0.729478 CTGTCTAGCACGTGTGACCG 60.729 60.000 24.36 18.47 0.00 4.79
176 179 3.108521 CTGTCTAGCACGTGTGACC 57.891 57.895 24.36 8.83 0.00 4.02
193 196 1.153939 GTCTCATGAGTCGCGTGCT 60.154 57.895 21.92 5.74 33.39 4.40
195 198 0.179127 ATGGTCTCATGAGTCGCGTG 60.179 55.000 21.92 0.00 34.72 5.34
203 206 4.920999 TGATTGGTCAAATGGTCTCATGA 58.079 39.130 0.00 0.00 33.18 3.07
204 207 5.847111 ATGATTGGTCAAATGGTCTCATG 57.153 39.130 0.00 0.00 38.01 3.07
209 212 7.910441 AAATTCAATGATTGGTCAAATGGTC 57.090 32.000 5.20 0.00 38.01 4.02
319 335 9.959749 ACTTGTTTCAAATTAGCGATCTTTTTA 57.040 25.926 0.00 0.00 0.00 1.52
326 342 6.970484 AGTGAACTTGTTTCAAATTAGCGAT 58.030 32.000 0.00 0.00 46.09 4.58
328 344 7.352739 ACTAGTGAACTTGTTTCAAATTAGCG 58.647 34.615 0.00 0.00 46.09 4.26
335 351 8.519526 ACATTCAAACTAGTGAACTTGTTTCAA 58.480 29.630 16.60 12.66 46.09 2.69
363 379 9.626045 GGAGTGGACTTTACAAATTCATAAAAG 57.374 33.333 0.00 0.00 34.19 2.27
557 630 1.005037 TCATCTTTCGCTGCACCGT 60.005 52.632 0.64 0.00 0.00 4.83
571 644 3.914426 AGACCAACCCATACTGTCATC 57.086 47.619 0.00 0.00 0.00 2.92
575 648 6.691255 TTTAAGTAGACCAACCCATACTGT 57.309 37.500 0.00 0.00 0.00 3.55
576 649 7.446013 TGTTTTTAAGTAGACCAACCCATACTG 59.554 37.037 0.00 0.00 0.00 2.74
586 659 6.592607 CCTTCGCTATGTTTTTAAGTAGACCA 59.407 38.462 0.00 0.00 0.00 4.02
648 722 6.756074 TGAACCAACAGCAAAGAAAAATAGTG 59.244 34.615 0.00 0.00 0.00 2.74
658 732 1.134753 TGCACTGAACCAACAGCAAAG 59.865 47.619 0.00 0.00 41.06 2.77
693 767 2.435234 TGATTGTACGCCACCCGC 60.435 61.111 0.00 0.00 41.76 6.13
764 1435 9.658799 CAACGGATAGATAATTGGACATAGAAT 57.341 33.333 0.00 0.00 0.00 2.40
921 1602 3.288484 CTGGACGGTCAGCTGCTA 58.712 61.111 9.47 0.00 0.00 3.49
992 1673 3.172106 GGGGGCTAGGAGAAGGGC 61.172 72.222 0.00 0.00 0.00 5.19
1044 1725 2.646244 CTCTCGCTCGCTCGTTCG 60.646 66.667 0.00 0.00 0.00 3.95
1046 1727 1.701545 CTCTCTCTCGCTCGCTCGTT 61.702 60.000 0.00 0.00 0.00 3.85
1047 1728 2.125472 TCTCTCTCGCTCGCTCGT 60.125 61.111 0.00 0.00 0.00 4.18
1048 1729 2.625906 CTCTCTCTCGCTCGCTCG 59.374 66.667 0.00 0.00 0.00 5.03
1050 1731 2.515991 CCCTCTCTCTCGCTCGCT 60.516 66.667 0.00 0.00 0.00 4.93
1051 1732 4.264638 GCCCTCTCTCTCGCTCGC 62.265 72.222 0.00 0.00 0.00 5.03
1052 1733 3.591835 GGCCCTCTCTCTCGCTCG 61.592 72.222 0.00 0.00 0.00 5.03
1053 1734 2.123897 AGGCCCTCTCTCTCGCTC 60.124 66.667 0.00 0.00 0.00 5.03
1054 1735 2.123897 GAGGCCCTCTCTCTCGCT 60.124 66.667 2.64 0.00 39.38 4.93
1055 1736 1.398958 AATGAGGCCCTCTCTCTCGC 61.399 60.000 12.94 0.00 42.86 5.03
1056 1737 0.673437 GAATGAGGCCCTCTCTCTCG 59.327 60.000 12.94 0.00 42.86 4.04
1312 1993 1.137872 CCAGATCTAAAGAGGTGCGCT 59.862 52.381 9.73 0.00 0.00 5.92
1333 2014 9.710979 GCATGAAACGCTAACTGTTAATAATAA 57.289 29.630 0.00 0.00 0.00 1.40
1334 2015 8.059502 CGCATGAAACGCTAACTGTTAATAATA 58.940 33.333 0.00 0.00 0.00 0.98
1335 2016 6.905076 CGCATGAAACGCTAACTGTTAATAAT 59.095 34.615 0.00 0.00 0.00 1.28
1386 2067 0.034616 CATCCGAGATCCCCTTCAGC 59.965 60.000 0.00 0.00 0.00 4.26
1456 2137 1.134848 AGATCAACGGAGCAAGAGAGC 60.135 52.381 0.00 0.00 0.00 4.09
1493 2174 8.738645 AAACTCCCAAATATGTAGCTTTCTAG 57.261 34.615 0.00 0.00 0.00 2.43
1494 2175 9.528489 AAAAACTCCCAAATATGTAGCTTTCTA 57.472 29.630 0.00 0.00 0.00 2.10
1507 2188 6.039605 CCAAAAATCTGCAAAAACTCCCAAAT 59.960 34.615 0.00 0.00 0.00 2.32
1712 2395 8.947055 AAACACTTGCAACTTGAATTTAGAAT 57.053 26.923 9.77 0.00 0.00 2.40
1894 2577 5.624738 CGCTTACCTAAGTGTCAAGGAGAAT 60.625 44.000 0.00 0.00 38.60 2.40
2481 3164 2.173758 TACCGCTTGCCGATTGACCA 62.174 55.000 0.00 0.00 40.02 4.02
2707 3391 1.195115 GGTCCAGCCACTGTATCAGA 58.805 55.000 3.70 0.00 35.18 3.27
2708 3392 0.904649 TGGTCCAGCCACTGTATCAG 59.095 55.000 0.00 0.00 43.61 2.90
2709 3393 3.081048 TGGTCCAGCCACTGTATCA 57.919 52.632 0.00 0.00 43.61 2.15
2822 3508 7.698836 ACAGCATAAAGAACAATTGACAAAC 57.301 32.000 13.59 0.00 0.00 2.93
2834 3520 7.225931 ACGTTTCTACTTGAACAGCATAAAGAA 59.774 33.333 0.00 0.00 33.88 2.52
2858 3544 5.942872 AGAACTCAAATGCCAATAAGAACG 58.057 37.500 0.00 0.00 0.00 3.95
3460 4147 5.414454 TGCAAACAACTACAAACTCAAGTCT 59.586 36.000 0.00 0.00 0.00 3.24
3494 4181 5.187687 AGGGAAGTTCAAAGTAACGAAACA 58.812 37.500 5.01 0.00 34.46 2.83
3500 4187 6.004574 AGATGGAAGGGAAGTTCAAAGTAAC 58.995 40.000 5.01 0.00 0.00 2.50
3644 4331 7.147949 GCACTTATACTTACAGGAGTCAACCTA 60.148 40.741 0.00 0.00 38.32 3.08
3745 4432 4.805192 CCAAAATATGCATTGCTTAACGCT 59.195 37.500 3.54 0.00 40.11 5.07
4107 4794 8.018677 TGAAACTAAGATTCAGCTTTAACTCG 57.981 34.615 0.00 0.00 33.15 4.18
4175 4862 2.537560 CGGCATAAAGAGCAGCCCG 61.538 63.158 0.00 0.00 44.18 6.13
4176 4863 1.452108 ACGGCATAAAGAGCAGCCC 60.452 57.895 0.00 0.00 44.18 5.19
4177 4864 1.026718 ACACGGCATAAAGAGCAGCC 61.027 55.000 0.00 0.00 43.61 4.85
4178 4865 0.804989 AACACGGCATAAAGAGCAGC 59.195 50.000 0.00 0.00 0.00 5.25
4179 4866 4.094887 ACATTAACACGGCATAAAGAGCAG 59.905 41.667 0.00 0.00 0.00 4.24
4180 4867 4.006989 ACATTAACACGGCATAAAGAGCA 58.993 39.130 0.00 0.00 0.00 4.26
4181 4868 4.616181 ACATTAACACGGCATAAAGAGC 57.384 40.909 0.00 0.00 0.00 4.09
4182 4869 6.903883 AGTACATTAACACGGCATAAAGAG 57.096 37.500 0.00 0.00 0.00 2.85
4183 4870 7.064134 CAGAAGTACATTAACACGGCATAAAGA 59.936 37.037 0.00 0.00 0.00 2.52
4184 4871 7.064134 TCAGAAGTACATTAACACGGCATAAAG 59.936 37.037 0.00 0.00 0.00 1.85
4185 4872 6.874664 TCAGAAGTACATTAACACGGCATAAA 59.125 34.615 0.00 0.00 0.00 1.40
4186 4873 6.399743 TCAGAAGTACATTAACACGGCATAA 58.600 36.000 0.00 0.00 0.00 1.90
4187 4874 5.968254 TCAGAAGTACATTAACACGGCATA 58.032 37.500 0.00 0.00 0.00 3.14
4188 4875 4.827692 TCAGAAGTACATTAACACGGCAT 58.172 39.130 0.00 0.00 0.00 4.40
4189 4876 4.260139 TCAGAAGTACATTAACACGGCA 57.740 40.909 0.00 0.00 0.00 5.69
4190 4877 5.178809 AGTTTCAGAAGTACATTAACACGGC 59.821 40.000 0.00 0.00 0.00 5.68
4191 4878 6.780706 AGTTTCAGAAGTACATTAACACGG 57.219 37.500 0.00 0.00 0.00 4.94
4204 4891 9.788960 GCACCCTAAATAATAAAGTTTCAGAAG 57.211 33.333 0.00 0.00 0.00 2.85
4332 5019 2.526304 TTTCTCGGACACTTCCACAG 57.474 50.000 0.00 0.00 43.00 3.66
4346 5033 8.621286 TGGTCTCTCAACAATAAAAGTTTTCTC 58.379 33.333 3.60 0.00 0.00 2.87
4368 5055 2.615912 GCTGAGAGGTTTGCATATGGTC 59.384 50.000 4.56 0.00 0.00 4.02
4659 5347 9.889128 CCATTTAACAGGTTATCAATTTTCCAT 57.111 29.630 0.00 0.00 0.00 3.41
4742 5430 2.478370 GCAACCATGATGATCACCAACG 60.478 50.000 0.00 0.00 0.00 4.10
5050 5741 3.508012 GCTCTCAGGTTCTCTTCACTACA 59.492 47.826 0.00 0.00 0.00 2.74
5152 5843 5.649970 TGAAACTAAGGACTGGGGTAAAA 57.350 39.130 0.00 0.00 0.00 1.52
5250 5941 0.603707 ACACACCATGAGTTGCCTCG 60.604 55.000 0.00 0.00 40.85 4.63
5268 5959 5.056480 TGATTGATTCCGGTATCACATGAC 58.944 41.667 21.95 12.27 34.41 3.06
5403 6095 9.736023 GAATGAACCAATATTAGTGTCAATTCC 57.264 33.333 0.00 0.00 0.00 3.01
5608 6300 4.234574 CACGTCTACAGTAATTGCTGTCA 58.765 43.478 29.16 16.30 45.63 3.58
5739 6431 1.376466 GCTCCTGGCAGTTTCCTCA 59.624 57.895 14.43 0.00 41.35 3.86
5764 6456 5.482908 CACTAAATCACTCCTGCTACTGTT 58.517 41.667 0.00 0.00 0.00 3.16
5765 6457 4.081420 CCACTAAATCACTCCTGCTACTGT 60.081 45.833 0.00 0.00 0.00 3.55
5790 6484 5.364446 TGGTCTTGGTACTCTAAAACAGTGA 59.636 40.000 0.00 0.00 0.00 3.41
5801 6495 3.819337 GGGTTTCTTTGGTCTTGGTACTC 59.181 47.826 0.00 0.00 0.00 2.59
5829 6523 6.014647 ACATTTGGGTGTAGACTACTGTAGA 58.985 40.000 21.01 0.00 0.00 2.59
5859 6553 4.737855 ATAATCGACAGGCAGTTAGTGT 57.262 40.909 0.00 0.00 0.00 3.55
5908 6602 7.506328 AAAAATAATTAGGATGGACTACCGC 57.494 36.000 0.00 0.00 39.42 5.68
6146 6840 5.527214 TGTATTCAGTGCCCTTTATCATTCG 59.473 40.000 0.00 0.00 0.00 3.34
6171 6865 0.326264 ATGAGACAGCCCTCCACAAC 59.674 55.000 0.00 0.00 32.32 3.32
6183 6877 0.322816 GCCTTCAAGCCCATGAGACA 60.323 55.000 0.00 0.00 0.00 3.41
6196 6890 3.306472 ACCAGTTTAGGTTTGCCTTCA 57.694 42.857 0.00 0.00 44.18 3.02
6208 6902 3.497227 GGAGTGGCCTTACAACCAGTTTA 60.497 47.826 3.32 0.00 39.76 2.01
6214 6908 0.035343 GAGGGAGTGGCCTTACAACC 60.035 60.000 3.32 1.01 36.66 3.77
6247 6941 2.159327 TAGGCGCATCATCACATCAG 57.841 50.000 10.83 0.00 0.00 2.90
6248 6942 2.037511 TCATAGGCGCATCATCACATCA 59.962 45.455 10.83 0.00 0.00 3.07
6249 6943 2.691927 TCATAGGCGCATCATCACATC 58.308 47.619 10.83 0.00 0.00 3.06
6250 6944 2.845363 TCATAGGCGCATCATCACAT 57.155 45.000 10.83 0.00 0.00 3.21
6251 6945 2.613595 GTTTCATAGGCGCATCATCACA 59.386 45.455 10.83 0.00 0.00 3.58
6252 6946 2.613595 TGTTTCATAGGCGCATCATCAC 59.386 45.455 10.83 0.00 0.00 3.06
6253 6947 2.916640 TGTTTCATAGGCGCATCATCA 58.083 42.857 10.83 0.00 0.00 3.07
6254 6948 3.424039 CGATGTTTCATAGGCGCATCATC 60.424 47.826 10.83 9.41 36.64 2.92
6255 6949 2.481568 CGATGTTTCATAGGCGCATCAT 59.518 45.455 10.83 0.00 36.64 2.45
6256 6950 1.866601 CGATGTTTCATAGGCGCATCA 59.133 47.619 10.83 0.00 36.64 3.07
6262 6956 0.947244 CTGCCCGATGTTTCATAGGC 59.053 55.000 13.12 13.12 40.87 3.93
6296 6990 0.321653 AAGCCCACACGGAGCTAAAG 60.322 55.000 0.00 0.00 37.70 1.85
6300 6994 2.032681 GAAAGCCCACACGGAGCT 59.967 61.111 0.00 0.00 39.62 4.09
6332 7026 0.180642 AGCTCTCATGCATGGTCCAG 59.819 55.000 25.97 15.83 34.99 3.86
6385 7079 2.224992 TGATGTTGTATGGGTTGTGCCT 60.225 45.455 0.00 0.00 37.43 4.75
6387 7081 4.881273 TCTATGATGTTGTATGGGTTGTGC 59.119 41.667 0.00 0.00 0.00 4.57
6388 7082 6.258727 GTCTCTATGATGTTGTATGGGTTGTG 59.741 42.308 0.00 0.00 0.00 3.33
6389 7083 6.070251 TGTCTCTATGATGTTGTATGGGTTGT 60.070 38.462 0.00 0.00 0.00 3.32
6390 7084 6.258727 GTGTCTCTATGATGTTGTATGGGTTG 59.741 42.308 0.00 0.00 0.00 3.77
6391 7085 6.349300 GTGTCTCTATGATGTTGTATGGGTT 58.651 40.000 0.00 0.00 0.00 4.11
6420 7114 2.215196 GTCGGTTTGGTTCTGCAGTTA 58.785 47.619 14.67 0.00 0.00 2.24
6464 7158 1.517257 CTTCTAGCCGCAGACCGTG 60.517 63.158 0.00 0.00 34.38 4.94
6473 7167 2.280628 GGTTTGATGGTCTTCTAGCCG 58.719 52.381 0.00 0.00 0.00 5.52
6518 7212 4.284829 TCCTGCTTTCATGTCATACACA 57.715 40.909 0.00 0.00 40.18 3.72
6520 7214 5.534278 TGTTTTCCTGCTTTCATGTCATACA 59.466 36.000 0.00 0.00 0.00 2.29
6534 7228 5.008118 GCTCTTATAGTGGATGTTTTCCTGC 59.992 44.000 0.00 0.00 45.68 4.85
6552 7246 2.135139 CGACTGTTGCACAAGCTCTTA 58.865 47.619 0.00 0.00 42.74 2.10
6638 7332 1.528309 CAAGGTTGGTGGCGGACTT 60.528 57.895 0.00 0.00 0.00 3.01
6644 7338 1.205893 TGTTTGTTCAAGGTTGGTGGC 59.794 47.619 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.