Multiple sequence alignment - TraesCS5A01G484300

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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 TraesCS5A01G484300 chr5A 100.000 4403 0 0 1 4403 655465022 655460620 0.000000e+00 8131
1 TraesCS5A01G484300 chr5A 85.161 2015 253 25 1229 3216 655990132 655992127 0.000000e+00 2023
2 TraesCS5A01G484300 chr5B 92.615 3453 188 31 863 4275 664685334 664681909 0.000000e+00 4902
3 TraesCS5A01G484300 chr5B 87.223 587 65 7 2635 3216 664948979 664949560 0.000000e+00 660
4 TraesCS5A01G484300 chr5B 80.519 385 56 10 18 392 664686324 664685949 1.210000e-70 278
5 TraesCS5A01G484300 chr5B 87.435 191 18 3 598 786 664685560 664685374 9.590000e-52 215
6 TraesCS5A01G484300 chr5D 93.574 2770 128 22 770 3505 527907597 527904844 0.000000e+00 4084
7 TraesCS5A01G484300 chr5D 85.228 2085 260 29 1156 3216 528141970 528144030 0.000000e+00 2100
8 TraesCS5A01G484300 chr5D 92.658 395 26 1 34 428 527919525 527919134 2.300000e-157 566
9 TraesCS5A01G484300 chr5D 92.658 395 26 1 34 428 527924888 527924497 2.300000e-157 566
10 TraesCS5A01G484300 chr5D 91.635 263 16 4 3488 3750 527903894 527903638 4.190000e-95 359
11 TraesCS5A01G484300 chr5D 91.803 122 7 3 637 755 527907704 527907583 2.720000e-37 167
12 TraesCS5A01G484300 chr5D 95.192 104 4 1 427 529 527907938 527907835 3.520000e-36 163
13 TraesCS5A01G484300 chrUn 94.372 1226 54 5 1949 3162 263457706 263458928 0.000000e+00 1868
14 TraesCS5A01G484300 chrUn 93.761 561 27 6 3488 4048 263460637 263461189 0.000000e+00 835
15 TraesCS5A01G484300 chrUn 92.507 347 18 5 4059 4403 263461244 263461584 1.420000e-134 490
16 TraesCS5A01G484300 chrUn 88.889 351 18 10 3164 3505 263459341 263459679 3.170000e-111 412
17 TraesCS5A01G484300 chrUn 92.271 207 6 7 770 967 263456596 263456801 7.210000e-73 285
18 TraesCS5A01G484300 chrUn 91.803 122 7 3 637 755 263456489 263456610 2.720000e-37 167
19 TraesCS5A01G484300 chrUn 95.192 104 4 1 427 529 263456255 263456358 3.520000e-36 163
20 TraesCS5A01G484300 chr2B 78.765 664 124 14 2212 2859 551638799 551639461 3.150000e-116 429
21 TraesCS5A01G484300 chr2D 78.306 673 120 16 2212 2859 472471434 472472105 1.140000e-110 411
22 TraesCS5A01G484300 chr2A 77.663 676 122 17 2212 2859 613992437 613993111 6.910000e-103 385
23 TraesCS5A01G484300 chr4D 73.107 383 77 22 2397 2766 38304593 38304962 3.600000e-21 113


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 TraesCS5A01G484300 chr5A 655460620 655465022 4402 True 8131.000000 8131 100.000000 1 4403 1 chr5A.!!$R1 4402
1 TraesCS5A01G484300 chr5A 655990132 655992127 1995 False 2023.000000 2023 85.161000 1229 3216 1 chr5A.!!$F1 1987
2 TraesCS5A01G484300 chr5B 664681909 664686324 4415 True 1798.333333 4902 86.856333 18 4275 3 chr5B.!!$R1 4257
3 TraesCS5A01G484300 chr5B 664948979 664949560 581 False 660.000000 660 87.223000 2635 3216 1 chr5B.!!$F1 581
4 TraesCS5A01G484300 chr5D 528141970 528144030 2060 False 2100.000000 2100 85.228000 1156 3216 1 chr5D.!!$F1 2060
5 TraesCS5A01G484300 chr5D 527903638 527907938 4300 True 1193.250000 4084 93.051000 427 3750 4 chr5D.!!$R3 3323
6 TraesCS5A01G484300 chrUn 263456255 263461584 5329 False 602.857143 1868 92.685000 427 4403 7 chrUn.!!$F1 3976
7 TraesCS5A01G484300 chr2B 551638799 551639461 662 False 429.000000 429 78.765000 2212 2859 1 chr2B.!!$F1 647
8 TraesCS5A01G484300 chr2D 472471434 472472105 671 False 411.000000 411 78.306000 2212 2859 1 chr2D.!!$F1 647
9 TraesCS5A01G484300 chr2A 613992437 613993111 674 False 385.000000 385 77.663000 2212 2859 1 chr2A.!!$F1 647

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
22 23 0.524862 GACGAGCAAGTCCGGTCTTA 59.475 55.0 13.73 0.00 35.22 2.10 F
398 407 0.618458 TGAGAATACTGGTGGCACCC 59.382 55.0 32.61 16.58 37.50 4.61 F
1355 1676 0.602905 CCAACGACACCAAGGAGACC 60.603 60.0 0.00 0.00 0.00 3.85 F
2189 2545 0.105964 CCGAGGAGGATGAGGAAGGA 60.106 60.0 0.00 0.00 45.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 1328 0.248296 GCAACGAACAGCCAACGAAA 60.248 50.0 0.00 0.0 0.00 3.46 R
2060 2393 0.980423 GTGCCAGGAGGAGAAGAAGT 59.020 55.0 0.00 0.0 36.89 3.01 R
2900 3283 0.879400 GGAGGACGAGCTCGACGATA 60.879 60.0 40.58 0.0 43.02 2.92 R
3650 5430 0.704076 TTCTAGGCCACCCATTGCTT 59.296 50.0 5.01 0.0 0.00 3.91 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 0.524862 GACGAGCAAGTCCGGTCTTA 59.475 55.000 13.73 0.00 35.22 2.10
27 28 3.435671 CGAGCAAGTCCGGTCTTAAAATT 59.564 43.478 13.73 0.00 0.00 1.82
31 32 6.177610 AGCAAGTCCGGTCTTAAAATTATGA 58.822 36.000 13.73 0.00 0.00 2.15
33 34 6.912591 GCAAGTCCGGTCTTAAAATTATGATG 59.087 38.462 13.73 0.00 0.00 3.07
35 36 9.104965 CAAGTCCGGTCTTAAAATTATGATGTA 57.895 33.333 13.73 0.00 0.00 2.29
36 37 8.888579 AGTCCGGTCTTAAAATTATGATGTAG 57.111 34.615 0.00 0.00 0.00 2.74
67 68 6.434965 TGAAAGTCAACATGTGATTGGATGAT 59.565 34.615 0.00 0.00 38.90 2.45
69 70 6.203808 AGTCAACATGTGATTGGATGATTG 57.796 37.500 0.00 0.00 38.90 2.67
78 79 4.025360 TGATTGGATGATTGGAAAGGTGG 58.975 43.478 0.00 0.00 0.00 4.61
79 80 3.824001 TTGGATGATTGGAAAGGTGGA 57.176 42.857 0.00 0.00 0.00 4.02
82 83 3.011595 TGGATGATTGGAAAGGTGGATGT 59.988 43.478 0.00 0.00 0.00 3.06
84 85 5.103558 TGGATGATTGGAAAGGTGGATGTAT 60.104 40.000 0.00 0.00 0.00 2.29
98 99 6.058183 GGTGGATGTATCTCATAGCAAACTT 58.942 40.000 0.00 0.00 36.83 2.66
106 114 5.426689 TCTCATAGCAAACTTGAGACCAT 57.573 39.130 0.00 0.00 40.59 3.55
110 118 6.653020 TCATAGCAAACTTGAGACCATACAT 58.347 36.000 0.00 0.00 0.00 2.29
112 120 4.910195 AGCAAACTTGAGACCATACATCA 58.090 39.130 0.00 0.00 0.00 3.07
120 128 6.801539 TTGAGACCATACATCAAGTTTGAC 57.198 37.500 0.00 0.00 40.49 3.18
142 150 7.090808 TGACGTCATATGTATCTCATTAAGGC 58.909 38.462 15.76 0.00 37.91 4.35
145 153 6.625081 CGTCATATGTATCTCATTAAGGCGGA 60.625 42.308 1.90 0.00 37.91 5.54
146 154 7.268586 GTCATATGTATCTCATTAAGGCGGAT 58.731 38.462 1.90 2.25 37.91 4.18
147 155 7.766278 GTCATATGTATCTCATTAAGGCGGATT 59.234 37.037 1.90 0.00 37.91 3.01
151 159 7.905604 TGTATCTCATTAAGGCGGATTATTG 57.094 36.000 2.01 0.00 0.00 1.90
156 164 5.441500 TCATTAAGGCGGATTATTGTTCCA 58.558 37.500 0.00 0.00 32.45 3.53
160 168 3.214328 AGGCGGATTATTGTTCCATCAC 58.786 45.455 0.00 0.00 32.45 3.06
167 175 2.814805 ATTGTTCCATCACTGGGAGG 57.185 50.000 0.00 0.00 43.34 4.30
172 180 3.016971 CATCACTGGGAGGGGGCA 61.017 66.667 0.00 0.00 0.00 5.36
178 186 1.149133 ACTGGGAGGGGGCATTTTCT 61.149 55.000 0.00 0.00 0.00 2.52
184 192 3.629796 GGGAGGGGGCATTTTCTTTGATA 60.630 47.826 0.00 0.00 0.00 2.15
185 193 4.030216 GGAGGGGGCATTTTCTTTGATAA 58.970 43.478 0.00 0.00 0.00 1.75
189 197 5.364735 AGGGGGCATTTTCTTTGATAATGAG 59.635 40.000 12.51 0.00 34.52 2.90
190 198 5.453762 GGGGGCATTTTCTTTGATAATGAGG 60.454 44.000 12.51 0.00 34.52 3.86
193 201 5.521372 GGCATTTTCTTTGATAATGAGGCAC 59.479 40.000 12.51 0.00 34.52 5.01
194 202 5.230726 GCATTTTCTTTGATAATGAGGCACG 59.769 40.000 12.51 0.00 34.52 5.34
206 214 1.002366 GAGGCACGTGTGATGACATC 58.998 55.000 18.38 8.59 33.63 3.06
234 242 4.329392 TCATAGACTCCACGACTACAACA 58.671 43.478 0.00 0.00 0.00 3.33
236 244 5.417894 TCATAGACTCCACGACTACAACATT 59.582 40.000 0.00 0.00 0.00 2.71
237 245 4.175787 AGACTCCACGACTACAACATTC 57.824 45.455 0.00 0.00 0.00 2.67
243 251 4.763279 TCCACGACTACAACATTCAGTAGA 59.237 41.667 6.60 0.00 40.02 2.59
244 252 5.096169 CCACGACTACAACATTCAGTAGAG 58.904 45.833 6.60 3.37 40.02 2.43
247 255 5.106237 ACGACTACAACATTCAGTAGAGGTC 60.106 44.000 6.60 0.00 40.02 3.85
256 264 2.860009 TCAGTAGAGGTCGTGTGAGTT 58.140 47.619 0.00 0.00 0.00 3.01
257 265 4.011966 TCAGTAGAGGTCGTGTGAGTTA 57.988 45.455 0.00 0.00 0.00 2.24
258 266 3.750130 TCAGTAGAGGTCGTGTGAGTTAC 59.250 47.826 0.00 0.00 0.00 2.50
262 270 6.760298 CAGTAGAGGTCGTGTGAGTTACTATA 59.240 42.308 0.00 0.00 0.00 1.31
263 271 7.441760 CAGTAGAGGTCGTGTGAGTTACTATAT 59.558 40.741 0.00 0.00 0.00 0.86
264 272 6.864360 AGAGGTCGTGTGAGTTACTATATC 57.136 41.667 0.00 0.00 0.00 1.63
265 273 6.354938 AGAGGTCGTGTGAGTTACTATATCA 58.645 40.000 0.00 0.00 0.00 2.15
308 316 9.252962 CTTTCTGAAACTTCTAAACATGCATTT 57.747 29.630 0.00 0.00 0.00 2.32
309 317 8.801715 TTCTGAAACTTCTAAACATGCATTTC 57.198 30.769 0.00 0.00 0.00 2.17
317 326 8.767085 ACTTCTAAACATGCATTTCACATTTTG 58.233 29.630 0.00 0.00 0.00 2.44
320 329 8.549548 TCTAAACATGCATTTCACATTTTGTTG 58.450 29.630 0.00 0.00 0.00 3.33
327 336 6.762187 TGCATTTCACATTTTGTTGAGAACAT 59.238 30.769 0.00 0.00 41.79 2.71
330 339 8.918658 CATTTCACATTTTGTTGAGAACATAGG 58.081 33.333 0.00 0.00 41.79 2.57
338 347 3.209410 GTTGAGAACATAGGGCTCCATG 58.791 50.000 0.00 0.00 0.00 3.66
339 348 2.481441 TGAGAACATAGGGCTCCATGT 58.519 47.619 0.00 0.00 36.96 3.21
342 351 2.370189 AGAACATAGGGCTCCATGTAGC 59.630 50.000 0.79 0.79 41.99 3.58
343 352 2.109229 ACATAGGGCTCCATGTAGCT 57.891 50.000 10.37 0.00 42.37 3.32
367 376 3.802866 AGAGCCAAGTTATTAGCAGCTC 58.197 45.455 0.00 0.00 44.31 4.09
370 379 2.285488 GCCAAGTTATTAGCAGCTCGAC 59.715 50.000 0.00 0.00 0.00 4.20
382 391 2.049959 CAGCTCGACGAATGCTATGAG 58.950 52.381 10.83 0.00 35.05 2.90
388 397 5.690997 TCGACGAATGCTATGAGAATACT 57.309 39.130 0.00 0.00 0.00 2.12
390 399 4.618912 CGACGAATGCTATGAGAATACTGG 59.381 45.833 0.00 0.00 0.00 4.00
391 400 5.533482 GACGAATGCTATGAGAATACTGGT 58.467 41.667 0.00 0.00 0.00 4.00
392 401 5.292765 ACGAATGCTATGAGAATACTGGTG 58.707 41.667 0.00 0.00 0.00 4.17
393 402 4.687948 CGAATGCTATGAGAATACTGGTGG 59.312 45.833 0.00 0.00 0.00 4.61
394 403 3.475566 TGCTATGAGAATACTGGTGGC 57.524 47.619 0.00 0.00 0.00 5.01
395 404 2.771372 TGCTATGAGAATACTGGTGGCA 59.229 45.455 0.00 0.00 0.00 4.92
396 405 3.134458 GCTATGAGAATACTGGTGGCAC 58.866 50.000 9.70 9.70 0.00 5.01
397 406 2.717639 ATGAGAATACTGGTGGCACC 57.282 50.000 29.75 29.75 39.22 5.01
398 407 0.618458 TGAGAATACTGGTGGCACCC 59.382 55.000 32.61 16.58 37.50 4.61
399 408 0.912486 GAGAATACTGGTGGCACCCT 59.088 55.000 32.61 21.07 37.50 4.34
400 409 1.282157 GAGAATACTGGTGGCACCCTT 59.718 52.381 32.61 21.49 37.50 3.95
401 410 2.504175 GAGAATACTGGTGGCACCCTTA 59.496 50.000 32.61 22.89 37.50 2.69
402 411 2.238898 AGAATACTGGTGGCACCCTTAC 59.761 50.000 32.61 18.30 37.50 2.34
403 412 1.966845 ATACTGGTGGCACCCTTACT 58.033 50.000 32.61 11.73 37.50 2.24
404 413 0.981183 TACTGGTGGCACCCTTACTG 59.019 55.000 32.61 17.26 37.50 2.74
405 414 1.060163 ACTGGTGGCACCCTTACTGT 61.060 55.000 32.61 17.85 37.50 3.55
406 415 0.981183 CTGGTGGCACCCTTACTGTA 59.019 55.000 32.61 11.43 37.50 2.74
407 416 1.559682 CTGGTGGCACCCTTACTGTAT 59.440 52.381 32.61 0.00 37.50 2.29
411 420 3.418047 GTGGCACCCTTACTGTATGTTT 58.582 45.455 6.29 0.00 0.00 2.83
415 424 4.196971 GCACCCTTACTGTATGTTTAGGG 58.803 47.826 16.51 16.51 46.44 3.53
544 685 1.734655 ACTTGGAGTGACCCTCATGT 58.265 50.000 0.00 0.00 42.40 3.21
552 693 4.327680 GAGTGACCCTCATGTTTTTAGCT 58.672 43.478 0.00 0.00 40.17 3.32
567 708 5.772825 TTTTAGCTGTGCAATCAAAGACT 57.227 34.783 0.00 0.00 28.54 3.24
568 709 5.772825 TTTAGCTGTGCAATCAAAGACTT 57.227 34.783 0.00 0.00 28.54 3.01
571 712 5.772825 AGCTGTGCAATCAAAGACTTTTA 57.227 34.783 0.00 0.00 28.54 1.52
579 721 5.915196 GCAATCAAAGACTTTTATATCCCGC 59.085 40.000 0.00 0.00 0.00 6.13
587 729 4.699637 ACTTTTATATCCCGCGTGATTCA 58.300 39.130 9.91 0.00 0.00 2.57
665 957 6.359545 TGACATGAATTTTGTAAGAACGTCG 58.640 36.000 0.00 0.00 0.00 5.12
720 1015 6.187125 GGGAAAACCTTCGTTACTATTTCC 57.813 41.667 5.95 5.95 34.88 3.13
726 1021 6.232139 ACCTTCGTTACTATTTCCAAAACG 57.768 37.500 0.00 0.00 43.07 3.60
744 1039 6.147164 CCAAAACGAGTGAGAAATGCTAAGTA 59.853 38.462 0.00 0.00 0.00 2.24
750 1045 8.467598 ACGAGTGAGAAATGCTAAGTAGAATAA 58.532 33.333 0.00 0.00 0.00 1.40
751 1046 8.963130 CGAGTGAGAAATGCTAAGTAGAATAAG 58.037 37.037 0.00 0.00 0.00 1.73
752 1047 9.810545 GAGTGAGAAATGCTAAGTAGAATAAGT 57.189 33.333 0.00 0.00 0.00 2.24
1016 1328 9.209175 GTACTCAATCACTCACTAGAAAACAAT 57.791 33.333 0.00 0.00 0.00 2.71
1192 1504 1.081556 CCGATCGTCGCCATGTTTCA 61.082 55.000 15.09 0.00 38.82 2.69
1355 1676 0.602905 CCAACGACACCAAGGAGACC 60.603 60.000 0.00 0.00 0.00 3.85
1515 1836 4.695231 CGCCGTCGGTCAACGTCT 62.695 66.667 13.94 0.00 44.69 4.18
1517 1838 2.640989 CCGTCGGTCAACGTCTCA 59.359 61.111 2.08 0.00 44.69 3.27
1526 1847 4.295119 AACGTCTCAGGCGCCGTT 62.295 61.111 23.20 17.25 38.57 4.44
1715 2036 1.441729 CGGGTACTGGCACGATGAT 59.558 57.895 0.00 0.00 37.48 2.45
1895 2216 3.745803 AACCTCTCGTCGGCCGTC 61.746 66.667 27.15 19.73 37.94 4.79
2060 2393 1.229951 ACCCAAGAGGAGGATGCCA 60.230 57.895 0.00 0.00 39.89 4.92
2066 2399 1.963985 AGAGGAGGATGCCACTTCTT 58.036 50.000 0.00 0.00 27.43 2.52
2069 2402 1.836802 AGGAGGATGCCACTTCTTCTC 59.163 52.381 0.00 0.00 0.00 2.87
2076 2412 0.251634 GCCACTTCTTCTCCTCCTGG 59.748 60.000 0.00 0.00 0.00 4.45
2090 2429 1.687146 CCTGGCACTGCTCCTCCTA 60.687 63.158 0.00 0.00 0.00 2.94
2100 2447 2.439701 TCCTCCTAGCCGTCGTGG 60.440 66.667 0.00 0.00 42.50 4.94
2139 2486 3.770040 CCATCGGGGTGCTCGTCA 61.770 66.667 0.00 0.00 0.00 4.35
2179 2535 3.760035 GCAGTTCGCCGAGGAGGA 61.760 66.667 0.00 0.00 45.00 3.71
2180 2536 3.082579 GCAGTTCGCCGAGGAGGAT 62.083 63.158 0.00 0.00 45.00 3.24
2189 2545 0.105964 CCGAGGAGGATGAGGAAGGA 60.106 60.000 0.00 0.00 45.00 3.36
2279 2641 4.471726 GACGTCATCGGCGTCGGT 62.472 66.667 10.62 0.00 46.85 4.69
2282 2644 4.430765 GTCATCGGCGTCGGTGGT 62.431 66.667 24.12 0.00 46.63 4.16
2802 3185 3.680786 CCACCACGAGCTCCGACA 61.681 66.667 8.47 0.00 41.76 4.35
3029 3412 4.079850 CTGCTCTGCTCGCACCCT 62.080 66.667 0.00 0.00 33.19 4.34
3080 3463 0.038599 TGGTGCAGATGCTGGAACAT 59.961 50.000 2.42 0.00 44.15 2.71
3470 4269 3.713858 TGTTTTGCACATGACTCAAGG 57.286 42.857 0.00 0.00 0.00 3.61
3483 4287 8.896744 CACATGACTCAAGGATGTATGTATTTT 58.103 33.333 0.00 0.00 0.00 1.82
3529 5307 8.880878 TGAAGTATTGCAATATGTATACGTGT 57.119 30.769 21.52 0.00 0.00 4.49
3586 5365 2.672908 CCAGCAGCACATCTCCCA 59.327 61.111 0.00 0.00 0.00 4.37
3596 5375 0.322816 ACATCTCCCATGCGCAACTT 60.323 50.000 17.11 0.00 0.00 2.66
3620 5399 2.816087 AGTTACCGTCGAAGCTAGTTGA 59.184 45.455 0.00 0.00 0.00 3.18
3621 5400 3.119919 AGTTACCGTCGAAGCTAGTTGAG 60.120 47.826 0.00 0.00 0.00 3.02
3638 5418 7.201652 GCTAGTTGAGTGAATTATTGACCTTCC 60.202 40.741 0.00 0.00 0.00 3.46
3650 5430 8.884124 ATTATTGACCTTCCAAGAATTTCTCA 57.116 30.769 0.00 0.00 35.24 3.27
3652 5432 6.639632 TTGACCTTCCAAGAATTTCTCAAG 57.360 37.500 0.00 3.18 0.00 3.02
3657 5437 5.867716 CCTTCCAAGAATTTCTCAAGCAATG 59.132 40.000 0.00 0.00 0.00 2.82
3679 5459 4.262617 GGGTGGCCTAGAAAAGAAAGTAG 58.737 47.826 3.32 0.00 0.00 2.57
3765 5545 2.679287 GGTCTCGGGGTCGACCTT 60.679 66.667 32.52 0.00 44.90 3.50
3820 5600 0.232303 GCTTCGATAAATGGCGGACG 59.768 55.000 0.00 0.00 0.00 4.79
3902 5682 2.950309 GCAGCCTGTGATCATTTCAGAT 59.050 45.455 12.20 0.13 34.17 2.90
3908 5688 8.843262 CAGCCTGTGATCATTTCAGATATTAAA 58.157 33.333 12.20 0.00 34.17 1.52
3942 5722 4.070716 GCCATTCCTCAAGACCATATCAG 58.929 47.826 0.00 0.00 0.00 2.90
3984 5764 9.639601 CTTTCACCAAAGATATCGCTATACATA 57.360 33.333 0.00 0.00 41.60 2.29
4018 5798 5.784750 AAGCTTGCAAAAGTTTCTTTCAC 57.215 34.783 0.00 0.00 0.00 3.18
4037 5817 8.756864 TCTTTCACGGCATTATTTTGTAAAAAC 58.243 29.630 0.00 0.00 0.00 2.43
4199 6023 5.179929 CGCATCATAACCTGCATCAAGAATA 59.820 40.000 0.00 0.00 38.30 1.75
4302 6126 3.624410 TGAGAAACATGCTGATTCATCCG 59.376 43.478 0.00 0.00 32.41 4.18
4310 6134 1.470098 GCTGATTCATCCGCACTTTGT 59.530 47.619 0.00 0.00 37.06 2.83
4318 6142 4.385825 TCATCCGCACTTTGTAGTTTCTT 58.614 39.130 0.00 0.00 30.26 2.52
4377 6201 8.616942 CCACATACCATCATAATTTAACAACGA 58.383 33.333 0.00 0.00 0.00 3.85
4378 6202 9.433317 CACATACCATCATAATTTAACAACGAC 57.567 33.333 0.00 0.00 0.00 4.34
4398 6222 0.108804 AAACCAGATGTCGTCGCGAT 60.109 50.000 14.06 0.00 38.42 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.599204 GACCGGACTTGCTCGTCAAA 60.599 55.000 9.46 0.00 35.63 2.69
1 2 1.006571 GACCGGACTTGCTCGTCAA 60.007 57.895 9.46 0.00 35.63 3.18
2 3 1.461091 AAGACCGGACTTGCTCGTCA 61.461 55.000 18.49 0.00 35.63 4.35
3 4 0.524862 TAAGACCGGACTTGCTCGTC 59.475 55.000 26.28 2.05 0.00 4.20
4 5 0.963962 TTAAGACCGGACTTGCTCGT 59.036 50.000 26.28 5.37 0.00 4.18
5 6 2.074547 TTTAAGACCGGACTTGCTCG 57.925 50.000 26.28 0.00 0.00 5.03
6 7 6.315393 TCATAATTTTAAGACCGGACTTGCTC 59.685 38.462 26.28 4.35 0.00 4.26
7 8 6.177610 TCATAATTTTAAGACCGGACTTGCT 58.822 36.000 26.28 5.67 0.00 3.91
8 9 6.431198 TCATAATTTTAAGACCGGACTTGC 57.569 37.500 26.28 2.50 0.00 4.01
9 10 7.985476 ACATCATAATTTTAAGACCGGACTTG 58.015 34.615 26.28 10.07 0.00 3.16
10 11 9.326413 CTACATCATAATTTTAAGACCGGACTT 57.674 33.333 22.37 22.37 0.00 3.01
11 12 7.441458 GCTACATCATAATTTTAAGACCGGACT 59.559 37.037 9.46 3.68 0.00 3.85
12 13 7.225931 TGCTACATCATAATTTTAAGACCGGAC 59.774 37.037 9.46 0.10 0.00 4.79
13 14 7.276658 TGCTACATCATAATTTTAAGACCGGA 58.723 34.615 9.46 0.00 0.00 5.14
14 15 7.490962 TGCTACATCATAATTTTAAGACCGG 57.509 36.000 0.00 0.00 0.00 5.28
15 16 8.612619 ACTTGCTACATCATAATTTTAAGACCG 58.387 33.333 0.00 0.00 0.00 4.79
27 28 7.977789 TTGACTTTCAACTTGCTACATCATA 57.022 32.000 0.00 0.00 30.26 2.15
45 46 6.350696 CCAATCATCCAATCACATGTTGACTT 60.351 38.462 0.00 0.00 36.92 3.01
48 49 5.262804 TCCAATCATCCAATCACATGTTGA 58.737 37.500 0.00 0.00 39.11 3.18
58 59 4.335735 TCCACCTTTCCAATCATCCAAT 57.664 40.909 0.00 0.00 0.00 3.16
67 68 5.715439 ATGAGATACATCCACCTTTCCAA 57.285 39.130 0.00 0.00 33.46 3.53
69 70 5.221722 TGCTATGAGATACATCCACCTTTCC 60.222 44.000 0.00 0.00 40.07 3.13
84 85 4.890158 TGGTCTCAAGTTTGCTATGAGA 57.110 40.909 0.82 0.82 45.34 3.27
98 99 4.929211 CGTCAAACTTGATGTATGGTCTCA 59.071 41.667 3.87 0.00 39.73 3.27
110 118 7.543756 TGAGATACATATGACGTCAAACTTGA 58.456 34.615 24.13 7.10 34.20 3.02
112 120 8.948631 AATGAGATACATATGACGTCAAACTT 57.051 30.769 24.13 8.61 38.38 2.66
120 128 5.516696 CCGCCTTAATGAGATACATATGACG 59.483 44.000 10.38 0.00 38.38 4.35
151 159 1.609783 CCCCTCCCAGTGATGGAAC 59.390 63.158 0.00 0.00 30.72 3.62
156 164 1.224003 AAATGCCCCCTCCCAGTGAT 61.224 55.000 0.00 0.00 0.00 3.06
160 168 0.041684 AAGAAAATGCCCCCTCCCAG 59.958 55.000 0.00 0.00 0.00 4.45
167 175 5.604565 CCTCATTATCAAAGAAAATGCCCC 58.395 41.667 0.00 0.00 31.98 5.80
168 176 5.052481 GCCTCATTATCAAAGAAAATGCCC 58.948 41.667 0.00 0.00 31.98 5.36
172 180 6.071952 ACACGTGCCTCATTATCAAAGAAAAT 60.072 34.615 17.22 0.00 0.00 1.82
178 186 3.669536 TCACACGTGCCTCATTATCAAA 58.330 40.909 17.22 0.00 0.00 2.69
184 192 1.270785 TGTCATCACACGTGCCTCATT 60.271 47.619 17.22 0.00 0.00 2.57
185 193 0.321346 TGTCATCACACGTGCCTCAT 59.679 50.000 17.22 0.00 0.00 2.90
189 197 1.372582 ATGATGTCATCACACGTGCC 58.627 50.000 17.74 0.00 43.01 5.01
206 214 5.193663 AGTCGTGGAGTCTATGATTGATG 57.806 43.478 1.33 0.00 0.00 3.07
234 242 3.422796 ACTCACACGACCTCTACTGAAT 58.577 45.455 0.00 0.00 0.00 2.57
236 244 2.563261 ACTCACACGACCTCTACTGA 57.437 50.000 0.00 0.00 0.00 3.41
237 245 3.752222 AGTAACTCACACGACCTCTACTG 59.248 47.826 0.00 0.00 0.00 2.74
243 251 5.531659 CCTGATATAGTAACTCACACGACCT 59.468 44.000 0.00 0.00 0.00 3.85
244 252 5.530171 TCCTGATATAGTAACTCACACGACC 59.470 44.000 0.00 0.00 0.00 4.79
247 255 8.697846 TTTTTCCTGATATAGTAACTCACACG 57.302 34.615 0.00 0.00 0.00 4.49
279 287 7.915397 TGCATGTTTAGAAGTTTCAGAAAGTTC 59.085 33.333 26.63 26.63 46.39 3.01
308 316 5.048083 GCCCTATGTTCTCAACAAAATGTGA 60.048 40.000 0.00 0.00 45.86 3.58
309 317 5.047802 AGCCCTATGTTCTCAACAAAATGTG 60.048 40.000 0.00 0.00 45.86 3.21
317 326 3.209410 CATGGAGCCCTATGTTCTCAAC 58.791 50.000 0.00 0.00 0.00 3.18
320 329 3.556004 GCTACATGGAGCCCTATGTTCTC 60.556 52.174 20.06 0.00 38.41 2.87
327 336 0.185175 TCGAGCTACATGGAGCCCTA 59.815 55.000 26.69 3.46 43.97 3.53
330 339 0.313672 CTCTCGAGCTACATGGAGCC 59.686 60.000 26.69 16.35 43.97 4.70
342 351 4.046938 TGCTAATAACTTGGCTCTCGAG 57.953 45.455 5.93 5.93 39.43 4.04
343 352 3.738281 GCTGCTAATAACTTGGCTCTCGA 60.738 47.826 0.00 0.00 39.43 4.04
345 354 3.802866 AGCTGCTAATAACTTGGCTCTC 58.197 45.455 0.00 0.00 39.43 3.20
361 370 0.506080 CATAGCATTCGTCGAGCTGC 59.494 55.000 16.76 17.85 39.30 5.25
367 376 4.618912 CCAGTATTCTCATAGCATTCGTCG 59.381 45.833 0.00 0.00 0.00 5.12
370 379 4.687948 CCACCAGTATTCTCATAGCATTCG 59.312 45.833 0.00 0.00 0.00 3.34
382 391 2.238898 AGTAAGGGTGCCACCAGTATTC 59.761 50.000 17.22 0.00 41.02 1.75
388 397 1.280710 CATACAGTAAGGGTGCCACCA 59.719 52.381 17.22 0.00 41.02 4.17
390 399 2.781681 ACATACAGTAAGGGTGCCAC 57.218 50.000 0.00 0.00 0.00 5.01
391 400 3.799432 AAACATACAGTAAGGGTGCCA 57.201 42.857 0.00 0.00 0.00 4.92
392 401 4.196971 CCTAAACATACAGTAAGGGTGCC 58.803 47.826 0.00 0.00 32.46 5.01
393 402 4.196971 CCCTAAACATACAGTAAGGGTGC 58.803 47.826 6.21 0.00 43.74 5.01
397 406 6.793505 AGAGACCCTAAACATACAGTAAGG 57.206 41.667 0.00 0.00 34.69 2.69
398 407 8.289939 TGTAGAGACCCTAAACATACAGTAAG 57.710 38.462 0.00 0.00 0.00 2.34
399 408 8.654485 TTGTAGAGACCCTAAACATACAGTAA 57.346 34.615 0.00 0.00 0.00 2.24
400 409 8.834004 ATTGTAGAGACCCTAAACATACAGTA 57.166 34.615 0.00 0.00 0.00 2.74
401 410 7.735326 ATTGTAGAGACCCTAAACATACAGT 57.265 36.000 0.00 0.00 0.00 3.55
402 411 9.449719 AAAATTGTAGAGACCCTAAACATACAG 57.550 33.333 0.00 0.00 0.00 2.74
403 412 9.802039 AAAAATTGTAGAGACCCTAAACATACA 57.198 29.630 0.00 0.00 0.00 2.29
406 415 9.588096 AAGAAAAATTGTAGAGACCCTAAACAT 57.412 29.630 0.00 0.00 0.00 2.71
407 416 8.990163 AAGAAAAATTGTAGAGACCCTAAACA 57.010 30.769 0.00 0.00 0.00 2.83
474 611 5.627172 TGATAGCGCAAAAGACATTGTAAC 58.373 37.500 11.47 0.00 32.80 2.50
538 679 5.463286 TGATTGCACAGCTAAAAACATGAG 58.537 37.500 0.00 0.00 0.00 2.90
541 682 6.421801 GTCTTTGATTGCACAGCTAAAAACAT 59.578 34.615 0.00 0.00 0.00 2.71
544 685 6.147864 AGTCTTTGATTGCACAGCTAAAAA 57.852 33.333 0.00 0.00 0.00 1.94
552 693 7.415095 CGGGATATAAAAGTCTTTGATTGCACA 60.415 37.037 0.24 0.00 0.00 4.57
567 708 6.438259 TTTTGAATCACGCGGGATATAAAA 57.562 33.333 27.68 27.68 0.00 1.52
568 709 6.038825 ACATTTTGAATCACGCGGGATATAAA 59.961 34.615 26.58 23.59 0.00 1.40
571 712 3.882888 ACATTTTGAATCACGCGGGATAT 59.117 39.130 26.58 14.88 0.00 1.63
579 721 5.229052 ACGTTTTGTGACATTTTGAATCACG 59.771 36.000 0.00 0.00 44.67 4.35
611 824 5.241506 ACAAAAATCCAACGTGATGACATCT 59.758 36.000 16.25 0.00 0.00 2.90
665 957 4.727507 TGAGCATGTCTTACCTCTCTTC 57.272 45.455 0.00 0.00 0.00 2.87
720 1015 5.990408 ACTTAGCATTTCTCACTCGTTTTG 58.010 37.500 0.00 0.00 0.00 2.44
726 1021 9.810545 ACTTATTCTACTTAGCATTTCTCACTC 57.189 33.333 0.00 0.00 0.00 3.51
764 1059 7.737972 TCTTGAAATTTATTCGACTTCACCA 57.262 32.000 0.00 0.00 0.00 4.17
863 1167 4.323417 TGATGCTCCTGACGTTAAAACAT 58.677 39.130 0.00 0.00 0.00 2.71
865 1169 4.742438 TTGATGCTCCTGACGTTAAAAC 57.258 40.909 0.00 0.00 0.00 2.43
870 1174 2.079158 CACATTGATGCTCCTGACGTT 58.921 47.619 0.00 0.00 0.00 3.99
875 1179 1.135199 GGTTGCACATTGATGCTCCTG 60.135 52.381 10.93 0.00 46.28 3.86
898 1202 4.156556 ACGCATTCAATTCAGCACAGTTAT 59.843 37.500 0.00 0.00 0.00 1.89
906 1210 2.280708 GCATCAACGCATTCAATTCAGC 59.719 45.455 0.00 0.00 0.00 4.26
1016 1328 0.248296 GCAACGAACAGCCAACGAAA 60.248 50.000 0.00 0.00 0.00 3.46
1526 1847 4.077184 CCGAGGTACTTGCCGGCA 62.077 66.667 29.03 29.03 41.55 5.69
1895 2216 3.989566 GACGTAGGTGTCGTCGGCG 62.990 68.421 1.15 1.15 45.64 6.46
2043 2376 1.225704 GTGGCATCCTCCTCTTGGG 59.774 63.158 0.00 0.00 0.00 4.12
2060 2393 0.980423 GTGCCAGGAGGAGAAGAAGT 59.020 55.000 0.00 0.00 36.89 3.01
2066 2399 1.986757 GAGCAGTGCCAGGAGGAGA 60.987 63.158 12.58 0.00 36.89 3.71
2069 2402 3.007920 AGGAGCAGTGCCAGGAGG 61.008 66.667 12.58 0.00 38.23 4.30
2076 2412 2.503546 GGCTAGGAGGAGCAGTGC 59.496 66.667 7.13 7.13 44.76 4.40
2100 2447 2.262915 CGACACCAGGAGCAGGAC 59.737 66.667 0.00 0.00 0.00 3.85
2152 2508 3.349006 CGAACTGCCAGCGTTGCT 61.349 61.111 0.00 0.00 40.77 3.91
2178 2534 3.246301 TCATCTCCCATCCTTCCTCATC 58.754 50.000 0.00 0.00 0.00 2.92
2179 2535 3.357482 TCATCTCCCATCCTTCCTCAT 57.643 47.619 0.00 0.00 0.00 2.90
2180 2536 2.875102 TCATCTCCCATCCTTCCTCA 57.125 50.000 0.00 0.00 0.00 3.86
2189 2545 4.093011 GGCTGTAGTCTATCATCTCCCAT 58.907 47.826 0.00 0.00 0.00 4.00
2279 2641 4.296593 TACACGCGGCCGAAACCA 62.297 61.111 33.48 7.29 38.29 3.67
2282 2644 4.296593 TGGTACACGCGGCCGAAA 62.297 61.111 33.48 5.12 38.29 3.46
2459 2824 4.391869 TCGTAGACGAGCACCAGT 57.608 55.556 0.00 0.00 44.22 4.00
2687 3070 4.105733 TCGTAGAGCCGCGCGAAA 62.106 61.111 34.63 8.49 0.00 3.46
2900 3283 0.879400 GGAGGACGAGCTCGACGATA 60.879 60.000 40.58 0.00 43.02 2.92
3414 4213 8.983724 GTGCAGAATAGGTTCTTATAGTCAATC 58.016 37.037 0.00 0.00 41.92 2.67
3451 4250 3.988379 TCCTTGAGTCATGTGCAAAAC 57.012 42.857 0.00 0.00 0.00 2.43
3452 4251 3.890756 ACATCCTTGAGTCATGTGCAAAA 59.109 39.130 0.00 0.00 29.36 2.44
3453 4252 3.489355 ACATCCTTGAGTCATGTGCAAA 58.511 40.909 0.00 0.00 29.36 3.68
3454 4253 3.144657 ACATCCTTGAGTCATGTGCAA 57.855 42.857 0.00 0.00 29.36 4.08
3455 4254 2.865119 ACATCCTTGAGTCATGTGCA 57.135 45.000 0.00 0.00 29.36 4.57
3483 4287 8.141268 ACTTCAGTTTCTTGAAAAGTTTTGTGA 58.859 29.630 5.36 0.00 46.34 3.58
3495 5273 9.013229 ACATATTGCAATACTTCAGTTTCTTGA 57.987 29.630 21.10 0.00 0.00 3.02
3565 5344 1.078637 GAGATGTGCTGCTGGCTCA 60.079 57.895 0.00 8.78 46.32 4.26
3586 5365 1.196808 CGGTAACTTCAAGTTGCGCAT 59.803 47.619 12.75 0.00 40.97 4.73
3596 5375 2.816087 ACTAGCTTCGACGGTAACTTCA 59.184 45.455 2.33 0.00 33.69 3.02
3620 5399 8.655935 AATTCTTGGAAGGTCAATAATTCACT 57.344 30.769 0.00 0.00 31.96 3.41
3621 5400 9.358872 GAAATTCTTGGAAGGTCAATAATTCAC 57.641 33.333 0.00 0.00 34.52 3.18
3638 5418 4.927425 CACCCATTGCTTGAGAAATTCTTG 59.073 41.667 0.00 0.00 0.00 3.02
3650 5430 0.704076 TTCTAGGCCACCCATTGCTT 59.296 50.000 5.01 0.00 0.00 3.91
3652 5432 1.478105 CTTTTCTAGGCCACCCATTGC 59.522 52.381 5.01 0.00 0.00 3.56
3657 5437 3.156288 ACTTTCTTTTCTAGGCCACCC 57.844 47.619 5.01 0.00 0.00 4.61
3679 5459 1.217882 CGGTGCCATTATCTCGGAAC 58.782 55.000 0.00 0.00 0.00 3.62
3765 5545 1.785321 GACGCGCTTCCGAAAATCA 59.215 52.632 5.73 0.00 36.29 2.57
3820 5600 1.363807 GGTGGAAGCTGTTGTTGGC 59.636 57.895 0.00 0.00 0.00 4.52
3824 5604 0.846693 AAGAGGGTGGAAGCTGTTGT 59.153 50.000 0.00 0.00 0.00 3.32
4018 5798 7.846592 ACGTTTTGTTTTTACAAAATAATGCCG 59.153 29.630 16.37 15.38 46.81 5.69
4037 5817 6.161381 ACCATACCTCACTACTAACGTTTTG 58.839 40.000 5.91 2.48 0.00 2.44
4041 5821 5.468072 CGATACCATACCTCACTACTAACGT 59.532 44.000 0.00 0.00 0.00 3.99
4302 6126 7.861630 TGTTAGATGAAGAAACTACAAAGTGC 58.138 34.615 0.00 0.00 35.62 4.40
4350 6174 8.402472 CGTTGTTAAATTATGATGGTATGTGGT 58.598 33.333 0.00 0.00 0.00 4.16
4351 6175 8.616942 TCGTTGTTAAATTATGATGGTATGTGG 58.383 33.333 0.00 0.00 0.00 4.17
4354 6178 9.995957 TTGTCGTTGTTAAATTATGATGGTATG 57.004 29.630 0.00 0.00 0.00 2.39
4377 6201 1.282248 CGCGACGACATCTGGTTTGT 61.282 55.000 0.00 0.00 0.00 2.83
4378 6202 1.006825 TCGCGACGACATCTGGTTTG 61.007 55.000 3.71 0.00 0.00 2.93


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

AutoCloner maintained by Alex Coulton.