Multiple sequence alignment - TraesCS7D01G178300

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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 TraesCS7D01G178300 chr7D 100.000 1661 0 0 802 2462 131597775 131599435 0.000000e+00 3068
1 TraesCS7D01G178300 chr7D 100.000 487 0 0 1 487 131596974 131597460 0.000000e+00 900
2 TraesCS7D01G178300 chr7A 86.827 1207 87 39 808 1973 130292532 130293707 0.000000e+00 1282
3 TraesCS7D01G178300 chr7A 88.068 352 22 8 66 405 130239924 130240267 1.370000e-107 399
4 TraesCS7D01G178300 chr7A 82.218 478 34 13 1994 2462 130293759 130294194 5.000000e-97 364
5 TraesCS7D01G178300 chr7A 98.684 76 1 0 1 76 130239827 130239902 4.270000e-28 135
6 TraesCS7D01G178300 chr7B 93.205 883 29 9 802 1675 92554807 92555667 0.000000e+00 1269
7 TraesCS7D01G178300 chr7B 93.919 296 14 1 1 292 92552623 92552918 6.250000e-121 444
8 TraesCS7D01G178300 chr7B 81.048 496 45 26 1994 2462 92556095 92556568 1.400000e-92 350
9 TraesCS7D01G178300 chr7B 91.262 206 13 4 1705 1907 92555666 92555869 2.410000e-70 276


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 TraesCS7D01G178300 chr7D 131596974 131599435 2461 False 1984.00 3068 100.0000 1 2462 2 chr7D.!!$F1 2461
1 TraesCS7D01G178300 chr7A 130292532 130294194 1662 False 823.00 1282 84.5225 808 2462 2 chr7A.!!$F2 1654
2 TraesCS7D01G178300 chr7B 92552623 92556568 3945 False 584.75 1269 89.8585 1 2462 4 chr7B.!!$F1 2461

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
357 370 0.303493 GACGCGCACAAGACTTTTGA 59.697 50.0 5.73 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 3317 0.033228 GCAGACTCAGCTGTCAGTGT 59.967 55.0 14.67 6.5 39.27 3.55 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
76 77 0.376852 AACGTGCATGTGTGTGTGTC 59.623 50.000 13.39 0.00 0.00 3.67
83 88 0.750249 ATGTGTGTGTGTCGAGGTGA 59.250 50.000 0.00 0.00 0.00 4.02
118 123 2.438795 CCGGGGTGGTGGAAATGT 59.561 61.111 0.00 0.00 0.00 2.71
132 137 2.609459 GGAAATGTGTGATGCTACGAGG 59.391 50.000 0.00 0.00 0.00 4.63
183 188 0.974383 ACTTTGGGTCCTCTGTACGG 59.026 55.000 0.00 0.00 0.00 4.02
187 192 1.982938 GGGTCCTCTGTACGGCTGT 60.983 63.158 2.42 2.42 0.00 4.40
216 221 2.502492 CCAGCCAGGACCGATCGAT 61.502 63.158 18.66 0.00 41.22 3.59
217 222 1.443407 CAGCCAGGACCGATCGATT 59.557 57.895 18.66 2.17 0.00 3.34
231 236 4.031652 CCGATCGATTTGGCATTGTTTTTC 59.968 41.667 18.66 0.00 0.00 2.29
238 243 2.621338 TGGCATTGTTTTTCGCACAAA 58.379 38.095 0.00 0.00 37.67 2.83
292 297 3.440872 ACGAACACTTTGCAAGTTGGTAA 59.559 39.130 13.53 0.00 40.46 2.85
293 298 4.097286 ACGAACACTTTGCAAGTTGGTAAT 59.903 37.500 13.53 0.00 40.46 1.89
294 299 5.040635 CGAACACTTTGCAAGTTGGTAATT 58.959 37.500 7.23 0.00 40.46 1.40
295 300 5.173131 CGAACACTTTGCAAGTTGGTAATTC 59.827 40.000 7.23 4.53 40.46 2.17
296 301 4.606961 ACACTTTGCAAGTTGGTAATTCG 58.393 39.130 4.75 0.00 40.46 3.34
297 302 3.425193 CACTTTGCAAGTTGGTAATTCGC 59.575 43.478 4.75 0.00 40.46 4.70
298 303 2.715737 TTGCAAGTTGGTAATTCGCC 57.284 45.000 4.75 0.00 0.00 5.54
300 305 1.268352 TGCAAGTTGGTAATTCGCCAC 59.732 47.619 4.75 0.00 35.46 5.01
302 307 2.745281 GCAAGTTGGTAATTCGCCACTA 59.255 45.455 4.75 0.00 35.46 2.74
304 309 4.495844 GCAAGTTGGTAATTCGCCACTATC 60.496 45.833 4.75 0.00 35.46 2.08
305 310 4.755266 AGTTGGTAATTCGCCACTATCT 57.245 40.909 1.57 0.00 35.46 1.98
306 311 4.442706 AGTTGGTAATTCGCCACTATCTG 58.557 43.478 1.57 0.00 35.46 2.90
308 313 4.322080 TGGTAATTCGCCACTATCTGAG 57.678 45.455 0.00 0.00 0.00 3.35
309 314 3.958147 TGGTAATTCGCCACTATCTGAGA 59.042 43.478 0.00 0.00 0.00 3.27
310 315 4.404394 TGGTAATTCGCCACTATCTGAGAA 59.596 41.667 0.00 0.00 0.00 2.87
322 335 2.496899 TCTGAGAATGCTGGGTTTCC 57.503 50.000 0.00 0.00 0.00 3.13
323 336 1.704628 TCTGAGAATGCTGGGTTTCCA 59.295 47.619 0.00 0.00 41.58 3.53
337 350 3.316308 GGGTTTCCAGATGATATGTGCAC 59.684 47.826 10.75 10.75 0.00 4.57
339 352 3.817709 TTCCAGATGATATGTGCACGA 57.182 42.857 13.13 2.60 0.00 4.35
340 353 3.097877 TCCAGATGATATGTGCACGAC 57.902 47.619 13.13 4.01 0.00 4.34
341 354 1.788886 CCAGATGATATGTGCACGACG 59.211 52.381 13.13 0.00 0.00 5.12
351 364 4.702826 GCACGACGCGCACAAGAC 62.703 66.667 5.73 0.00 0.00 3.01
352 365 3.030308 CACGACGCGCACAAGACT 61.030 61.111 5.73 0.00 0.00 3.24
353 366 2.279252 ACGACGCGCACAAGACTT 60.279 55.556 5.73 0.00 0.00 3.01
354 367 1.881252 ACGACGCGCACAAGACTTT 60.881 52.632 5.73 0.00 0.00 2.66
355 368 1.275657 CGACGCGCACAAGACTTTT 59.724 52.632 5.73 0.00 0.00 2.27
356 369 0.986874 CGACGCGCACAAGACTTTTG 60.987 55.000 5.73 0.00 0.00 2.44
357 370 0.303493 GACGCGCACAAGACTTTTGA 59.697 50.000 5.73 0.00 0.00 2.69
358 371 0.944386 ACGCGCACAAGACTTTTGAT 59.056 45.000 5.73 0.00 0.00 2.57
359 372 1.069906 ACGCGCACAAGACTTTTGATC 60.070 47.619 5.73 0.00 0.00 2.92
360 373 1.725931 CGCGCACAAGACTTTTGATCC 60.726 52.381 8.75 0.00 0.00 3.36
363 376 3.070018 CGCACAAGACTTTTGATCCTCT 58.930 45.455 5.52 0.00 0.00 3.69
366 379 4.320057 GCACAAGACTTTTGATCCTCTGTG 60.320 45.833 5.52 0.00 0.00 3.66
369 382 2.373169 AGACTTTTGATCCTCTGTGCCA 59.627 45.455 0.00 0.00 0.00 4.92
370 383 2.485814 GACTTTTGATCCTCTGTGCCAC 59.514 50.000 0.00 0.00 0.00 5.01
372 385 3.327757 ACTTTTGATCCTCTGTGCCACTA 59.672 43.478 0.00 0.00 0.00 2.74
384 397 1.054406 TGCCACTATACCCTGGGCTC 61.054 60.000 14.08 0.00 44.85 4.70
385 398 1.769716 GCCACTATACCCTGGGCTCC 61.770 65.000 14.08 0.00 41.39 4.70
386 399 0.399949 CCACTATACCCTGGGCTCCA 60.400 60.000 14.08 0.00 0.00 3.86
387 400 1.507140 CACTATACCCTGGGCTCCAA 58.493 55.000 14.08 0.00 30.80 3.53
390 411 0.771127 TATACCCTGGGCTCCAATGC 59.229 55.000 14.08 0.00 30.80 3.56
393 414 2.056223 CCCTGGGCTCCAATGCTTG 61.056 63.158 0.00 0.00 30.80 4.01
409 430 7.413644 CCAATGCTTGGTTTTATTTTTCGTTT 58.586 30.769 6.74 0.00 45.93 3.60
415 436 8.279800 GCTTGGTTTTATTTTTCGTTTGCTATT 58.720 29.630 0.00 0.00 0.00 1.73
416 437 9.579610 CTTGGTTTTATTTTTCGTTTGCTATTG 57.420 29.630 0.00 0.00 0.00 1.90
417 438 8.649973 TGGTTTTATTTTTCGTTTGCTATTGT 57.350 26.923 0.00 0.00 0.00 2.71
418 439 8.543774 TGGTTTTATTTTTCGTTTGCTATTGTG 58.456 29.630 0.00 0.00 0.00 3.33
439 1714 2.335752 CAACAGCACAAACACTTTGCA 58.664 42.857 0.00 0.00 44.39 4.08
441 1716 2.609350 ACAGCACAAACACTTTGCAAG 58.391 42.857 0.00 0.00 44.39 4.01
443 1718 3.119029 ACAGCACAAACACTTTGCAAGAT 60.119 39.130 0.00 0.00 44.39 2.40
444 1719 3.488310 CAGCACAAACACTTTGCAAGATC 59.512 43.478 0.00 0.00 44.39 2.75
447 1722 4.567959 GCACAAACACTTTGCAAGATCTTT 59.432 37.500 4.86 0.00 44.39 2.52
449 1724 6.255453 GCACAAACACTTTGCAAGATCTTTTA 59.745 34.615 4.86 0.00 44.39 1.52
454 1729 7.100458 ACACTTTGCAAGATCTTTTACAACT 57.900 32.000 4.86 0.00 0.00 3.16
456 1731 8.682710 ACACTTTGCAAGATCTTTTACAACTAA 58.317 29.630 4.86 0.00 0.00 2.24
459 1734 9.515020 CTTTGCAAGATCTTTTACAACTAAACA 57.485 29.630 4.86 0.00 0.00 2.83
460 1735 9.515020 TTTGCAAGATCTTTTACAACTAAACAG 57.485 29.630 4.86 0.00 0.00 3.16
461 1736 7.138736 TGCAAGATCTTTTACAACTAAACAGC 58.861 34.615 4.86 1.54 0.00 4.40
463 1738 7.535599 GCAAGATCTTTTACAACTAAACAGCTC 59.464 37.037 4.86 0.00 0.00 4.09
464 1739 7.674471 AGATCTTTTACAACTAAACAGCTCC 57.326 36.000 0.00 0.00 0.00 4.70
467 1742 6.588204 TCTTTTACAACTAAACAGCTCCTGA 58.412 36.000 0.00 0.00 35.18 3.86
468 1743 6.482308 TCTTTTACAACTAAACAGCTCCTGAC 59.518 38.462 0.00 0.00 35.18 3.51
469 1744 5.546621 TTACAACTAAACAGCTCCTGACT 57.453 39.130 0.00 0.00 35.18 3.41
470 1745 3.733337 ACAACTAAACAGCTCCTGACTG 58.267 45.455 0.00 0.00 41.08 3.51
474 1749 3.798758 ACAGCTCCTGACTGTCCC 58.201 61.111 5.17 0.00 45.06 4.46
477 1752 3.775654 GCTCCTGACTGTCCCCCG 61.776 72.222 5.17 0.00 0.00 5.73
478 1753 3.775654 CTCCTGACTGTCCCCCGC 61.776 72.222 5.17 0.00 0.00 6.13
479 1754 4.631740 TCCTGACTGTCCCCCGCA 62.632 66.667 5.17 0.00 0.00 5.69
482 1757 1.228124 CTGACTGTCCCCCGCAAAA 60.228 57.895 5.17 0.00 0.00 2.44
972 2378 2.054453 GCCACCAATCTTCCAGCCC 61.054 63.158 0.00 0.00 0.00 5.19
975 2381 3.204827 CCAATCTTCCAGCCCGCG 61.205 66.667 0.00 0.00 0.00 6.46
1254 2660 2.191375 CTGGGGATGCTGATGCGT 59.809 61.111 0.00 0.00 43.34 5.24
1504 2919 2.432628 GGTCAGTCGGTTGAGCGG 60.433 66.667 2.57 0.00 36.06 5.52
1508 2923 2.034879 CAGTCGGTTGAGCGGCATT 61.035 57.895 9.91 0.00 0.00 3.56
1509 2924 2.034879 AGTCGGTTGAGCGGCATTG 61.035 57.895 9.91 0.00 0.00 2.82
1510 2925 2.745884 TCGGTTGAGCGGCATTGG 60.746 61.111 1.45 0.00 0.00 3.16
1511 2926 3.055719 CGGTTGAGCGGCATTGGT 61.056 61.111 1.45 0.00 0.00 3.67
1512 2927 2.877691 GGTTGAGCGGCATTGGTC 59.122 61.111 1.45 0.00 36.91 4.02
1513 2928 2.700773 GGTTGAGCGGCATTGGTCC 61.701 63.158 1.45 0.00 35.53 4.46
1515 2930 4.776322 TGAGCGGCATTGGTCCGG 62.776 66.667 1.45 0.00 46.51 5.14
1538 2953 1.134640 GGTTGGTTGGTTGGTTGGTTC 60.135 52.381 0.00 0.00 0.00 3.62
1607 3046 2.625790 GGATCACCTGCTCGTCTAATCT 59.374 50.000 0.00 0.00 0.00 2.40
1639 3078 1.487482 GCTGTTTCTTTCGGGTTTGC 58.513 50.000 0.00 0.00 0.00 3.68
1767 3206 0.523072 TCCAATGAAAGAGCTTGCGC 59.477 50.000 0.00 0.00 0.00 6.09
1813 3256 1.080366 CGTTTCCCCGTCACGATCA 60.080 57.895 0.00 0.00 35.93 2.92
1817 3260 0.320946 TTCCCCGTCACGATCAAACC 60.321 55.000 0.00 0.00 0.00 3.27
1846 3290 3.114616 CTTGTCGTGCTGGCGAGG 61.115 66.667 0.00 0.00 41.85 4.63
1851 3295 3.114616 CGTGCTGGCGAGGTTCAG 61.115 66.667 0.00 0.00 0.00 3.02
1892 3336 0.033228 ACACTGACAGCTGAGTCTGC 59.967 55.000 23.35 13.72 40.02 4.26
1907 3351 5.178061 TGAGTCTGCCAATATTGTACAGTG 58.822 41.667 24.16 8.51 34.17 3.66
1908 3352 5.165961 AGTCTGCCAATATTGTACAGTGT 57.834 39.130 24.16 15.32 34.17 3.55
1909 3353 6.071051 TGAGTCTGCCAATATTGTACAGTGTA 60.071 38.462 24.16 0.00 34.17 2.90
1910 3354 6.106673 AGTCTGCCAATATTGTACAGTGTAC 58.893 40.000 23.85 23.85 34.17 2.90
1911 3355 6.070767 AGTCTGCCAATATTGTACAGTGTACT 60.071 38.462 28.78 19.67 34.17 2.73
1912 3356 7.123697 AGTCTGCCAATATTGTACAGTGTACTA 59.876 37.037 28.78 23.51 34.17 1.82
1913 3357 7.435488 GTCTGCCAATATTGTACAGTGTACTAG 59.565 40.741 28.78 13.65 34.17 2.57
1935 3398 6.380095 AGTTTTGTTGGAATAAGCGTGTTA 57.620 33.333 0.00 0.00 0.00 2.41
1949 3412 3.625764 AGCGTGTTAGTTTTGCTTCAGAA 59.374 39.130 0.00 0.00 30.27 3.02
1991 3454 2.271821 AAAAACAGGCACGAACACAC 57.728 45.000 0.00 0.00 0.00 3.82
1992 3455 0.454196 AAAACAGGCACGAACACACC 59.546 50.000 0.00 0.00 0.00 4.16
2009 3619 3.130516 CACACCTAGAGCTCCGAAACATA 59.869 47.826 10.93 0.00 0.00 2.29
2017 3627 4.083271 AGAGCTCCGAAACATAAAAACTGC 60.083 41.667 10.93 0.00 0.00 4.40
2023 3633 4.505922 CCGAAACATAAAAACTGCTTGCAA 59.494 37.500 0.00 0.00 0.00 4.08
2027 3637 5.009854 ACATAAAAACTGCTTGCAACTGT 57.990 34.783 0.00 0.41 0.00 3.55
2029 3639 2.584492 AAAACTGCTTGCAACTGTCC 57.416 45.000 0.00 0.00 0.00 4.02
2030 3640 1.767759 AAACTGCTTGCAACTGTCCT 58.232 45.000 0.00 0.00 0.00 3.85
2031 3641 1.027357 AACTGCTTGCAACTGTCCTG 58.973 50.000 0.00 0.00 0.00 3.86
2033 3643 1.027357 CTGCTTGCAACTGTCCTGTT 58.973 50.000 0.00 0.00 0.00 3.16
2036 3656 2.159254 TGCTTGCAACTGTCCTGTTTTC 60.159 45.455 0.00 0.00 0.00 2.29
2038 3658 3.491447 GCTTGCAACTGTCCTGTTTTCAT 60.491 43.478 0.00 0.00 0.00 2.57
2041 3661 3.316029 TGCAACTGTCCTGTTTTCATCAG 59.684 43.478 0.00 0.00 33.12 2.90
2051 3671 2.290260 TGTTTTCATCAGCAGGGACGAT 60.290 45.455 0.00 0.00 0.00 3.73
2053 3673 1.489481 TTCATCAGCAGGGACGATCT 58.511 50.000 0.00 0.00 0.00 2.75
2084 3704 3.165058 TCGAGACCATCACATAACTGC 57.835 47.619 0.00 0.00 0.00 4.40
2085 3705 2.159099 TCGAGACCATCACATAACTGCC 60.159 50.000 0.00 0.00 0.00 4.85
2093 3713 5.648092 ACCATCACATAACTGCCTTAAGTTC 59.352 40.000 0.97 0.00 40.77 3.01
2121 3741 1.004745 ACATCCTTCGCCATTTGAGGT 59.995 47.619 0.00 0.00 0.00 3.85
2147 3767 9.056005 TGAATTTGTGACCTATATACATTCTGC 57.944 33.333 0.00 0.00 0.00 4.26
2148 3768 7.986085 ATTTGTGACCTATATACATTCTGCC 57.014 36.000 0.00 0.00 0.00 4.85
2149 3769 5.483685 TGTGACCTATATACATTCTGCCC 57.516 43.478 0.00 0.00 0.00 5.36
2152 3772 5.013183 GTGACCTATATACATTCTGCCCCTT 59.987 44.000 0.00 0.00 0.00 3.95
2154 3774 4.223032 ACCTATATACATTCTGCCCCTTCG 59.777 45.833 0.00 0.00 0.00 3.79
2177 3804 1.569548 TCTCTTCGGGGATCCTGTACT 59.430 52.381 12.58 0.00 0.00 2.73
2182 3809 1.567649 TCGGGGATCCTGTACTGTACT 59.432 52.381 17.98 0.00 0.00 2.73
2183 3810 1.681793 CGGGGATCCTGTACTGTACTG 59.318 57.143 17.98 16.65 0.00 2.74
2184 3811 2.748388 GGGGATCCTGTACTGTACTGT 58.252 52.381 17.98 10.46 0.00 3.55
2185 3812 3.686405 CGGGGATCCTGTACTGTACTGTA 60.686 52.174 17.98 8.40 0.00 2.74
2190 3817 6.125029 GGATCCTGTACTGTACTGTACCTAA 58.875 44.000 29.33 19.04 41.34 2.69
2191 3818 6.604795 GGATCCTGTACTGTACTGTACCTAAA 59.395 42.308 29.33 17.75 41.34 1.85
2195 3822 8.526147 TCCTGTACTGTACTGTACCTAAATTTC 58.474 37.037 29.33 10.84 41.34 2.17
2211 3838 9.369672 ACCTAAATTTCTCTATACCTCCTGTAG 57.630 37.037 0.00 0.00 31.61 2.74
2212 3839 8.308207 CCTAAATTTCTCTATACCTCCTGTAGC 58.692 40.741 0.00 0.00 31.61 3.58
2213 3840 7.676683 AAATTTCTCTATACCTCCTGTAGCA 57.323 36.000 0.00 0.00 31.61 3.49
2214 3841 7.676683 AATTTCTCTATACCTCCTGTAGCAA 57.323 36.000 0.00 0.00 31.61 3.91
2218 3845 5.536538 TCTCTATACCTCCTGTAGCAACATG 59.463 44.000 0.00 0.00 34.37 3.21
2262 3889 2.503356 ACCTCCCTTTCTGCATCTACAG 59.497 50.000 0.00 0.00 39.12 2.74
2263 3890 2.559440 CTCCCTTTCTGCATCTACAGC 58.441 52.381 0.00 0.00 37.59 4.40
2265 3892 1.293924 CCTTTCTGCATCTACAGCCG 58.706 55.000 0.00 0.00 37.59 5.52
2266 3893 1.293924 CTTTCTGCATCTACAGCCGG 58.706 55.000 0.00 0.00 37.59 6.13
2267 3894 0.901827 TTTCTGCATCTACAGCCGGA 59.098 50.000 5.05 0.00 37.59 5.14
2270 3897 0.176680 CTGCATCTACAGCCGGAACT 59.823 55.000 5.05 0.00 0.00 3.01
2271 3898 0.613260 TGCATCTACAGCCGGAACTT 59.387 50.000 5.05 0.00 0.00 2.66
2272 3899 1.003118 TGCATCTACAGCCGGAACTTT 59.997 47.619 5.05 0.00 0.00 2.66
2274 3901 2.935238 GCATCTACAGCCGGAACTTTCA 60.935 50.000 5.05 0.00 0.00 2.69
2275 3902 3.535561 CATCTACAGCCGGAACTTTCAT 58.464 45.455 5.05 0.00 0.00 2.57
2276 3903 3.247006 TCTACAGCCGGAACTTTCATC 57.753 47.619 5.05 0.00 0.00 2.92
2342 3979 1.156736 GGACATGTCAAACCACCTCG 58.843 55.000 26.47 0.00 0.00 4.63
2343 3980 1.270625 GGACATGTCAAACCACCTCGA 60.271 52.381 26.47 0.00 0.00 4.04
2344 3981 1.798813 GACATGTCAAACCACCTCGAC 59.201 52.381 21.07 0.00 0.00 4.20
2345 3982 1.140052 ACATGTCAAACCACCTCGACA 59.860 47.619 0.00 0.00 42.19 4.35
2346 3983 1.531149 CATGTCAAACCACCTCGACAC 59.469 52.381 0.00 0.00 40.91 3.67
2347 3984 0.179067 TGTCAAACCACCTCGACACC 60.179 55.000 0.00 0.00 33.61 4.16
2348 3985 0.106149 GTCAAACCACCTCGACACCT 59.894 55.000 0.00 0.00 0.00 4.00
2349 3986 0.391597 TCAAACCACCTCGACACCTC 59.608 55.000 0.00 0.00 0.00 3.85
2350 3987 0.944311 CAAACCACCTCGACACCTCG 60.944 60.000 0.00 0.00 41.65 4.63
2415 4052 2.492088 CTCGTCAAGGTACTCCACATCA 59.508 50.000 0.00 0.00 38.49 3.07
2416 4053 2.894765 TCGTCAAGGTACTCCACATCAA 59.105 45.455 0.00 0.00 38.49 2.57
2436 4073 3.414700 CGTGGGTTGCTCGAGTGC 61.415 66.667 15.13 1.33 0.00 4.40
2444 4081 1.221466 TTGCTCGAGTGCCGTTTCAG 61.221 55.000 15.13 0.00 39.75 3.02
2445 4082 1.664965 GCTCGAGTGCCGTTTCAGT 60.665 57.895 15.13 0.00 39.75 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 119 1.743772 GCCCTCGTAGCATCACACATT 60.744 52.381 0.00 0.00 0.00 2.71
118 123 1.987306 TGGCCCTCGTAGCATCACA 60.987 57.895 0.00 0.00 0.00 3.58
132 137 1.450134 TGCACAGATCATCGTGGCC 60.450 57.895 0.00 0.00 33.62 5.36
187 192 3.626996 CTGGCTGGAACCGATGGCA 62.627 63.158 0.00 0.00 0.00 4.92
216 221 2.621338 TGTGCGAAAAACAATGCCAAA 58.379 38.095 0.00 0.00 0.00 3.28
217 222 2.299993 TGTGCGAAAAACAATGCCAA 57.700 40.000 0.00 0.00 0.00 4.52
231 236 3.963340 AAAGAAAAACGTGTTTGTGCG 57.037 38.095 8.82 0.00 32.36 5.34
238 243 4.090786 CCGCAAAAGAAAAGAAAAACGTGT 59.909 37.500 0.00 0.00 0.00 4.49
292 297 3.070734 AGCATTCTCAGATAGTGGCGAAT 59.929 43.478 0.00 0.00 31.11 3.34
293 298 2.432146 AGCATTCTCAGATAGTGGCGAA 59.568 45.455 0.00 0.00 0.00 4.70
294 299 2.034878 AGCATTCTCAGATAGTGGCGA 58.965 47.619 0.00 0.00 0.00 5.54
295 300 2.133553 CAGCATTCTCAGATAGTGGCG 58.866 52.381 0.00 0.00 0.00 5.69
296 301 2.492012 CCAGCATTCTCAGATAGTGGC 58.508 52.381 0.00 0.00 0.00 5.01
297 302 2.437281 ACCCAGCATTCTCAGATAGTGG 59.563 50.000 0.00 0.00 0.00 4.00
298 303 3.834489 ACCCAGCATTCTCAGATAGTG 57.166 47.619 0.00 0.00 0.00 2.74
300 305 4.133078 GGAAACCCAGCATTCTCAGATAG 58.867 47.826 0.00 0.00 0.00 2.08
302 307 2.309755 TGGAAACCCAGCATTCTCAGAT 59.690 45.455 0.00 0.00 0.00 2.90
304 309 2.089980 CTGGAAACCCAGCATTCTCAG 58.910 52.381 0.00 0.00 44.11 3.35
305 310 2.205022 CTGGAAACCCAGCATTCTCA 57.795 50.000 0.00 0.00 44.11 3.27
322 335 1.190984 GCGTCGTGCACATATCATCTG 59.809 52.381 18.64 0.00 45.45 2.90
323 336 1.491670 GCGTCGTGCACATATCATCT 58.508 50.000 18.64 0.00 45.45 2.90
337 350 0.986874 CAAAAGTCTTGTGCGCGTCG 60.987 55.000 8.43 0.00 0.00 5.12
339 352 0.944386 ATCAAAAGTCTTGTGCGCGT 59.056 45.000 8.43 0.00 0.00 6.01
340 353 1.595609 GATCAAAAGTCTTGTGCGCG 58.404 50.000 0.00 0.00 0.00 6.86
341 354 1.537202 AGGATCAAAAGTCTTGTGCGC 59.463 47.619 0.00 0.00 0.00 6.09
351 364 2.787994 AGTGGCACAGAGGATCAAAAG 58.212 47.619 21.41 0.00 41.80 2.27
352 365 2.957402 AGTGGCACAGAGGATCAAAA 57.043 45.000 21.41 0.00 41.80 2.44
353 366 4.141711 GGTATAGTGGCACAGAGGATCAAA 60.142 45.833 21.41 0.00 41.80 2.69
354 367 3.388024 GGTATAGTGGCACAGAGGATCAA 59.612 47.826 21.41 0.00 41.80 2.57
355 368 2.965831 GGTATAGTGGCACAGAGGATCA 59.034 50.000 21.41 0.00 41.80 2.92
356 369 2.300437 GGGTATAGTGGCACAGAGGATC 59.700 54.545 21.41 0.09 41.80 3.36
357 370 2.090494 AGGGTATAGTGGCACAGAGGAT 60.090 50.000 21.41 7.25 41.80 3.24
358 371 1.291033 AGGGTATAGTGGCACAGAGGA 59.709 52.381 21.41 0.00 41.80 3.71
359 372 1.414181 CAGGGTATAGTGGCACAGAGG 59.586 57.143 21.41 0.00 41.80 3.69
360 373 1.414181 CCAGGGTATAGTGGCACAGAG 59.586 57.143 21.41 0.47 41.80 3.35
363 376 1.632018 GCCCAGGGTATAGTGGCACA 61.632 60.000 21.41 6.31 41.76 4.57
366 379 1.755384 GAGCCCAGGGTATAGTGGC 59.245 63.158 7.55 0.00 42.48 5.01
369 382 2.057922 CATTGGAGCCCAGGGTATAGT 58.942 52.381 7.55 0.00 33.81 2.12
370 383 1.271597 GCATTGGAGCCCAGGGTATAG 60.272 57.143 7.55 0.00 33.81 1.31
372 385 0.995675 AGCATTGGAGCCCAGGGTAT 60.996 55.000 7.55 0.00 33.81 2.73
386 399 6.909895 GCAAACGAAAAATAAAACCAAGCATT 59.090 30.769 0.00 0.00 0.00 3.56
387 400 6.259829 AGCAAACGAAAAATAAAACCAAGCAT 59.740 30.769 0.00 0.00 0.00 3.79
390 411 9.579610 CAATAGCAAACGAAAAATAAAACCAAG 57.420 29.630 0.00 0.00 0.00 3.61
393 414 7.529185 GCACAATAGCAAACGAAAAATAAAACC 59.471 33.333 0.00 0.00 0.00 3.27
394 415 8.058915 TGCACAATAGCAAACGAAAAATAAAAC 58.941 29.630 0.00 0.00 42.46 2.43
417 438 3.496630 GCAAAGTGTTTGTGCTGTTGCA 61.497 45.455 0.00 0.00 42.91 4.08
418 439 1.060986 GCAAAGTGTTTGTGCTGTTGC 59.939 47.619 1.62 0.00 42.56 4.17
422 443 2.878580 TCTTGCAAAGTGTTTGTGCTG 58.121 42.857 0.00 0.00 46.34 4.41
423 444 3.382546 AGATCTTGCAAAGTGTTTGTGCT 59.617 39.130 0.00 0.00 46.34 4.40
424 445 3.709987 AGATCTTGCAAAGTGTTTGTGC 58.290 40.909 0.00 0.00 46.34 4.57
427 1702 7.754069 TGTAAAAGATCTTGCAAAGTGTTTG 57.246 32.000 9.17 0.00 46.34 2.93
434 1709 9.515020 CTGTTTAGTTGTAAAAGATCTTGCAAA 57.485 29.630 9.17 0.00 33.52 3.68
439 1714 7.939588 AGGAGCTGTTTAGTTGTAAAAGATCTT 59.060 33.333 0.88 0.88 30.61 2.40
441 1716 7.387948 TCAGGAGCTGTTTAGTTGTAAAAGATC 59.612 37.037 0.00 0.00 32.61 2.75
443 1718 6.482308 GTCAGGAGCTGTTTAGTTGTAAAAGA 59.518 38.462 0.00 0.00 32.61 2.52
444 1719 6.483640 AGTCAGGAGCTGTTTAGTTGTAAAAG 59.516 38.462 0.00 0.00 32.61 2.27
447 1722 5.163343 ACAGTCAGGAGCTGTTTAGTTGTAA 60.163 40.000 0.00 0.00 43.87 2.41
449 1724 3.134804 ACAGTCAGGAGCTGTTTAGTTGT 59.865 43.478 0.00 0.00 43.87 3.32
454 1729 1.623811 GGGACAGTCAGGAGCTGTTTA 59.376 52.381 2.17 0.00 45.99 2.01
456 1731 1.484444 GGGGACAGTCAGGAGCTGTT 61.484 60.000 2.17 0.00 45.99 3.16
459 1734 2.284995 GGGGGACAGTCAGGAGCT 60.285 66.667 2.17 0.00 0.00 4.09
460 1735 3.775654 CGGGGGACAGTCAGGAGC 61.776 72.222 2.17 0.00 0.00 4.70
461 1736 3.775654 GCGGGGGACAGTCAGGAG 61.776 72.222 2.17 0.00 0.00 3.69
463 1738 2.690653 TTTTGCGGGGGACAGTCAGG 62.691 60.000 2.17 0.00 0.00 3.86
464 1739 0.821711 TTTTTGCGGGGGACAGTCAG 60.822 55.000 2.17 0.00 0.00 3.51
952 2351 2.054453 GCTGGAAGATTGGTGGCCC 61.054 63.158 0.00 0.00 34.07 5.80
972 2378 2.895865 TCTAGCTCGGAGGACGCG 60.896 66.667 3.53 3.53 43.86 6.01
1278 2684 2.046023 TCCTGCTTGCCGTGATGG 60.046 61.111 0.00 0.00 42.50 3.51
1279 2685 2.110967 CCTCCTGCTTGCCGTGATG 61.111 63.158 0.00 0.00 0.00 3.07
1280 2686 2.270205 CCTCCTGCTTGCCGTGAT 59.730 61.111 0.00 0.00 0.00 3.06
1311 2723 0.544223 GCTTCTTCTTCTCCCCCTCC 59.456 60.000 0.00 0.00 0.00 4.30
1314 2726 1.222113 CGGCTTCTTCTTCTCCCCC 59.778 63.158 0.00 0.00 0.00 5.40
1504 2919 1.288752 CAACCAACCGGACCAATGC 59.711 57.895 9.46 0.00 35.59 3.56
1508 2923 1.454111 CAACCAACCAACCGGACCA 60.454 57.895 9.46 0.00 35.59 4.02
1509 2924 2.197605 CCAACCAACCAACCGGACC 61.198 63.158 9.46 0.00 35.59 4.46
1510 2925 1.038681 AACCAACCAACCAACCGGAC 61.039 55.000 9.46 0.00 35.59 4.79
1511 2926 1.038130 CAACCAACCAACCAACCGGA 61.038 55.000 9.46 0.00 35.59 5.14
1512 2927 1.439644 CAACCAACCAACCAACCGG 59.560 57.895 0.00 0.00 38.77 5.28
1513 2928 1.324005 ACCAACCAACCAACCAACCG 61.324 55.000 0.00 0.00 0.00 4.44
1514 2929 0.906066 AACCAACCAACCAACCAACC 59.094 50.000 0.00 0.00 0.00 3.77
1515 2930 1.406205 CCAACCAACCAACCAACCAAC 60.406 52.381 0.00 0.00 0.00 3.77
1813 3256 2.621526 GACAAGAAACATCCACCGGTTT 59.378 45.455 2.97 0.00 39.74 3.27
1817 3260 1.194547 CACGACAAGAAACATCCACCG 59.805 52.381 0.00 0.00 0.00 4.94
1846 3290 2.877335 CAACCTACGGAGCTACTGAAC 58.123 52.381 0.00 0.00 0.00 3.18
1851 3295 0.815734 TCTGCAACCTACGGAGCTAC 59.184 55.000 0.00 0.00 0.00 3.58
1870 3314 2.029200 CAGACTCAGCTGTCAGTGTCAT 60.029 50.000 14.67 3.99 39.27 3.06
1872 3316 1.934399 GCAGACTCAGCTGTCAGTGTC 60.934 57.143 14.67 14.18 39.27 3.67
1873 3317 0.033228 GCAGACTCAGCTGTCAGTGT 59.967 55.000 14.67 6.50 39.27 3.55
1874 3318 0.669932 GGCAGACTCAGCTGTCAGTG 60.670 60.000 14.67 8.86 40.18 3.66
1875 3319 1.117749 TGGCAGACTCAGCTGTCAGT 61.118 55.000 14.67 10.92 44.84 3.41
1907 3351 7.013529 CACGCTTATTCCAACAAAACTAGTAC 58.986 38.462 0.00 0.00 0.00 2.73
1908 3352 6.707161 ACACGCTTATTCCAACAAAACTAGTA 59.293 34.615 0.00 0.00 0.00 1.82
1909 3353 5.529800 ACACGCTTATTCCAACAAAACTAGT 59.470 36.000 0.00 0.00 0.00 2.57
1910 3354 5.997385 ACACGCTTATTCCAACAAAACTAG 58.003 37.500 0.00 0.00 0.00 2.57
1911 3355 6.380095 AACACGCTTATTCCAACAAAACTA 57.620 33.333 0.00 0.00 0.00 2.24
1912 3356 4.911514 ACACGCTTATTCCAACAAAACT 57.088 36.364 0.00 0.00 0.00 2.66
1913 3357 6.203647 ACTAACACGCTTATTCCAACAAAAC 58.796 36.000 0.00 0.00 0.00 2.43
1949 3412 0.832983 TGCTTCCCATTTTGCCTGCT 60.833 50.000 0.00 0.00 0.00 4.24
1973 3436 0.454196 GGTGTGTTCGTGCCTGTTTT 59.546 50.000 0.00 0.00 0.00 2.43
1974 3437 0.393808 AGGTGTGTTCGTGCCTGTTT 60.394 50.000 0.00 0.00 0.00 2.83
1976 3439 0.033504 CTAGGTGTGTTCGTGCCTGT 59.966 55.000 0.00 0.00 32.90 4.00
1977 3440 0.317160 TCTAGGTGTGTTCGTGCCTG 59.683 55.000 0.00 0.00 32.90 4.85
1979 3442 1.014564 GCTCTAGGTGTGTTCGTGCC 61.015 60.000 0.00 0.00 0.00 5.01
1980 3443 0.038159 AGCTCTAGGTGTGTTCGTGC 60.038 55.000 0.00 0.00 0.00 5.34
1981 3444 1.402984 GGAGCTCTAGGTGTGTTCGTG 60.403 57.143 14.64 0.00 0.00 4.35
1982 3445 0.889306 GGAGCTCTAGGTGTGTTCGT 59.111 55.000 14.64 0.00 0.00 3.85
1984 3447 1.174783 TCGGAGCTCTAGGTGTGTTC 58.825 55.000 14.64 0.00 0.00 3.18
1985 3448 1.629043 TTCGGAGCTCTAGGTGTGTT 58.371 50.000 14.64 0.00 0.00 3.32
1986 3449 1.272769 GTTTCGGAGCTCTAGGTGTGT 59.727 52.381 14.64 0.00 0.00 3.72
1987 3450 1.272490 TGTTTCGGAGCTCTAGGTGTG 59.728 52.381 14.64 0.00 0.00 3.82
1988 3451 1.629043 TGTTTCGGAGCTCTAGGTGT 58.371 50.000 14.64 0.00 0.00 4.16
1989 3452 2.969628 ATGTTTCGGAGCTCTAGGTG 57.030 50.000 14.64 0.00 0.00 4.00
1990 3453 5.416271 TTTTATGTTTCGGAGCTCTAGGT 57.584 39.130 14.64 0.00 0.00 3.08
1991 3454 5.875359 AGTTTTTATGTTTCGGAGCTCTAGG 59.125 40.000 14.64 3.65 0.00 3.02
1992 3455 6.673316 GCAGTTTTTATGTTTCGGAGCTCTAG 60.673 42.308 14.64 8.52 0.00 2.43
2009 3619 2.497273 AGGACAGTTGCAAGCAGTTTTT 59.503 40.909 0.00 0.00 0.00 1.94
2017 3627 3.781079 TGAAAACAGGACAGTTGCAAG 57.219 42.857 0.00 0.00 0.00 4.01
2023 3633 3.144506 CTGCTGATGAAAACAGGACAGT 58.855 45.455 0.00 0.00 37.20 3.55
2029 3639 1.466167 CGTCCCTGCTGATGAAAACAG 59.534 52.381 0.00 0.00 40.09 3.16
2030 3640 1.071542 TCGTCCCTGCTGATGAAAACA 59.928 47.619 0.00 0.00 0.00 2.83
2031 3641 1.808411 TCGTCCCTGCTGATGAAAAC 58.192 50.000 0.00 0.00 0.00 2.43
2033 3643 1.833630 AGATCGTCCCTGCTGATGAAA 59.166 47.619 0.00 0.00 34.15 2.69
2036 3656 2.208431 GAAAGATCGTCCCTGCTGATG 58.792 52.381 0.00 0.00 0.00 3.07
2038 3658 0.173481 CGAAAGATCGTCCCTGCTGA 59.827 55.000 0.00 0.00 44.06 4.26
2051 3671 2.073816 GGTCTCGAAAATGGCGAAAGA 58.926 47.619 0.00 0.00 37.32 2.52
2053 3673 1.885560 TGGTCTCGAAAATGGCGAAA 58.114 45.000 0.00 0.00 37.32 3.46
2121 3741 9.056005 GCAGAATGTATATAGGTCACAAATTCA 57.944 33.333 0.00 0.00 39.31 2.57
2146 3766 1.019805 CCGAAGAGAAACGAAGGGGC 61.020 60.000 0.00 0.00 0.00 5.80
2147 3767 0.391263 CCCGAAGAGAAACGAAGGGG 60.391 60.000 0.00 0.00 33.97 4.79
2148 3768 0.391263 CCCCGAAGAGAAACGAAGGG 60.391 60.000 0.00 0.00 37.20 3.95
2149 3769 0.606604 TCCCCGAAGAGAAACGAAGG 59.393 55.000 0.00 0.00 0.00 3.46
2152 3772 0.822164 GGATCCCCGAAGAGAAACGA 59.178 55.000 0.00 0.00 0.00 3.85
2154 3774 1.555533 ACAGGATCCCCGAAGAGAAAC 59.444 52.381 8.55 0.00 37.58 2.78
2182 3809 9.144298 CAGGAGGTATAGAGAAATTTAGGTACA 57.856 37.037 0.00 0.00 0.00 2.90
2183 3810 9.145442 ACAGGAGGTATAGAGAAATTTAGGTAC 57.855 37.037 0.00 0.00 0.00 3.34
2185 3812 9.369672 CTACAGGAGGTATAGAGAAATTTAGGT 57.630 37.037 0.00 0.00 0.00 3.08
2190 3817 7.125811 TGTTGCTACAGGAGGTATAGAGAAATT 59.874 37.037 0.00 0.00 0.00 1.82
2191 3818 6.611642 TGTTGCTACAGGAGGTATAGAGAAAT 59.388 38.462 0.00 0.00 0.00 2.17
2195 3822 5.303078 ACATGTTGCTACAGGAGGTATAGAG 59.697 44.000 19.29 0.00 38.29 2.43
2205 3832 1.645034 CTCGGACATGTTGCTACAGG 58.355 55.000 11.31 11.31 41.65 4.00
2262 3889 3.798202 AGAGTATGATGAAAGTTCCGGC 58.202 45.455 0.00 0.00 0.00 6.13
2263 3890 6.574350 AGTTAGAGTATGATGAAAGTTCCGG 58.426 40.000 0.00 0.00 0.00 5.14
2265 3892 8.669243 CCAAAGTTAGAGTATGATGAAAGTTCC 58.331 37.037 0.00 0.00 0.00 3.62
2266 3893 9.436957 TCCAAAGTTAGAGTATGATGAAAGTTC 57.563 33.333 0.00 0.00 0.00 3.01
2267 3894 9.220767 GTCCAAAGTTAGAGTATGATGAAAGTT 57.779 33.333 0.00 0.00 0.00 2.66
2270 3897 9.166173 CATGTCCAAAGTTAGAGTATGATGAAA 57.834 33.333 0.00 0.00 0.00 2.69
2271 3898 8.321353 ACATGTCCAAAGTTAGAGTATGATGAA 58.679 33.333 0.00 0.00 0.00 2.57
2272 3899 7.851228 ACATGTCCAAAGTTAGAGTATGATGA 58.149 34.615 0.00 0.00 0.00 2.92
2274 3901 7.766278 GTGACATGTCCAAAGTTAGAGTATGAT 59.234 37.037 22.85 0.00 0.00 2.45
2275 3902 7.097192 GTGACATGTCCAAAGTTAGAGTATGA 58.903 38.462 22.85 0.00 0.00 2.15
2276 3903 6.873605 TGTGACATGTCCAAAGTTAGAGTATG 59.126 38.462 22.85 0.00 0.00 2.39
2342 3979 0.656259 TCGATGATCGACGAGGTGTC 59.344 55.000 14.25 0.00 44.82 3.67
2343 3980 2.776659 TCGATGATCGACGAGGTGT 58.223 52.632 14.25 0.00 44.82 4.16
2444 4081 3.936535 ACGAGATCTTCCGGGGAC 58.063 61.111 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.