Multiple sequence alignment - TraesCS2A01G396600

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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 TraesCS2A01G396600 chr2A 100.000 3140 0 0 1 3140 650261319 650258180 0.000000e+00 5799.0
1 TraesCS2A01G396600 chr2D 89.452 2228 75 47 1 2142 505842818 505840665 0.000000e+00 2665.0
2 TraesCS2A01G396600 chr2D 87.328 363 17 16 2198 2542 505840649 505840298 3.800000e-104 388.0
3 TraesCS2A01G396600 chr2D 86.875 320 24 8 2825 3140 505839903 505839598 3.000000e-90 342.0
4 TraesCS2A01G396600 chr2D 88.278 273 25 6 2544 2813 505840264 505839996 1.410000e-83 320.0
5 TraesCS2A01G396600 chr2B 87.601 2218 111 74 664 2813 593018509 593016388 0.000000e+00 2422.0
6 TraesCS2A01G396600 chr2B 88.710 620 40 12 46 652 593021759 593021157 0.000000e+00 730.0
7 TraesCS2A01G396600 chr2B 86.056 251 19 7 2850 3089 593016286 593016041 4.020000e-64 255.0
8 TraesCS2A01G396600 chr6A 74.185 368 69 20 1002 1356 480310349 480310703 2.540000e-26 130.0
9 TraesCS2A01G396600 chr6D 72.283 368 76 19 1002 1356 340212374 340212728 1.200000e-14 91.6


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 TraesCS2A01G396600 chr2A 650258180 650261319 3139 True 5799.000000 5799 100.000000 1 3140 1 chr2A.!!$R1 3139
1 TraesCS2A01G396600 chr2D 505839598 505842818 3220 True 928.750000 2665 87.983250 1 3140 4 chr2D.!!$R1 3139
2 TraesCS2A01G396600 chr2B 593016041 593021759 5718 True 1135.666667 2422 87.455667 46 3089 3 chr2B.!!$R1 3043

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
857 3529 0.037326 TTCTTCGTCGCTGGCTTCAT 60.037 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 4927 0.03438 TCTACCAGGAGCAGCTACGT 60.034 55.0 0.0 0.0 0.0 3.57 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 2.223525 GCCGCTACAGAACCTACTACAG 60.224 54.545 0.00 0.00 0.00 2.74
62 63 1.826385 AAGAAATCACCTCCTTGGCG 58.174 50.000 0.00 0.00 40.22 5.69
91 92 1.864435 GCATCGGGTACACTCACGATC 60.864 57.143 0.81 0.00 43.38 3.69
252 253 4.115199 GCGGCACCCTCCATTCCT 62.115 66.667 0.00 0.00 0.00 3.36
253 254 2.124570 CGGCACCCTCCATTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
254 255 2.669133 CGGCACCCTCCATTCCTGA 61.669 63.158 0.00 0.00 0.00 3.86
255 256 1.077429 GGCACCCTCCATTCCTGAC 60.077 63.158 0.00 0.00 0.00 3.51
256 257 1.077429 GCACCCTCCATTCCTGACC 60.077 63.158 0.00 0.00 0.00 4.02
257 258 1.609783 CACCCTCCATTCCTGACCC 59.390 63.158 0.00 0.00 0.00 4.46
258 259 1.995626 ACCCTCCATTCCTGACCCG 60.996 63.158 0.00 0.00 0.00 5.28
259 260 1.689233 CCCTCCATTCCTGACCCGA 60.689 63.158 0.00 0.00 0.00 5.14
260 261 1.690219 CCCTCCATTCCTGACCCGAG 61.690 65.000 0.00 0.00 0.00 4.63
303 304 5.006746 GCACAAAATCTATCCTGGTTCTACG 59.993 44.000 0.00 0.00 0.00 3.51
377 378 3.562639 GCGAGTGCGTCCATATGTA 57.437 52.632 1.24 0.00 40.36 2.29
383 385 4.381863 CGAGTGCGTCCATATGTAATGTAC 59.618 45.833 1.24 5.06 0.00 2.90
386 388 4.147653 GTGCGTCCATATGTAATGTACGAC 59.852 45.833 7.20 0.00 0.00 4.34
397 399 1.695893 ATGTACGACTGCACATGCGC 61.696 55.000 0.00 0.00 45.83 6.09
414 416 1.503818 CGCGGGGGCATACATAACAC 61.504 60.000 0.00 0.00 0.00 3.32
415 417 1.503818 GCGGGGGCATACATAACACG 61.504 60.000 0.00 0.00 0.00 4.49
416 418 0.179067 CGGGGGCATACATAACACGT 60.179 55.000 0.00 0.00 0.00 4.49
417 419 1.068895 CGGGGGCATACATAACACGTA 59.931 52.381 0.00 0.00 0.00 3.57
418 420 2.486918 GGGGGCATACATAACACGTAC 58.513 52.381 0.00 0.00 0.00 3.67
419 421 2.486918 GGGGCATACATAACACGTACC 58.513 52.381 0.00 0.00 0.00 3.34
456 459 0.293723 GTGCGCGTAATGAGTACACG 59.706 55.000 8.43 0.00 40.46 4.49
462 465 1.838345 CGTAATGAGTACACGACAGCG 59.162 52.381 0.00 0.00 44.79 5.18
489 503 3.074412 GTTGGTGTATTCTGTGGGAGTG 58.926 50.000 0.00 0.00 0.00 3.51
494 508 2.304761 TGTATTCTGTGGGAGTGGTTCC 59.695 50.000 0.00 0.00 46.00 3.62
507 521 0.535335 TGGTTCCGCTGTATCTGTCC 59.465 55.000 0.00 0.00 0.00 4.02
554 568 2.960129 GCCGGCGTAATGAGGACG 60.960 66.667 12.58 0.00 41.74 4.79
579 606 1.678970 AATGGCCGGTCAGCTTTCC 60.679 57.895 16.89 0.00 0.00 3.13
599 626 2.026990 CGTTCTGCGCGTATTTATTGC 58.973 47.619 8.43 0.00 0.00 3.56
622 649 1.300620 CGCGACAGTGGTTTGGAGA 60.301 57.895 0.00 0.00 0.00 3.71
646 673 1.522580 GGAGATCTGCTTCACGGCC 60.523 63.158 7.03 0.00 0.00 6.13
668 3340 7.603024 CGGCCTAGTAAATTATTAGCTTAGCTT 59.397 37.037 13.44 0.00 40.44 3.74
669 3341 9.939802 GGCCTAGTAAATTATTAGCTTAGCTTA 57.060 33.333 13.44 3.00 40.44 3.09
673 3345 8.535690 AGTAAATTATTAGCTTAGCTTAGCGG 57.464 34.615 18.29 0.00 45.82 5.52
674 3346 8.365647 AGTAAATTATTAGCTTAGCTTAGCGGA 58.634 33.333 18.29 11.59 45.82 5.54
675 3347 7.659652 AAATTATTAGCTTAGCTTAGCGGAG 57.340 36.000 18.29 1.97 45.82 4.63
676 3348 5.786264 TTATTAGCTTAGCTTAGCGGAGT 57.214 39.130 18.29 10.24 45.82 3.85
721 3393 1.810755 GTGTCTTTAAGCGAAAGGGGG 59.189 52.381 12.47 0.00 44.18 5.40
722 3394 1.700739 TGTCTTTAAGCGAAAGGGGGA 59.299 47.619 12.47 0.00 44.18 4.81
723 3395 2.082231 GTCTTTAAGCGAAAGGGGGAC 58.918 52.381 12.47 2.72 44.18 4.46
724 3396 1.084289 CTTTAAGCGAAAGGGGGACG 58.916 55.000 6.32 0.00 40.89 4.79
725 3397 0.321830 TTTAAGCGAAAGGGGGACGG 60.322 55.000 0.00 0.00 0.00 4.79
794 3466 3.777925 GCGTACGCAGTGGCAGTG 61.778 66.667 33.90 18.01 45.73 3.66
796 3468 2.357517 GTACGCAGTGGCAGTGCT 60.358 61.111 36.32 26.90 45.73 4.40
797 3469 1.080093 GTACGCAGTGGCAGTGCTA 60.080 57.895 36.32 26.03 45.73 3.49
798 3470 1.080093 TACGCAGTGGCAGTGCTAC 60.080 57.895 36.32 22.87 45.73 3.58
799 3471 1.811645 TACGCAGTGGCAGTGCTACA 61.812 55.000 36.32 22.23 45.73 2.74
800 3472 1.742880 CGCAGTGGCAGTGCTACAT 60.743 57.895 36.32 14.60 42.47 2.29
801 3473 1.798735 GCAGTGGCAGTGCTACATG 59.201 57.895 34.11 24.06 42.47 3.21
802 3474 0.957395 GCAGTGGCAGTGCTACATGT 60.957 55.000 34.11 10.03 42.47 3.21
803 3475 1.675714 GCAGTGGCAGTGCTACATGTA 60.676 52.381 34.11 5.25 42.47 2.29
804 3476 2.002586 CAGTGGCAGTGCTACATGTAC 58.997 52.381 30.17 5.43 42.47 2.90
805 3477 1.902508 AGTGGCAGTGCTACATGTACT 59.097 47.619 30.17 8.56 42.47 2.73
806 3478 2.093973 AGTGGCAGTGCTACATGTACTC 60.094 50.000 30.17 3.97 42.47 2.59
807 3479 2.093973 GTGGCAGTGCTACATGTACTCT 60.094 50.000 25.01 3.29 39.61 3.24
808 3480 3.130516 GTGGCAGTGCTACATGTACTCTA 59.869 47.826 25.01 0.00 39.61 2.43
809 3481 3.130516 TGGCAGTGCTACATGTACTCTAC 59.869 47.826 16.11 0.00 39.61 2.59
852 3524 1.153823 TAGCTTCTTCGTCGCTGGC 60.154 57.895 0.00 0.00 35.33 4.85
853 3525 1.595993 TAGCTTCTTCGTCGCTGGCT 61.596 55.000 0.00 0.00 35.33 4.75
854 3526 2.029844 GCTTCTTCGTCGCTGGCTT 61.030 57.895 0.00 0.00 0.00 4.35
855 3527 1.960994 GCTTCTTCGTCGCTGGCTTC 61.961 60.000 0.00 0.00 0.00 3.86
856 3528 0.667487 CTTCTTCGTCGCTGGCTTCA 60.667 55.000 0.00 0.00 0.00 3.02
857 3529 0.037326 TTCTTCGTCGCTGGCTTCAT 60.037 50.000 0.00 0.00 0.00 2.57
858 3530 0.815095 TCTTCGTCGCTGGCTTCATA 59.185 50.000 0.00 0.00 0.00 2.15
859 3531 1.203758 TCTTCGTCGCTGGCTTCATAA 59.796 47.619 0.00 0.00 0.00 1.90
864 3536 1.324736 GTCGCTGGCTTCATAACTTCG 59.675 52.381 0.00 0.00 0.00 3.79
921 3593 1.556373 TATGCCACTGTGAGCTGCCT 61.556 55.000 9.86 0.00 0.00 4.75
964 3646 2.668632 GGCCACCGTCCAAGATCA 59.331 61.111 0.00 0.00 0.00 2.92
972 3659 0.608130 CGTCCAAGATCACTGTGGGA 59.392 55.000 8.11 3.31 32.95 4.37
1194 3903 3.608662 TCGGTGTCCACGTCCACC 61.609 66.667 15.37 15.37 46.20 4.61
1233 3942 2.131067 CGCCTCCTCCTCCTTCCTC 61.131 68.421 0.00 0.00 0.00 3.71
1497 4218 0.323178 ACAAGCCCAGCATCCAAGAG 60.323 55.000 0.00 0.00 0.00 2.85
1506 4227 3.411517 ATCCAAGAGGGCCACGGG 61.412 66.667 6.18 7.38 36.21 5.28
1604 4325 1.370900 GCGTTGACAAAGCCAGCAG 60.371 57.895 14.32 0.00 0.00 4.24
1903 4624 4.143333 ACTTCCGGCGGTCGATGG 62.143 66.667 27.32 12.52 42.43 3.51
2157 4902 1.514657 GTGCCGCATCACGTACGTA 60.515 57.895 22.34 10.16 41.42 3.57
2158 4903 1.514657 TGCCGCATCACGTACGTAC 60.515 57.895 22.34 15.90 41.42 3.67
2168 4913 1.226379 CGTACGTACGTGGCCGATT 60.226 57.895 33.95 3.43 44.13 3.34
2170 4915 0.867329 GTACGTACGTGGCCGATTCC 60.867 60.000 30.25 3.59 37.88 3.01
2171 4916 1.031571 TACGTACGTGGCCGATTCCT 61.032 55.000 30.25 1.29 37.88 3.36
2172 4917 1.876714 CGTACGTGGCCGATTCCTG 60.877 63.158 7.22 0.00 37.88 3.86
2173 4918 2.171725 GTACGTGGCCGATTCCTGC 61.172 63.158 0.00 0.00 37.88 4.85
2174 4919 2.651105 TACGTGGCCGATTCCTGCA 61.651 57.895 0.00 0.00 37.88 4.41
2175 4920 2.173758 TACGTGGCCGATTCCTGCAA 62.174 55.000 0.00 0.00 37.88 4.08
2176 4921 2.114670 CGTGGCCGATTCCTGCAAT 61.115 57.895 0.00 0.00 35.63 3.56
2177 4922 1.434696 GTGGCCGATTCCTGCAATG 59.565 57.895 0.00 0.00 0.00 2.82
2178 4923 1.001020 TGGCCGATTCCTGCAATGT 60.001 52.632 0.00 0.00 0.00 2.71
2179 4924 0.254462 TGGCCGATTCCTGCAATGTA 59.746 50.000 0.00 0.00 0.00 2.29
2180 4925 0.947244 GGCCGATTCCTGCAATGTAG 59.053 55.000 0.00 0.00 0.00 2.74
2181 4926 1.668419 GCCGATTCCTGCAATGTAGT 58.332 50.000 0.00 0.00 0.00 2.73
2182 4927 2.484770 GGCCGATTCCTGCAATGTAGTA 60.485 50.000 0.00 0.00 0.00 1.82
2183 4928 2.544267 GCCGATTCCTGCAATGTAGTAC 59.456 50.000 0.00 0.00 0.00 2.73
2184 4929 2.794910 CCGATTCCTGCAATGTAGTACG 59.205 50.000 0.00 0.00 0.00 3.67
2185 4930 3.444916 CGATTCCTGCAATGTAGTACGT 58.555 45.455 0.00 0.00 0.00 3.57
2186 4931 4.498513 CCGATTCCTGCAATGTAGTACGTA 60.499 45.833 0.00 0.00 0.00 3.57
2187 4932 4.675565 CGATTCCTGCAATGTAGTACGTAG 59.324 45.833 0.00 0.00 0.00 3.51
2188 4933 3.431922 TCCTGCAATGTAGTACGTAGC 57.568 47.619 0.00 0.00 0.00 3.58
2189 4934 3.021695 TCCTGCAATGTAGTACGTAGCT 58.978 45.455 0.00 0.00 0.00 3.32
2190 4935 3.116300 CCTGCAATGTAGTACGTAGCTG 58.884 50.000 0.00 9.89 0.00 4.24
2191 4936 2.535984 CTGCAATGTAGTACGTAGCTGC 59.464 50.000 9.72 9.72 0.00 5.25
2192 4937 2.165641 TGCAATGTAGTACGTAGCTGCT 59.834 45.455 7.57 7.57 0.00 4.24
2193 4938 2.789893 GCAATGTAGTACGTAGCTGCTC 59.210 50.000 4.91 0.00 0.00 4.26
2194 4939 3.372954 CAATGTAGTACGTAGCTGCTCC 58.627 50.000 4.91 0.00 0.00 4.70
2195 4940 2.414994 TGTAGTACGTAGCTGCTCCT 57.585 50.000 4.91 0.00 0.00 3.69
2196 4941 2.014857 TGTAGTACGTAGCTGCTCCTG 58.985 52.381 4.91 0.00 0.00 3.86
2215 4960 3.944015 CCTGGTAGATTGCTTCCAAGAAG 59.056 47.826 0.00 0.00 40.52 2.85
2216 4961 4.323792 CCTGGTAGATTGCTTCCAAGAAGA 60.324 45.833 8.50 0.00 40.52 2.87
2217 4962 5.241403 TGGTAGATTGCTTCCAAGAAGAA 57.759 39.130 8.50 0.00 38.47 2.52
2218 4963 5.630121 TGGTAGATTGCTTCCAAGAAGAAA 58.370 37.500 8.50 4.40 38.47 2.52
2219 4964 6.248433 TGGTAGATTGCTTCCAAGAAGAAAT 58.752 36.000 9.81 9.81 38.47 2.17
2225 4975 2.094417 GCTTCCAAGAAGAAATCGTCGG 59.906 50.000 8.50 0.00 0.00 4.79
2256 5006 2.094762 AACACGAATCTACCTGGTGC 57.905 50.000 10.23 0.00 32.00 5.01
2260 5010 1.532238 GAATCTACCTGGTGCCCCC 59.468 63.158 10.23 0.00 0.00 5.40
2284 5040 3.713858 TCATCCAGCACACACTTTTTG 57.286 42.857 0.00 0.00 0.00 2.44
2300 5056 5.519927 CACTTTTTGGTTTGAATGTCCACTC 59.480 40.000 0.00 0.00 0.00 3.51
2303 5059 2.582052 TGGTTTGAATGTCCACTCACC 58.418 47.619 0.00 0.00 0.00 4.02
2304 5060 2.092158 TGGTTTGAATGTCCACTCACCA 60.092 45.455 0.00 0.00 0.00 4.17
2305 5061 2.293399 GGTTTGAATGTCCACTCACCAC 59.707 50.000 0.00 0.00 0.00 4.16
2306 5062 3.214328 GTTTGAATGTCCACTCACCACT 58.786 45.455 0.00 0.00 0.00 4.00
2307 5063 2.549064 TGAATGTCCACTCACCACTG 57.451 50.000 0.00 0.00 0.00 3.66
2308 5064 2.046292 TGAATGTCCACTCACCACTGA 58.954 47.619 0.00 0.00 0.00 3.41
2309 5065 2.224281 TGAATGTCCACTCACCACTGAC 60.224 50.000 0.00 0.00 0.00 3.51
2310 5066 1.423584 ATGTCCACTCACCACTGACA 58.576 50.000 0.00 0.00 39.95 3.58
2311 5067 0.464036 TGTCCACTCACCACTGACAC 59.536 55.000 0.00 0.00 31.45 3.67
2312 5068 0.464036 GTCCACTCACCACTGACACA 59.536 55.000 0.00 0.00 0.00 3.72
2313 5069 0.464036 TCCACTCACCACTGACACAC 59.536 55.000 0.00 0.00 0.00 3.82
2314 5070 0.177836 CCACTCACCACTGACACACA 59.822 55.000 0.00 0.00 0.00 3.72
2315 5071 1.290203 CACTCACCACTGACACACAC 58.710 55.000 0.00 0.00 0.00 3.82
2316 5072 1.134699 CACTCACCACTGACACACACT 60.135 52.381 0.00 0.00 0.00 3.55
2317 5073 1.555075 ACTCACCACTGACACACACTT 59.445 47.619 0.00 0.00 0.00 3.16
2357 5119 3.381949 GCTTTCTAGCATGGGTACGTAG 58.618 50.000 0.00 0.00 46.95 3.51
2392 5154 2.916502 TTTGCGACACGTCTGGCACT 62.917 55.000 0.00 0.00 34.72 4.40
2393 5155 3.406361 GCGACACGTCTGGCACTG 61.406 66.667 0.00 0.00 0.00 3.66
2394 5156 2.734723 CGACACGTCTGGCACTGG 60.735 66.667 0.00 0.00 0.00 4.00
2395 5157 2.421739 GACACGTCTGGCACTGGT 59.578 61.111 0.00 0.00 0.00 4.00
2396 5158 1.663739 GACACGTCTGGCACTGGTA 59.336 57.895 0.00 0.00 0.00 3.25
2397 5159 0.388649 GACACGTCTGGCACTGGTAG 60.389 60.000 0.00 0.00 0.00 3.18
2398 5160 1.079819 CACGTCTGGCACTGGTAGG 60.080 63.158 0.00 0.00 0.00 3.18
2399 5161 2.283529 ACGTCTGGCACTGGTAGGG 61.284 63.158 0.00 0.00 0.00 3.53
2400 5162 1.982395 CGTCTGGCACTGGTAGGGA 60.982 63.158 0.00 0.00 0.00 4.20
2401 5163 1.901085 GTCTGGCACTGGTAGGGAG 59.099 63.158 0.00 0.00 0.00 4.30
2526 5289 2.082629 AAACAGGCGGAAAAAGGGCG 62.083 55.000 0.00 0.00 0.00 6.13
2582 5377 2.895372 GTGCGCGGAGTTATGGGG 60.895 66.667 8.83 0.00 0.00 4.96
2659 5459 3.539107 GCGGACGTTAACGCGAGG 61.539 66.667 27.07 14.86 46.58 4.63
2687 5487 1.865788 CTGATGGTGCCCAAACACGG 61.866 60.000 0.00 0.00 41.65 4.94
2728 5528 0.181114 TCTCCATCCGGAAATGCCAG 59.819 55.000 9.01 2.04 42.21 4.85
2741 5543 2.403252 ATGCCAGGACTTTAACTCCG 57.597 50.000 0.00 0.00 32.45 4.63
2750 5552 1.004679 TTTAACTCCGTCCACCGCC 60.005 57.895 0.00 0.00 34.38 6.13
2752 5554 2.162338 TTAACTCCGTCCACCGCCAG 62.162 60.000 0.00 0.00 34.38 4.85
2784 5586 1.657822 GCTCCTCGGAGGAATTTCAC 58.342 55.000 25.95 9.10 45.28 3.18
2813 5615 3.289062 TCGTTGACGGCCTGACGA 61.289 61.111 13.37 13.37 41.62 4.20
2818 5620 2.102553 GACGGCCTGACGAGTAGC 59.897 66.667 0.00 0.00 37.61 3.58
2819 5621 2.361357 ACGGCCTGACGAGTAGCT 60.361 61.111 0.00 0.00 37.61 3.32
2838 5747 2.290093 GCTAAATGCTGAAGCTAGCCAG 59.710 50.000 12.13 13.63 43.02 4.85
2841 5750 2.894387 GCTGAAGCTAGCCAGGCG 60.894 66.667 18.87 0.00 37.73 5.52
2848 5757 2.963854 CTAGCCAGGCGCACGATG 60.964 66.667 10.83 1.50 41.38 3.84
2873 5782 4.363034 GGCTAGCACCGCCTTATC 57.637 61.111 18.24 0.00 44.17 1.75
2904 5813 1.068541 GGGACGAATGGTTCTTGTTGC 60.069 52.381 0.00 0.00 0.00 4.17
2963 5876 3.883744 AAGCTCGTCCAACTGGCGG 62.884 63.158 11.04 0.00 36.10 6.13
2964 5877 4.373116 GCTCGTCCAACTGGCGGA 62.373 66.667 0.00 0.00 36.10 5.54
2970 5883 4.308458 CCAACTGGCGGACACGGA 62.308 66.667 0.00 0.00 41.36 4.69
2971 5884 2.280524 CAACTGGCGGACACGGAA 60.281 61.111 0.00 0.00 41.36 4.30
2972 5885 1.671054 CAACTGGCGGACACGGAAT 60.671 57.895 0.00 0.00 41.36 3.01
2973 5886 1.375523 AACTGGCGGACACGGAATC 60.376 57.895 0.00 0.00 41.36 2.52
2974 5887 2.885644 CTGGCGGACACGGAATCG 60.886 66.667 0.00 0.00 41.36 3.34
2975 5888 3.350909 CTGGCGGACACGGAATCGA 62.351 63.158 0.00 0.00 41.36 3.59
2982 5895 3.043876 CGGACACGGAATCGAAAGAGAG 61.044 54.545 0.00 0.00 39.30 3.20
3016 5933 1.384191 GTCCATCCAGTTTGGGCCT 59.616 57.895 4.53 0.00 38.32 5.19
3031 5948 0.108019 GGCCTTCCCCCGTGTATAAG 59.892 60.000 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.539142 CGCTGTAGTAGGTTCTGTAGCG 60.539 54.545 0.00 0.00 41.05 4.26
22 23 5.405571 TCTTATCTTAATCAAAGCCGATCGC 59.594 40.000 10.32 5.46 34.97 4.58
38 39 5.196695 GCCAAGGAGGTGATTTCTTATCTT 58.803 41.667 0.00 0.00 40.61 2.40
91 92 0.597637 CCCATCGACCGAATCTTCCG 60.598 60.000 0.00 0.00 0.00 4.30
252 253 1.228644 TTCCTTCGGACTCGGGTCA 60.229 57.895 18.98 0.00 43.77 4.02
253 254 1.214853 GTTCCTTCGGACTCGGGTC 59.785 63.158 6.97 6.97 41.43 4.46
254 255 1.117142 TTGTTCCTTCGGACTCGGGT 61.117 55.000 0.00 0.00 36.95 5.28
255 256 0.249398 ATTGTTCCTTCGGACTCGGG 59.751 55.000 0.00 0.00 36.95 5.14
256 257 1.641577 GATTGTTCCTTCGGACTCGG 58.358 55.000 0.00 0.00 36.95 4.63
257 258 1.269166 CGATTGTTCCTTCGGACTCG 58.731 55.000 0.00 0.00 37.82 4.18
316 317 4.828296 CCCTGCCATGGGTCTGCC 62.828 72.222 15.13 0.00 42.25 4.85
377 378 0.721154 CGCATGTGCAGTCGTACATT 59.279 50.000 5.77 0.00 44.98 2.71
397 399 0.179067 ACGTGTTATGTATGCCCCCG 60.179 55.000 0.00 0.00 0.00 5.73
415 417 1.457643 GGGGTAGGGGTACGGGTAC 60.458 68.421 0.30 0.30 35.40 3.34
416 418 0.329039 TAGGGGTAGGGGTACGGGTA 60.329 60.000 0.00 0.00 0.00 3.69
417 419 1.625565 TAGGGGTAGGGGTACGGGT 60.626 63.158 0.00 0.00 0.00 5.28
418 420 1.152461 GTAGGGGTAGGGGTACGGG 60.152 68.421 0.00 0.00 0.00 5.28
419 421 1.529244 CGTAGGGGTAGGGGTACGG 60.529 68.421 0.00 0.00 35.68 4.02
444 446 1.468565 GGCGCTGTCGTGTACTCATTA 60.469 52.381 7.64 0.00 38.14 1.90
471 474 1.628846 ACCACTCCCACAGAATACACC 59.371 52.381 0.00 0.00 0.00 4.16
473 476 2.304761 GGAACCACTCCCACAGAATACA 59.695 50.000 0.00 0.00 38.44 2.29
489 503 0.535335 TGGACAGATACAGCGGAACC 59.465 55.000 0.00 0.00 0.00 3.62
494 508 1.854743 CGATGTTGGACAGATACAGCG 59.145 52.381 0.00 0.00 43.69 5.18
495 509 1.594862 GCGATGTTGGACAGATACAGC 59.405 52.381 0.00 0.00 0.00 4.40
507 521 3.864686 CCCTTCGCGGCGATGTTG 61.865 66.667 26.95 16.47 35.23 3.33
543 557 4.051922 CCATTGTAGCTCGTCCTCATTAC 58.948 47.826 0.00 0.00 0.00 1.89
554 568 0.811616 CTGACCGGCCATTGTAGCTC 60.812 60.000 0.00 0.00 0.00 4.09
599 626 1.660575 AAACCACTGTCGCGACGAG 60.661 57.895 31.88 28.69 36.23 4.18
622 649 2.158986 CGTGAAGCAGATCTCCTCCAAT 60.159 50.000 0.00 0.00 0.00 3.16
672 3344 2.036089 GGTCAGTTGGATCGGATACTCC 59.964 54.545 1.22 0.00 0.00 3.85
673 3345 2.693591 TGGTCAGTTGGATCGGATACTC 59.306 50.000 1.22 0.00 0.00 2.59
674 3346 2.747177 TGGTCAGTTGGATCGGATACT 58.253 47.619 1.22 0.00 0.00 2.12
675 3347 3.069586 TGATGGTCAGTTGGATCGGATAC 59.930 47.826 0.00 0.00 0.00 2.24
676 3348 3.304829 TGATGGTCAGTTGGATCGGATA 58.695 45.455 0.00 0.00 0.00 2.59
698 3370 2.157085 CCCTTTCGCTTAAAGACACGAC 59.843 50.000 9.33 0.00 46.44 4.34
724 3396 4.867599 GATCCGCACCGTCCGTCC 62.868 72.222 0.00 0.00 0.00 4.79
788 3460 2.969628 AGAGTACATGTAGCACTGCC 57.030 50.000 5.62 0.00 0.00 4.85
790 3462 6.679327 TGTAGTAGAGTACATGTAGCACTG 57.321 41.667 5.62 0.00 0.00 3.66
799 3471 3.303857 GCGTCGCATGTAGTAGAGTACAT 60.304 47.826 13.44 4.48 43.13 2.29
800 3472 2.031314 GCGTCGCATGTAGTAGAGTACA 59.969 50.000 13.44 0.00 37.32 2.90
801 3473 2.031314 TGCGTCGCATGTAGTAGAGTAC 59.969 50.000 17.58 0.00 31.71 2.73
802 3474 2.282407 TGCGTCGCATGTAGTAGAGTA 58.718 47.619 17.58 0.00 31.71 2.59
803 3475 1.064208 CTGCGTCGCATGTAGTAGAGT 59.936 52.381 22.03 0.00 38.13 3.24
804 3476 1.747956 CTGCGTCGCATGTAGTAGAG 58.252 55.000 22.03 1.25 38.13 2.43
805 3477 0.248498 GCTGCGTCGCATGTAGTAGA 60.248 55.000 22.03 0.00 38.13 2.59
806 3478 0.248661 AGCTGCGTCGCATGTAGTAG 60.249 55.000 22.03 8.23 38.13 2.57
807 3479 0.525455 CAGCTGCGTCGCATGTAGTA 60.525 55.000 22.03 0.00 38.13 1.82
808 3480 1.807165 CAGCTGCGTCGCATGTAGT 60.807 57.895 22.03 0.62 38.13 2.73
809 3481 1.477826 CTCAGCTGCGTCGCATGTAG 61.478 60.000 22.03 10.20 38.13 2.74
852 3524 4.110482 CCCCGAGTTACGAAGTTATGAAG 58.890 47.826 0.00 0.00 37.78 3.02
853 3525 3.119029 CCCCCGAGTTACGAAGTTATGAA 60.119 47.826 0.00 0.00 37.78 2.57
854 3526 2.428171 CCCCCGAGTTACGAAGTTATGA 59.572 50.000 0.00 0.00 37.78 2.15
855 3527 2.167075 ACCCCCGAGTTACGAAGTTATG 59.833 50.000 0.00 0.00 37.78 1.90
856 3528 2.428530 GACCCCCGAGTTACGAAGTTAT 59.571 50.000 0.00 0.00 37.78 1.89
857 3529 1.818674 GACCCCCGAGTTACGAAGTTA 59.181 52.381 0.00 0.00 37.78 2.24
858 3530 0.605083 GACCCCCGAGTTACGAAGTT 59.395 55.000 0.00 0.00 37.78 2.66
859 3531 1.589716 CGACCCCCGAGTTACGAAGT 61.590 60.000 0.00 0.00 45.77 3.01
864 3536 2.362889 TCCCGACCCCCGAGTTAC 60.363 66.667 0.00 0.00 41.76 2.50
926 3598 0.737715 GCCGGCCTTATATCGCAGAG 60.738 60.000 18.11 0.00 43.63 3.35
964 3646 2.345244 CTCGCAGCTTCCCACAGT 59.655 61.111 0.00 0.00 0.00 3.55
972 3659 4.379243 CCCGGTCACTCGCAGCTT 62.379 66.667 0.00 0.00 0.00 3.74
1258 3979 2.089349 GCTTGCACTCGACCTCGTC 61.089 63.158 0.00 0.00 40.80 4.20
1259 3980 2.049063 GCTTGCACTCGACCTCGT 60.049 61.111 0.00 0.00 40.80 4.18
1260 3981 3.175240 CGCTTGCACTCGACCTCG 61.175 66.667 0.84 0.00 41.45 4.63
1261 3982 2.811317 CCGCTTGCACTCGACCTC 60.811 66.667 8.21 0.00 0.00 3.85
1383 4104 4.681978 GGCGGTGGCGAGAAGTGT 62.682 66.667 0.00 0.00 41.24 3.55
1497 4218 4.097361 GAGAAGTCCCCGTGGCCC 62.097 72.222 0.00 0.00 0.00 5.80
1545 4266 2.668550 GTTGGGACCTGCACGGAC 60.669 66.667 8.91 3.23 36.31 4.79
1549 4270 3.357079 CTGCGTTGGGACCTGCAC 61.357 66.667 0.00 0.00 33.12 4.57
1686 4407 0.830648 TATTGTCCTCCTCGGCCTTG 59.169 55.000 0.00 0.00 0.00 3.61
1690 4411 4.695928 GGATTTATTATTGTCCTCCTCGGC 59.304 45.833 0.00 0.00 0.00 5.54
1707 4428 5.547465 TCGTCTTCTTTGCTCTTGGATTTA 58.453 37.500 0.00 0.00 0.00 1.40
1708 4429 4.389374 TCGTCTTCTTTGCTCTTGGATTT 58.611 39.130 0.00 0.00 0.00 2.17
1709 4430 3.999663 CTCGTCTTCTTTGCTCTTGGATT 59.000 43.478 0.00 0.00 0.00 3.01
1795 4516 4.700365 GAAGCCGTTGCCGTTGCC 62.700 66.667 0.00 0.00 38.69 4.52
1903 4624 3.999229 GTTCTCCACGATCATGTTCAC 57.001 47.619 4.71 0.00 0.00 3.18
2142 4887 3.580498 CGTACGTACGTGATGCGG 58.420 61.111 33.95 9.02 46.52 5.69
2157 4902 2.819984 ATTGCAGGAATCGGCCACGT 62.820 55.000 2.24 0.00 41.85 4.49
2158 4903 2.114670 ATTGCAGGAATCGGCCACG 61.115 57.895 2.24 0.00 42.74 4.94
2159 4904 1.315257 ACATTGCAGGAATCGGCCAC 61.315 55.000 2.24 0.00 33.09 5.01
2160 4905 0.254462 TACATTGCAGGAATCGGCCA 59.746 50.000 2.24 0.00 33.09 5.36
2162 4907 1.668419 ACTACATTGCAGGAATCGGC 58.332 50.000 0.00 0.00 34.65 5.54
2163 4908 2.794910 CGTACTACATTGCAGGAATCGG 59.205 50.000 0.00 0.00 0.00 4.18
2164 4909 3.444916 ACGTACTACATTGCAGGAATCG 58.555 45.455 0.00 0.00 0.00 3.34
2165 4910 4.444720 GCTACGTACTACATTGCAGGAATC 59.555 45.833 0.00 0.00 0.00 2.52
2166 4911 4.099573 AGCTACGTACTACATTGCAGGAAT 59.900 41.667 0.00 0.00 0.00 3.01
2168 4913 3.021695 AGCTACGTACTACATTGCAGGA 58.978 45.455 0.00 0.00 0.00 3.86
2170 4915 2.535984 GCAGCTACGTACTACATTGCAG 59.464 50.000 0.00 0.00 0.00 4.41
2171 4916 2.165641 AGCAGCTACGTACTACATTGCA 59.834 45.455 0.00 0.00 33.00 4.08
2172 4917 2.789893 GAGCAGCTACGTACTACATTGC 59.210 50.000 0.00 0.00 0.00 3.56
2173 4918 3.066900 AGGAGCAGCTACGTACTACATTG 59.933 47.826 0.00 0.00 0.00 2.82
2174 4919 3.066900 CAGGAGCAGCTACGTACTACATT 59.933 47.826 0.00 0.00 0.00 2.71
2175 4920 2.619177 CAGGAGCAGCTACGTACTACAT 59.381 50.000 0.00 0.00 0.00 2.29
2176 4921 2.014857 CAGGAGCAGCTACGTACTACA 58.985 52.381 0.00 0.00 0.00 2.74
2177 4922 1.334243 CCAGGAGCAGCTACGTACTAC 59.666 57.143 0.00 0.00 0.00 2.73
2178 4923 1.064906 ACCAGGAGCAGCTACGTACTA 60.065 52.381 0.00 0.00 0.00 1.82
2179 4924 0.323542 ACCAGGAGCAGCTACGTACT 60.324 55.000 0.00 0.00 0.00 2.73
2180 4925 1.334243 CTACCAGGAGCAGCTACGTAC 59.666 57.143 0.00 0.00 0.00 3.67
2181 4926 1.211212 TCTACCAGGAGCAGCTACGTA 59.789 52.381 0.00 0.00 0.00 3.57
2182 4927 0.034380 TCTACCAGGAGCAGCTACGT 60.034 55.000 0.00 0.00 0.00 3.57
2183 4928 1.323412 ATCTACCAGGAGCAGCTACG 58.677 55.000 0.00 0.00 0.00 3.51
2184 4929 2.804933 GCAATCTACCAGGAGCAGCTAC 60.805 54.545 0.00 0.00 0.00 3.58
2185 4930 1.414181 GCAATCTACCAGGAGCAGCTA 59.586 52.381 0.00 0.00 0.00 3.32
2186 4931 0.179936 GCAATCTACCAGGAGCAGCT 59.820 55.000 0.00 0.00 0.00 4.24
2187 4932 0.179936 AGCAATCTACCAGGAGCAGC 59.820 55.000 0.00 0.00 0.00 5.25
2188 4933 2.559440 GAAGCAATCTACCAGGAGCAG 58.441 52.381 0.00 0.00 0.00 4.24
2189 4934 1.210478 GGAAGCAATCTACCAGGAGCA 59.790 52.381 0.00 0.00 0.00 4.26
2190 4935 1.210478 TGGAAGCAATCTACCAGGAGC 59.790 52.381 0.00 0.00 0.00 4.70
2191 4936 3.198635 TCTTGGAAGCAATCTACCAGGAG 59.801 47.826 0.00 0.00 34.49 3.69
2192 4937 3.181329 TCTTGGAAGCAATCTACCAGGA 58.819 45.455 0.00 0.00 36.45 3.86
2193 4938 3.634397 TCTTGGAAGCAATCTACCAGG 57.366 47.619 0.00 0.00 33.85 4.45
2194 4939 4.836825 TCTTCTTGGAAGCAATCTACCAG 58.163 43.478 2.74 0.00 33.85 4.00
2195 4940 4.908601 TCTTCTTGGAAGCAATCTACCA 57.091 40.909 2.74 0.00 0.00 3.25
2196 4941 6.457528 CGATTTCTTCTTGGAAGCAATCTACC 60.458 42.308 20.86 5.62 0.00 3.18
2215 4960 1.139095 AGCCGAGACCGACGATTTC 59.861 57.895 0.00 0.00 38.22 2.17
2216 4961 1.153823 CAGCCGAGACCGACGATTT 60.154 57.895 0.00 0.00 38.22 2.17
2217 4962 1.384989 ATCAGCCGAGACCGACGATT 61.385 55.000 0.00 0.00 38.22 3.34
2218 4963 0.534427 TATCAGCCGAGACCGACGAT 60.534 55.000 0.00 0.00 38.22 3.73
2219 4964 0.745486 TTATCAGCCGAGACCGACGA 60.745 55.000 0.00 0.00 38.22 4.20
2225 4975 2.273370 TTCGTGTTATCAGCCGAGAC 57.727 50.000 0.00 0.00 0.00 3.36
2256 5006 1.379044 GTGCTGGATGAACAGGGGG 60.379 63.158 0.00 0.00 38.90 5.40
2260 5010 1.888215 AGTGTGTGCTGGATGAACAG 58.112 50.000 0.00 0.00 34.24 3.16
2284 5040 2.293399 GTGGTGAGTGGACATTCAAACC 59.707 50.000 0.00 0.00 0.00 3.27
2300 5056 1.737838 ACAAGTGTGTGTCAGTGGTG 58.262 50.000 0.00 0.00 36.31 4.17
2303 5059 2.607635 GTGGTACAAGTGTGTGTCAGTG 59.392 50.000 0.00 0.00 44.16 3.66
2304 5060 2.419574 GGTGGTACAAGTGTGTGTCAGT 60.420 50.000 0.00 0.00 44.16 3.41
2305 5061 2.210116 GGTGGTACAAGTGTGTGTCAG 58.790 52.381 0.00 0.00 44.16 3.51
2306 5062 1.555533 TGGTGGTACAAGTGTGTGTCA 59.444 47.619 0.00 0.00 44.16 3.58
2307 5063 1.937899 GTGGTGGTACAAGTGTGTGTC 59.062 52.381 0.00 0.00 44.16 3.67
2308 5064 1.407712 GGTGGTGGTACAAGTGTGTGT 60.408 52.381 0.00 0.00 44.16 3.72
2309 5065 1.305201 GGTGGTGGTACAAGTGTGTG 58.695 55.000 0.00 0.00 44.16 3.82
2310 5066 0.913205 TGGTGGTGGTACAAGTGTGT 59.087 50.000 0.00 0.00 44.16 3.72
2311 5067 1.134220 AGTGGTGGTGGTACAAGTGTG 60.134 52.381 0.00 0.00 44.16 3.82
2312 5068 1.209621 AGTGGTGGTGGTACAAGTGT 58.790 50.000 0.00 0.00 44.16 3.55
2313 5069 2.341846 AAGTGGTGGTGGTACAAGTG 57.658 50.000 0.00 0.00 44.16 3.16
2314 5070 2.422377 GGAAAGTGGTGGTGGTACAAGT 60.422 50.000 0.00 0.00 44.16 3.16
2315 5071 2.227194 GGAAAGTGGTGGTGGTACAAG 58.773 52.381 0.00 0.00 44.16 3.16
2316 5072 1.475392 CGGAAAGTGGTGGTGGTACAA 60.475 52.381 0.00 0.00 44.16 2.41
2317 5073 0.107081 CGGAAAGTGGTGGTGGTACA 59.893 55.000 0.00 0.00 0.00 2.90
2398 5160 3.020237 GCTCTCACGGGGTTCCTCC 62.020 68.421 0.00 0.00 0.00 4.30
2399 5161 1.985116 AGCTCTCACGGGGTTCCTC 60.985 63.158 0.00 0.00 0.00 3.71
2400 5162 2.120718 AGCTCTCACGGGGTTCCT 59.879 61.111 0.00 0.00 0.00 3.36
2401 5163 1.827399 TTCAGCTCTCACGGGGTTCC 61.827 60.000 0.00 0.00 0.00 3.62
2435 5198 1.139095 CCTAGAACGTCTCGTGGCC 59.861 63.158 0.00 0.00 39.99 5.36
2582 5377 3.966543 CCACCACCTCCACCACCC 61.967 72.222 0.00 0.00 0.00 4.61
2585 5385 3.174987 CACCCACCACCTCCACCA 61.175 66.667 0.00 0.00 0.00 4.17
2659 5459 2.048603 GCACCATCAGCAGGTTCCC 61.049 63.158 0.00 0.00 37.23 3.97
2687 5487 0.099436 GAGGTTGCGCATTGATGTCC 59.901 55.000 12.75 5.67 0.00 4.02
2689 5489 1.538047 AAGAGGTTGCGCATTGATGT 58.462 45.000 12.75 0.00 0.00 3.06
2818 5620 2.877168 CCTGGCTAGCTTCAGCATTTAG 59.123 50.000 15.72 3.37 43.67 1.85
2819 5621 2.923121 CCTGGCTAGCTTCAGCATTTA 58.077 47.619 15.72 0.00 43.67 1.40
2827 5736 3.198489 GTGCGCCTGGCTAGCTTC 61.198 66.667 17.92 7.66 44.05 3.86
2841 5750 4.564116 GCCAGCCATGCATCGTGC 62.564 66.667 0.00 0.00 45.29 5.34
2863 5772 2.027745 CCATGCAGATAGATAAGGCGGT 60.028 50.000 0.00 0.00 0.00 5.68
2865 5774 2.625737 CCCATGCAGATAGATAAGGCG 58.374 52.381 0.00 0.00 0.00 5.52
2870 5779 3.169512 TCGTCCCCATGCAGATAGATA 57.830 47.619 0.00 0.00 0.00 1.98
2871 5780 2.015456 TCGTCCCCATGCAGATAGAT 57.985 50.000 0.00 0.00 0.00 1.98
2872 5781 1.788229 TTCGTCCCCATGCAGATAGA 58.212 50.000 0.00 0.00 0.00 1.98
2873 5782 2.420642 CATTCGTCCCCATGCAGATAG 58.579 52.381 0.00 0.00 0.00 2.08
2904 5813 2.618053 GACCACTCCCACGTGATAAAG 58.382 52.381 19.30 10.68 37.06 1.85
2963 5876 2.163815 TCCTCTCTTTCGATTCCGTGTC 59.836 50.000 0.00 0.00 37.05 3.67
2964 5877 2.164624 CTCCTCTCTTTCGATTCCGTGT 59.835 50.000 0.00 0.00 37.05 4.49
2966 5879 2.424246 GTCTCCTCTCTTTCGATTCCGT 59.576 50.000 0.00 0.00 37.05 4.69
2967 5880 2.539953 CGTCTCCTCTCTTTCGATTCCG 60.540 54.545 0.00 0.00 37.07 4.30
2968 5881 2.683867 TCGTCTCCTCTCTTTCGATTCC 59.316 50.000 0.00 0.00 0.00 3.01
2970 5883 3.082548 TGTCGTCTCCTCTCTTTCGATT 58.917 45.455 0.00 0.00 0.00 3.34
2971 5884 2.712709 TGTCGTCTCCTCTCTTTCGAT 58.287 47.619 0.00 0.00 0.00 3.59
2972 5885 2.180432 TGTCGTCTCCTCTCTTTCGA 57.820 50.000 0.00 0.00 0.00 3.71
2973 5886 2.586900 GTTGTCGTCTCCTCTCTTTCG 58.413 52.381 0.00 0.00 0.00 3.46
2974 5887 2.586900 CGTTGTCGTCTCCTCTCTTTC 58.413 52.381 0.00 0.00 0.00 2.62
2975 5888 1.336056 GCGTTGTCGTCTCCTCTCTTT 60.336 52.381 0.00 0.00 39.49 2.52
2982 5895 4.353437 ACCGGCGTTGTCGTCTCC 62.353 66.667 6.01 0.00 39.73 3.71
3016 5933 0.620990 TGGCCTTATACACGGGGGAA 60.621 55.000 3.32 0.00 0.00 3.97
3093 6016 3.018840 GAAAAGCGTACGGGGCGTG 62.019 63.158 18.39 0.00 41.39 5.34
3096 6019 1.079336 AGAGAAAAGCGTACGGGGC 60.079 57.895 18.39 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.