Multiple sequence alignment - TraesCS2A01G535500

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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 TraesCS2A01G535500 chr2A 100.000 2386 0 0 1 2386 750329667 750332052 0.000000e+00 4407
1 TraesCS2A01G535500 chr2A 91.280 883 39 3 1 866 4645029 4644168 0.000000e+00 1170
2 TraesCS2A01G535500 chr2A 85.970 670 83 6 1537 2201 750190736 750190073 0.000000e+00 706
3 TraesCS2A01G535500 chr2A 90.341 176 14 3 2212 2386 750423409 750423582 6.630000e-56 228
4 TraesCS2A01G535500 chr2B 88.062 1424 121 13 872 2286 757536232 757537615 0.000000e+00 1642
5 TraesCS2A01G535500 chr2B 84.172 1352 165 24 872 2196 757230951 757232280 0.000000e+00 1266
6 TraesCS2A01G535500 chr2B 91.564 889 52 7 1 866 77816522 77815634 0.000000e+00 1205
7 TraesCS2A01G535500 chr2B 90.572 891 57 10 1 866 77860566 77859678 0.000000e+00 1155
8 TraesCS2A01G535500 chr2B 84.175 733 79 16 1473 2196 757390576 757391280 0.000000e+00 676
9 TraesCS2A01G535500 chr2B 82.192 730 91 23 1422 2134 757451215 757451922 2.040000e-165 592
10 TraesCS2A01G535500 chr2B 82.724 301 45 4 875 1173 757279253 757279548 6.540000e-66 261
11 TraesCS2A01G535500 chr1D 86.642 1340 147 18 872 2201 77452626 77451309 0.000000e+00 1454
12 TraesCS2A01G535500 chr1B 86.269 1340 153 17 872 2200 121014235 121012916 0.000000e+00 1426
13 TraesCS2A01G535500 chr1B 90.333 900 63 8 1 876 589496985 589496086 0.000000e+00 1158
14 TraesCS2A01G535500 chr1A 86.991 1253 136 16 872 2117 108780418 108779186 0.000000e+00 1386
15 TraesCS2A01G535500 chr1A 90.827 883 44 7 1 866 495322448 495321586 0.000000e+00 1147
16 TraesCS2A01G535500 chr7A 85.650 1338 150 18 875 2201 477184665 477183359 0.000000e+00 1369
17 TraesCS2A01G535500 chr7A 91.723 882 52 7 2 866 79633314 79634191 0.000000e+00 1205
18 TraesCS2A01G535500 chr7A 90.476 882 43 8 2 866 648738113 648738970 0.000000e+00 1125
19 TraesCS2A01G535500 chr7A 93.449 748 49 0 122 869 603933518 603932771 0.000000e+00 1110
20 TraesCS2A01G535500 chr6A 93.115 886 44 1 1 869 109140491 109139606 0.000000e+00 1282
21 TraesCS2A01G535500 chr5A 92.463 889 43 8 1 870 585087021 585087904 0.000000e+00 1249
22 TraesCS2A01G535500 chr5A 91.676 889 56 7 1 871 476452913 476453801 0.000000e+00 1216
23 TraesCS2A01G535500 chr3A 91.986 886 54 1 1 869 81654490 81653605 0.000000e+00 1227
24 TraesCS2A01G535500 chr3A 90.993 866 57 2 1 866 696704768 696703924 0.000000e+00 1147
25 TraesCS2A01G535500 chrUn 91.451 889 53 7 1 866 245560265 245559377 0.000000e+00 1199
26 TraesCS2A01G535500 chrUn 91.451 889 53 7 1 866 272850398 272849510 0.000000e+00 1199
27 TraesCS2A01G535500 chr2D 88.556 734 64 9 966 1688 619311041 619311765 0.000000e+00 872
28 TraesCS2A01G535500 chr2D 83.307 641 80 9 1357 1990 619262304 619262924 1.240000e-157 566
29 TraesCS2A01G535500 chr7B 88.478 703 38 19 205 866 145519827 145519127 0.000000e+00 809
30 TraesCS2A01G535500 chr7D 84.470 264 31 2 1221 1484 498242823 498243076 3.940000e-63 252


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 TraesCS2A01G535500 chr2A 750329667 750332052 2385 False 4407 4407 100.000 1 2386 1 chr2A.!!$F1 2385
1 TraesCS2A01G535500 chr2A 4644168 4645029 861 True 1170 1170 91.280 1 866 1 chr2A.!!$R1 865
2 TraesCS2A01G535500 chr2A 750190073 750190736 663 True 706 706 85.970 1537 2201 1 chr2A.!!$R2 664
3 TraesCS2A01G535500 chr2B 757536232 757537615 1383 False 1642 1642 88.062 872 2286 1 chr2B.!!$F5 1414
4 TraesCS2A01G535500 chr2B 757230951 757232280 1329 False 1266 1266 84.172 872 2196 1 chr2B.!!$F1 1324
5 TraesCS2A01G535500 chr2B 77815634 77816522 888 True 1205 1205 91.564 1 866 1 chr2B.!!$R1 865
6 TraesCS2A01G535500 chr2B 77859678 77860566 888 True 1155 1155 90.572 1 866 1 chr2B.!!$R2 865
7 TraesCS2A01G535500 chr2B 757390576 757391280 704 False 676 676 84.175 1473 2196 1 chr2B.!!$F3 723
8 TraesCS2A01G535500 chr2B 757451215 757451922 707 False 592 592 82.192 1422 2134 1 chr2B.!!$F4 712
9 TraesCS2A01G535500 chr1D 77451309 77452626 1317 True 1454 1454 86.642 872 2201 1 chr1D.!!$R1 1329
10 TraesCS2A01G535500 chr1B 121012916 121014235 1319 True 1426 1426 86.269 872 2200 1 chr1B.!!$R1 1328
11 TraesCS2A01G535500 chr1B 589496086 589496985 899 True 1158 1158 90.333 1 876 1 chr1B.!!$R2 875
12 TraesCS2A01G535500 chr1A 108779186 108780418 1232 True 1386 1386 86.991 872 2117 1 chr1A.!!$R1 1245
13 TraesCS2A01G535500 chr1A 495321586 495322448 862 True 1147 1147 90.827 1 866 1 chr1A.!!$R2 865
14 TraesCS2A01G535500 chr7A 477183359 477184665 1306 True 1369 1369 85.650 875 2201 1 chr7A.!!$R1 1326
15 TraesCS2A01G535500 chr7A 79633314 79634191 877 False 1205 1205 91.723 2 866 1 chr7A.!!$F1 864
16 TraesCS2A01G535500 chr7A 648738113 648738970 857 False 1125 1125 90.476 2 866 1 chr7A.!!$F2 864
17 TraesCS2A01G535500 chr7A 603932771 603933518 747 True 1110 1110 93.449 122 869 1 chr7A.!!$R2 747
18 TraesCS2A01G535500 chr6A 109139606 109140491 885 True 1282 1282 93.115 1 869 1 chr6A.!!$R1 868
19 TraesCS2A01G535500 chr5A 585087021 585087904 883 False 1249 1249 92.463 1 870 1 chr5A.!!$F2 869
20 TraesCS2A01G535500 chr5A 476452913 476453801 888 False 1216 1216 91.676 1 871 1 chr5A.!!$F1 870
21 TraesCS2A01G535500 chr3A 81653605 81654490 885 True 1227 1227 91.986 1 869 1 chr3A.!!$R1 868
22 TraesCS2A01G535500 chr3A 696703924 696704768 844 True 1147 1147 90.993 1 866 1 chr3A.!!$R2 865
23 TraesCS2A01G535500 chrUn 245559377 245560265 888 True 1199 1199 91.451 1 866 1 chrUn.!!$R1 865
24 TraesCS2A01G535500 chrUn 272849510 272850398 888 True 1199 1199 91.451 1 866 1 chrUn.!!$R2 865
25 TraesCS2A01G535500 chr2D 619311041 619311765 724 False 872 872 88.556 966 1688 1 chr2D.!!$F2 722
26 TraesCS2A01G535500 chr2D 619262304 619262924 620 False 566 566 83.307 1357 1990 1 chr2D.!!$F1 633
27 TraesCS2A01G535500 chr7B 145519127 145519827 700 True 809 809 88.478 205 866 1 chr7B.!!$R1 661

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
895 964 0.670546 GTTGCTCGTTGGCTCAGCTA 60.671 55.0 0.0 0.0 34.03 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2294 2423 0.101759 CTGAGCCCATTGCCGAATTG 59.898 55.0 0.0 0.0 42.71 2.32 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
91 92 2.159043 AGGTTGAGAGCCATATGTCGTG 60.159 50.000 1.24 0.00 0.00 4.35
125 129 2.758979 GTCCGAGGTGAAGAATGACCTA 59.241 50.000 0.00 0.00 42.95 3.08
129 133 3.133003 CGAGGTGAAGAATGACCTACCAT 59.867 47.826 0.00 0.00 42.95 3.55
131 135 3.456277 AGGTGAAGAATGACCTACCATCC 59.544 47.826 0.00 0.00 41.01 3.51
159 163 3.881952 ATGCCGCACTGCTCGTTCA 62.882 57.895 0.00 0.00 0.00 3.18
173 177 1.227853 GTTCACCACTGCCTTCCGT 60.228 57.895 0.00 0.00 0.00 4.69
871 940 1.277273 TGTTGGAGATGCTCTGAGGTG 59.723 52.381 6.83 0.00 0.00 4.00
872 941 1.277557 GTTGGAGATGCTCTGAGGTGT 59.722 52.381 6.83 0.00 0.00 4.16
873 942 0.900421 TGGAGATGCTCTGAGGTGTG 59.100 55.000 6.83 0.00 0.00 3.82
877 946 1.539869 ATGCTCTGAGGTGTGGGGT 60.540 57.895 6.83 0.00 0.00 4.95
878 947 1.136329 ATGCTCTGAGGTGTGGGGTT 61.136 55.000 6.83 0.00 0.00 4.11
885 954 2.203294 GGTGTGGGGTTGCTCGTT 60.203 61.111 0.00 0.00 0.00 3.85
895 964 0.670546 GTTGCTCGTTGGCTCAGCTA 60.671 55.000 0.00 0.00 34.03 3.32
916 985 1.135199 TCGTTGGGATGTACGAGAAGC 60.135 52.381 0.00 0.00 41.38 3.86
926 995 1.703438 TACGAGAAGCGCGGAGAGAC 61.703 60.000 8.83 0.00 46.04 3.36
958 1027 2.033424 CGGAGAGTGTTCGATAGCATCA 59.967 50.000 0.00 0.00 0.00 3.07
960 1029 3.376540 GAGAGTGTTCGATAGCATCACC 58.623 50.000 0.00 0.00 33.62 4.02
964 1033 1.749063 TGTTCGATAGCATCACCGACT 59.251 47.619 0.00 0.00 0.00 4.18
974 1044 0.744874 ATCACCGACTGGATACCGTG 59.255 55.000 0.00 0.00 39.21 4.94
999 1069 1.072331 GGAATGCTATGATCACCGGGT 59.928 52.381 6.32 0.00 0.00 5.28
1001 1071 3.055094 GGAATGCTATGATCACCGGGTAT 60.055 47.826 6.32 0.00 0.00 2.73
1013 1085 1.891150 ACCGGGTATGTATCGATGGAC 59.109 52.381 8.54 0.00 0.00 4.02
1020 1092 4.525487 GGTATGTATCGATGGACCCACTTA 59.475 45.833 8.54 0.00 0.00 2.24
1041 1116 8.383619 CACTTAGGTTCTCATTTCGAAATACTG 58.616 37.037 22.33 12.78 0.00 2.74
1118 1205 5.010617 TGTGTATGATGATGCAGGTACGTAT 59.989 40.000 0.00 0.00 0.00 3.06
1135 1230 4.772046 CGTATAACGTCATGTCAAAGGG 57.228 45.455 0.00 0.00 36.74 3.95
1162 1257 1.689984 TCCTTGTTTCACAGCATGCA 58.310 45.000 21.98 0.00 42.53 3.96
1292 1387 2.187958 AGAGGCCTGTACAGCAATGTA 58.812 47.619 12.00 0.00 0.00 2.29
1320 1415 2.301346 GGACTGCTTTGGTGGATATGG 58.699 52.381 0.00 0.00 0.00 2.74
1324 1419 3.010584 ACTGCTTTGGTGGATATGGACTT 59.989 43.478 0.00 0.00 0.00 3.01
1325 1420 3.355378 TGCTTTGGTGGATATGGACTTG 58.645 45.455 0.00 0.00 0.00 3.16
1337 1432 3.814504 ATGGACTTGGAAGTGTGGAAT 57.185 42.857 0.00 0.00 39.88 3.01
1399 1494 3.726557 AGAATGAAGCCTCATGGAACA 57.273 42.857 0.00 0.00 41.66 3.18
1416 1511 3.253432 GGAACACCTTGATTTGTGGTCTC 59.747 47.826 7.52 0.00 46.13 3.36
1424 1519 3.071479 TGATTTGTGGTCTCGCCTTTAC 58.929 45.455 0.00 0.00 38.35 2.01
1560 1662 1.349067 AGGGTTACTGAAAGACGGCT 58.651 50.000 0.00 0.00 37.43 5.52
1642 1746 4.352009 TCCTGCATGGTTGATTTATTGGT 58.648 39.130 0.00 0.00 37.07 3.67
1659 1763 1.001624 GGTACGTGCCGGACATTTAC 58.998 55.000 5.05 8.24 43.28 2.01
1716 1820 1.026182 GGCAGATGCGGTGATGTTGA 61.026 55.000 0.00 0.00 43.26 3.18
1731 1835 1.152860 TTGAGGGTTTTGCTCGCCA 60.153 52.632 0.00 0.00 0.00 5.69
1760 1864 7.392113 TGTCGGAAATGTATAAATGTTGAGGTT 59.608 33.333 0.00 0.00 0.00 3.50
1784 1888 2.628178 CGCTAGGGTCATCAACAGGATA 59.372 50.000 0.00 0.00 33.95 2.59
1885 1989 0.534652 GACCCTGCATGGATGAGAGC 60.535 60.000 15.66 0.00 38.35 4.09
2041 2159 4.573900 CTTGTTGATGAGCTAAGACTGGT 58.426 43.478 0.00 0.00 0.00 4.00
2042 2160 4.193826 TGTTGATGAGCTAAGACTGGTC 57.806 45.455 0.00 0.00 0.00 4.02
2103 2227 6.000219 AGATGCAGTTCAACTTCAGTATTGT 59.000 36.000 0.00 0.00 0.00 2.71
2226 2355 4.637534 GCTAAGTCATCTGCAAAGATTGGA 59.362 41.667 0.00 0.00 0.00 3.53
2236 2365 3.575256 TGCAAAGATTGGATGCTTGAGTT 59.425 39.130 0.00 0.00 40.66 3.01
2245 2374 4.910195 TGGATGCTTGAGTTGTGTCTATT 58.090 39.130 0.00 0.00 0.00 1.73
2291 2420 7.017498 GCTATTAGCTACCCTTGAAACTTTC 57.983 40.000 8.47 0.00 38.45 2.62
2292 2421 6.598064 GCTATTAGCTACCCTTGAAACTTTCA 59.402 38.462 8.47 0.00 38.45 2.69
2293 2422 7.120726 GCTATTAGCTACCCTTGAAACTTTCAA 59.879 37.037 14.79 14.79 41.71 2.69
2294 2423 6.628919 TTAGCTACCCTTGAAACTTTCAAC 57.371 37.500 12.12 3.27 44.21 3.18
2295 2424 4.532834 AGCTACCCTTGAAACTTTCAACA 58.467 39.130 12.12 0.00 44.21 3.33
2296 2425 4.953579 AGCTACCCTTGAAACTTTCAACAA 59.046 37.500 12.12 0.00 44.21 2.83
2297 2426 5.598417 AGCTACCCTTGAAACTTTCAACAAT 59.402 36.000 12.12 4.39 44.21 2.71
2298 2427 6.098266 AGCTACCCTTGAAACTTTCAACAATT 59.902 34.615 12.12 1.89 44.21 2.32
2299 2428 6.420903 GCTACCCTTGAAACTTTCAACAATTC 59.579 38.462 12.12 0.00 44.21 2.17
2300 2429 5.348164 ACCCTTGAAACTTTCAACAATTCG 58.652 37.500 12.12 3.20 44.21 3.34
2301 2430 4.744631 CCCTTGAAACTTTCAACAATTCGG 59.255 41.667 12.12 10.62 44.21 4.30
2302 2431 4.209080 CCTTGAAACTTTCAACAATTCGGC 59.791 41.667 12.12 0.00 44.21 5.54
2303 2432 4.377839 TGAAACTTTCAACAATTCGGCA 57.622 36.364 1.47 0.00 36.59 5.69
2304 2433 4.748892 TGAAACTTTCAACAATTCGGCAA 58.251 34.783 1.47 0.00 36.59 4.52
2305 2434 5.355596 TGAAACTTTCAACAATTCGGCAAT 58.644 33.333 1.47 0.00 36.59 3.56
2306 2435 5.233902 TGAAACTTTCAACAATTCGGCAATG 59.766 36.000 1.47 0.00 36.59 2.82
2307 2436 3.652274 ACTTTCAACAATTCGGCAATGG 58.348 40.909 0.00 0.00 0.00 3.16
2308 2437 2.739885 TTCAACAATTCGGCAATGGG 57.260 45.000 0.00 0.00 0.00 4.00
2309 2438 0.246086 TCAACAATTCGGCAATGGGC 59.754 50.000 0.00 0.00 43.74 5.36
2310 2439 0.247185 CAACAATTCGGCAATGGGCT 59.753 50.000 0.00 0.00 44.01 5.19
2311 2440 0.532115 AACAATTCGGCAATGGGCTC 59.468 50.000 0.00 0.00 44.01 4.70
2312 2441 0.611618 ACAATTCGGCAATGGGCTCA 60.612 50.000 0.00 0.00 44.01 4.26
2313 2442 0.101759 CAATTCGGCAATGGGCTCAG 59.898 55.000 0.00 0.00 44.01 3.35
2314 2443 0.323725 AATTCGGCAATGGGCTCAGT 60.324 50.000 0.00 0.00 44.01 3.41
2315 2444 0.323725 ATTCGGCAATGGGCTCAGTT 60.324 50.000 0.00 0.00 44.01 3.16
2316 2445 0.326595 TTCGGCAATGGGCTCAGTTA 59.673 50.000 0.00 0.00 44.01 2.24
2317 2446 0.326595 TCGGCAATGGGCTCAGTTAA 59.673 50.000 0.00 0.00 44.01 2.01
2318 2447 1.064758 TCGGCAATGGGCTCAGTTAAT 60.065 47.619 0.00 0.00 44.01 1.40
2319 2448 1.750778 CGGCAATGGGCTCAGTTAATT 59.249 47.619 0.00 0.00 44.01 1.40
2320 2449 2.166254 CGGCAATGGGCTCAGTTAATTT 59.834 45.455 0.00 0.00 44.01 1.82
2321 2450 3.368323 CGGCAATGGGCTCAGTTAATTTT 60.368 43.478 0.00 0.00 44.01 1.82
2322 2451 3.934579 GGCAATGGGCTCAGTTAATTTTG 59.065 43.478 0.00 0.00 44.01 2.44
2323 2452 3.371898 GCAATGGGCTCAGTTAATTTTGC 59.628 43.478 3.26 3.26 40.25 3.68
2324 2453 4.567971 CAATGGGCTCAGTTAATTTTGCA 58.432 39.130 0.00 0.00 0.00 4.08
2325 2454 4.888326 ATGGGCTCAGTTAATTTTGCAA 57.112 36.364 0.00 0.00 0.00 4.08
2326 2455 4.255833 TGGGCTCAGTTAATTTTGCAAG 57.744 40.909 0.00 0.00 0.00 4.01
2327 2456 2.995939 GGGCTCAGTTAATTTTGCAAGC 59.004 45.455 0.00 0.00 0.00 4.01
2328 2457 3.306294 GGGCTCAGTTAATTTTGCAAGCT 60.306 43.478 0.00 0.00 0.00 3.74
2329 2458 3.676646 GGCTCAGTTAATTTTGCAAGCTG 59.323 43.478 0.00 0.00 0.00 4.24
2330 2459 4.301628 GCTCAGTTAATTTTGCAAGCTGT 58.698 39.130 0.00 0.00 0.00 4.40
2331 2460 4.383948 GCTCAGTTAATTTTGCAAGCTGTC 59.616 41.667 0.00 0.00 0.00 3.51
2332 2461 5.512753 TCAGTTAATTTTGCAAGCTGTCA 57.487 34.783 0.00 0.00 0.00 3.58
2333 2462 5.522456 TCAGTTAATTTTGCAAGCTGTCAG 58.478 37.500 0.00 0.00 0.00 3.51
2334 2463 5.299028 TCAGTTAATTTTGCAAGCTGTCAGA 59.701 36.000 3.32 0.00 0.00 3.27
2335 2464 5.978919 CAGTTAATTTTGCAAGCTGTCAGAA 59.021 36.000 3.32 0.00 0.00 3.02
2336 2465 6.476380 CAGTTAATTTTGCAAGCTGTCAGAAA 59.524 34.615 3.32 0.00 0.00 2.52
2337 2466 7.170320 CAGTTAATTTTGCAAGCTGTCAGAAAT 59.830 33.333 3.32 0.00 0.00 2.17
2338 2467 5.917541 AATTTTGCAAGCTGTCAGAAATG 57.082 34.783 3.32 0.00 0.00 2.32
2339 2468 2.427232 TTGCAAGCTGTCAGAAATGC 57.573 45.000 3.32 10.56 0.00 3.56
2340 2469 1.612676 TGCAAGCTGTCAGAAATGCT 58.387 45.000 19.27 2.84 37.37 3.79
2341 2470 2.781923 TGCAAGCTGTCAGAAATGCTA 58.218 42.857 19.27 8.60 35.09 3.49
2342 2471 2.745821 TGCAAGCTGTCAGAAATGCTAG 59.254 45.455 19.27 0.00 35.09 3.42
2343 2472 3.005554 GCAAGCTGTCAGAAATGCTAGA 58.994 45.455 3.32 0.00 35.09 2.43
2344 2473 3.626670 GCAAGCTGTCAGAAATGCTAGAT 59.373 43.478 3.32 0.00 35.09 1.98
2345 2474 4.096081 GCAAGCTGTCAGAAATGCTAGATT 59.904 41.667 3.32 0.00 35.09 2.40
2346 2475 5.295292 GCAAGCTGTCAGAAATGCTAGATTA 59.705 40.000 3.32 0.00 35.09 1.75
2347 2476 6.713520 CAAGCTGTCAGAAATGCTAGATTAC 58.286 40.000 3.32 0.00 35.09 1.89
2348 2477 5.363939 AGCTGTCAGAAATGCTAGATTACC 58.636 41.667 3.32 0.00 33.64 2.85
2349 2478 4.210120 GCTGTCAGAAATGCTAGATTACCG 59.790 45.833 3.32 0.00 0.00 4.02
2350 2479 5.339008 TGTCAGAAATGCTAGATTACCGT 57.661 39.130 0.00 0.00 0.00 4.83
2351 2480 5.109210 TGTCAGAAATGCTAGATTACCGTG 58.891 41.667 0.00 0.00 0.00 4.94
2352 2481 5.105513 TGTCAGAAATGCTAGATTACCGTGA 60.106 40.000 0.00 0.00 0.00 4.35
2353 2482 5.810587 GTCAGAAATGCTAGATTACCGTGAA 59.189 40.000 0.00 0.00 0.00 3.18
2354 2483 6.480320 GTCAGAAATGCTAGATTACCGTGAAT 59.520 38.462 0.00 0.00 0.00 2.57
2355 2484 7.652105 GTCAGAAATGCTAGATTACCGTGAATA 59.348 37.037 0.00 0.00 0.00 1.75
2356 2485 8.367911 TCAGAAATGCTAGATTACCGTGAATAT 58.632 33.333 0.00 0.00 0.00 1.28
2357 2486 8.651588 CAGAAATGCTAGATTACCGTGAATATC 58.348 37.037 0.00 0.00 0.00 1.63
2358 2487 7.542477 AGAAATGCTAGATTACCGTGAATATCG 59.458 37.037 0.00 0.00 0.00 2.92
2369 2498 4.427438 CGTGAATATCGGAAAACCGTAC 57.573 45.455 8.46 0.00 34.52 3.67
2370 2499 4.107622 CGTGAATATCGGAAAACCGTACT 58.892 43.478 8.46 0.00 34.52 2.73
2371 2500 4.563976 CGTGAATATCGGAAAACCGTACTT 59.436 41.667 8.46 1.37 34.52 2.24
2372 2501 5.276067 CGTGAATATCGGAAAACCGTACTTC 60.276 44.000 8.46 9.59 34.52 3.01
2373 2502 5.006068 GTGAATATCGGAAAACCGTACTTCC 59.994 44.000 8.46 2.26 38.20 3.46
2374 2503 5.105228 TGAATATCGGAAAACCGTACTTCCT 60.105 40.000 8.46 0.00 39.23 3.36
2375 2504 6.096705 TGAATATCGGAAAACCGTACTTCCTA 59.903 38.462 8.46 0.44 39.23 2.94
2376 2505 4.806640 ATCGGAAAACCGTACTTCCTAA 57.193 40.909 8.46 0.04 39.23 2.69
2377 2506 4.599047 TCGGAAAACCGTACTTCCTAAA 57.401 40.909 8.46 0.00 39.23 1.85
2378 2507 4.559153 TCGGAAAACCGTACTTCCTAAAG 58.441 43.478 8.46 0.00 39.23 1.85
2379 2508 4.280677 TCGGAAAACCGTACTTCCTAAAGA 59.719 41.667 8.46 0.00 39.23 2.52
2380 2509 4.624452 CGGAAAACCGTACTTCCTAAAGAG 59.376 45.833 9.28 0.00 39.23 2.85
2381 2510 5.545588 GGAAAACCGTACTTCCTAAAGAGT 58.454 41.667 4.72 0.00 38.48 3.24
2382 2511 6.570378 CGGAAAACCGTACTTCCTAAAGAGTA 60.570 42.308 9.28 0.00 39.23 2.59
2383 2512 7.326454 GGAAAACCGTACTTCCTAAAGAGTAT 58.674 38.462 4.72 0.00 38.48 2.12
2384 2513 7.490725 GGAAAACCGTACTTCCTAAAGAGTATC 59.509 40.741 4.72 0.00 38.48 2.24
2385 2514 7.472334 AAACCGTACTTCCTAAAGAGTATCA 57.528 36.000 0.00 0.00 37.82 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 129 2.833582 ATCGTCTCCGCGGATGGT 60.834 61.111 31.19 15.44 0.00 3.55
144 148 3.414700 GGTGAACGAGCAGTGCGG 61.415 66.667 10.00 8.60 0.00 5.69
159 163 1.227853 GTCAACGGAAGGCAGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
845 914 3.422303 GCATCTCCAACACGCGCA 61.422 61.111 5.73 0.00 0.00 6.09
871 940 3.670377 GCCAACGAGCAACCCCAC 61.670 66.667 0.00 0.00 0.00 4.61
872 941 3.842925 GAGCCAACGAGCAACCCCA 62.843 63.158 0.00 0.00 34.23 4.96
873 942 3.056328 GAGCCAACGAGCAACCCC 61.056 66.667 0.00 0.00 34.23 4.95
877 946 0.250234 ATAGCTGAGCCAACGAGCAA 59.750 50.000 0.00 0.00 35.03 3.91
878 947 0.179100 GATAGCTGAGCCAACGAGCA 60.179 55.000 0.00 0.00 35.03 4.26
885 954 0.975556 TCCCAACGATAGCTGAGCCA 60.976 55.000 0.00 0.00 42.67 4.75
895 964 2.481449 GCTTCTCGTACATCCCAACGAT 60.481 50.000 0.00 0.00 46.05 3.73
926 995 3.578272 CTCTCCGAGACTCCGCCG 61.578 72.222 0.00 0.00 0.00 6.46
934 1003 1.941294 GCTATCGAACACTCTCCGAGA 59.059 52.381 0.00 0.00 35.70 4.04
952 1021 0.753262 GGTATCCAGTCGGTGATGCT 59.247 55.000 0.00 0.00 0.00 3.79
958 1027 2.718073 GCCACGGTATCCAGTCGGT 61.718 63.158 0.00 0.00 0.00 4.69
960 1029 0.806102 CAAGCCACGGTATCCAGTCG 60.806 60.000 0.00 0.00 0.00 4.18
964 1033 0.916086 ATTCCAAGCCACGGTATCCA 59.084 50.000 0.00 0.00 0.00 3.41
974 1044 2.555757 GGTGATCATAGCATTCCAAGCC 59.444 50.000 0.00 0.00 0.00 4.35
999 1069 4.770531 CCTAAGTGGGTCCATCGATACATA 59.229 45.833 0.00 0.00 0.00 2.29
1001 1071 2.963101 CCTAAGTGGGTCCATCGATACA 59.037 50.000 0.00 0.00 0.00 2.29
1013 1085 4.202245 TCGAAATGAGAACCTAAGTGGG 57.798 45.455 0.00 0.00 41.11 4.61
1020 1092 6.591834 CAGACAGTATTTCGAAATGAGAACCT 59.408 38.462 29.20 16.89 0.00 3.50
1059 1134 7.756395 ATGATCAGGCCACATAAGATAAAAG 57.244 36.000 5.01 0.00 0.00 2.27
1061 1136 7.560991 ACAAATGATCAGGCCACATAAGATAAA 59.439 33.333 5.01 0.00 0.00 1.40
1071 1146 3.067180 CCATACACAAATGATCAGGCCAC 59.933 47.826 5.01 0.00 0.00 5.01
1118 1205 2.614481 GGCTCCCTTTGACATGACGTTA 60.614 50.000 0.00 0.00 0.00 3.18
1123 1212 2.905415 AATGGCTCCCTTTGACATGA 57.095 45.000 0.00 0.00 32.79 3.07
1203 1298 0.597118 GCAGCATAGACCGAGAGCAG 60.597 60.000 0.00 0.00 0.00 4.24
1292 1387 3.091545 CACCAAAGCAGTCCCAATGTAT 58.908 45.455 0.00 0.00 0.00 2.29
1320 1415 4.214332 GTGAGAATTCCACACTTCCAAGTC 59.786 45.833 19.47 2.09 37.08 3.01
1324 1419 2.441375 TGGTGAGAATTCCACACTTCCA 59.559 45.455 23.21 15.21 36.31 3.53
1325 1420 3.077359 CTGGTGAGAATTCCACACTTCC 58.923 50.000 23.21 13.50 36.31 3.46
1337 1432 2.906389 ACTTGTATGGCTCTGGTGAGAA 59.094 45.455 0.00 0.00 42.73 2.87
1399 1494 1.523758 GCGAGACCACAAATCAAGGT 58.476 50.000 0.00 0.00 38.63 3.50
1494 1596 8.178313 GCAAAAAGTACTCCTATGAAAGTGATC 58.822 37.037 0.00 0.00 0.00 2.92
1540 1642 2.232941 CAGCCGTCTTTCAGTAACCCTA 59.767 50.000 0.00 0.00 0.00 3.53
1560 1662 0.178975 AGGGAATTGAACCAACGCCA 60.179 50.000 0.00 0.00 0.00 5.69
1659 1763 5.126545 TCTCAATGAAATCCCATGCTTCTTG 59.873 40.000 0.00 0.00 0.00 3.02
1716 1820 1.152756 AAGTGGCGAGCAAAACCCT 60.153 52.632 0.00 0.00 0.00 4.34
1731 1835 8.330466 TCAACATTTATACATTTCCGACAAGT 57.670 30.769 0.00 0.00 0.00 3.16
1760 1864 1.220749 GTTGATGACCCTAGCGCCA 59.779 57.895 2.29 0.00 0.00 5.69
1863 1967 1.142262 TCTCATCCATGCAGGGTCATG 59.858 52.381 18.43 14.62 42.53 3.07
1885 1989 1.339610 CACCCCTCTCTCTTATCAGCG 59.660 57.143 0.00 0.00 0.00 5.18
1994 2112 6.933521 GCATGTTGAGGAGTTGATACATATCT 59.066 38.462 0.00 0.00 33.88 1.98
2033 2151 1.348064 TTGGACCATCGACCAGTCTT 58.652 50.000 0.00 0.00 37.48 3.01
2041 2159 4.445453 CAGATCAAGATTTGGACCATCGA 58.555 43.478 0.00 0.00 0.00 3.59
2042 2160 3.562973 CCAGATCAAGATTTGGACCATCG 59.437 47.826 12.90 0.00 43.60 3.84
2210 2339 4.112634 CAAGCATCCAATCTTTGCAGATG 58.887 43.478 5.69 5.69 39.00 2.90
2268 2397 8.561738 TTGAAAGTTTCAAGGGTAGCTAATAG 57.438 34.615 23.91 0.00 44.21 1.73
2286 2415 3.554752 CCCATTGCCGAATTGTTGAAAGT 60.555 43.478 0.00 0.00 0.00 2.66
2287 2416 2.995258 CCCATTGCCGAATTGTTGAAAG 59.005 45.455 0.00 0.00 0.00 2.62
2288 2417 2.869636 GCCCATTGCCGAATTGTTGAAA 60.870 45.455 0.00 0.00 0.00 2.69
2289 2418 1.337635 GCCCATTGCCGAATTGTTGAA 60.338 47.619 0.00 0.00 0.00 2.69
2290 2419 0.246086 GCCCATTGCCGAATTGTTGA 59.754 50.000 0.00 0.00 0.00 3.18
2291 2420 0.247185 AGCCCATTGCCGAATTGTTG 59.753 50.000 0.00 0.00 42.71 3.33
2292 2421 0.532115 GAGCCCATTGCCGAATTGTT 59.468 50.000 0.00 0.00 42.71 2.83
2293 2422 0.611618 TGAGCCCATTGCCGAATTGT 60.612 50.000 0.00 0.00 42.71 2.71
2294 2423 0.101759 CTGAGCCCATTGCCGAATTG 59.898 55.000 0.00 0.00 42.71 2.32
2295 2424 0.323725 ACTGAGCCCATTGCCGAATT 60.324 50.000 0.00 0.00 42.71 2.17
2296 2425 0.323725 AACTGAGCCCATTGCCGAAT 60.324 50.000 0.00 0.00 42.71 3.34
2297 2426 0.326595 TAACTGAGCCCATTGCCGAA 59.673 50.000 0.00 0.00 42.71 4.30
2298 2427 0.326595 TTAACTGAGCCCATTGCCGA 59.673 50.000 0.00 0.00 42.71 5.54
2299 2428 1.392589 ATTAACTGAGCCCATTGCCG 58.607 50.000 0.00 0.00 42.71 5.69
2300 2429 3.893326 AAATTAACTGAGCCCATTGCC 57.107 42.857 0.00 0.00 42.71 4.52
2301 2430 3.371898 GCAAAATTAACTGAGCCCATTGC 59.628 43.478 0.00 0.00 41.71 3.56
2302 2431 4.567971 TGCAAAATTAACTGAGCCCATTG 58.432 39.130 0.00 0.00 0.00 2.82
2303 2432 4.888326 TGCAAAATTAACTGAGCCCATT 57.112 36.364 0.00 0.00 0.00 3.16
2304 2433 4.824289 CTTGCAAAATTAACTGAGCCCAT 58.176 39.130 0.00 0.00 0.00 4.00
2305 2434 3.554752 GCTTGCAAAATTAACTGAGCCCA 60.555 43.478 0.00 0.00 0.00 5.36
2306 2435 2.995939 GCTTGCAAAATTAACTGAGCCC 59.004 45.455 0.00 0.00 0.00 5.19
2307 2436 3.676646 CAGCTTGCAAAATTAACTGAGCC 59.323 43.478 0.00 0.00 0.00 4.70
2308 2437 4.301628 ACAGCTTGCAAAATTAACTGAGC 58.698 39.130 0.00 0.00 0.00 4.26
2309 2438 5.522456 TGACAGCTTGCAAAATTAACTGAG 58.478 37.500 0.00 0.00 0.00 3.35
2310 2439 5.299028 TCTGACAGCTTGCAAAATTAACTGA 59.701 36.000 0.00 0.00 0.00 3.41
2311 2440 5.522456 TCTGACAGCTTGCAAAATTAACTG 58.478 37.500 0.00 4.38 0.00 3.16
2312 2441 5.772825 TCTGACAGCTTGCAAAATTAACT 57.227 34.783 0.00 0.00 0.00 2.24
2313 2442 6.826893 TTTCTGACAGCTTGCAAAATTAAC 57.173 33.333 0.00 0.00 0.00 2.01
2314 2443 6.073657 GCATTTCTGACAGCTTGCAAAATTAA 60.074 34.615 15.09 0.00 0.00 1.40
2315 2444 5.406175 GCATTTCTGACAGCTTGCAAAATTA 59.594 36.000 15.09 0.00 0.00 1.40
2316 2445 4.212636 GCATTTCTGACAGCTTGCAAAATT 59.787 37.500 15.09 0.00 0.00 1.82
2317 2446 3.744426 GCATTTCTGACAGCTTGCAAAAT 59.256 39.130 15.09 5.76 0.00 1.82
2318 2447 3.125316 GCATTTCTGACAGCTTGCAAAA 58.875 40.909 15.09 3.97 0.00 2.44
2319 2448 2.363038 AGCATTTCTGACAGCTTGCAAA 59.637 40.909 19.49 7.51 32.52 3.68
2320 2449 1.958579 AGCATTTCTGACAGCTTGCAA 59.041 42.857 19.49 0.00 32.52 4.08
2321 2450 1.612676 AGCATTTCTGACAGCTTGCA 58.387 45.000 19.49 0.00 32.52 4.08
2322 2451 3.005554 TCTAGCATTTCTGACAGCTTGC 58.994 45.455 13.16 13.16 38.47 4.01
2323 2452 5.814764 AATCTAGCATTTCTGACAGCTTG 57.185 39.130 0.00 2.68 38.47 4.01
2324 2453 5.819901 GGTAATCTAGCATTTCTGACAGCTT 59.180 40.000 0.00 0.00 38.47 3.74
2325 2454 5.363939 GGTAATCTAGCATTTCTGACAGCT 58.636 41.667 0.00 0.00 40.92 4.24
2326 2455 4.210120 CGGTAATCTAGCATTTCTGACAGC 59.790 45.833 0.00 0.00 0.00 4.40
2327 2456 5.233050 CACGGTAATCTAGCATTTCTGACAG 59.767 44.000 0.00 0.00 0.00 3.51
2328 2457 5.105513 TCACGGTAATCTAGCATTTCTGACA 60.106 40.000 0.00 0.00 0.00 3.58
2329 2458 5.348986 TCACGGTAATCTAGCATTTCTGAC 58.651 41.667 0.00 0.00 0.00 3.51
2330 2459 5.592104 TCACGGTAATCTAGCATTTCTGA 57.408 39.130 0.00 0.00 0.00 3.27
2331 2460 6.851222 ATTCACGGTAATCTAGCATTTCTG 57.149 37.500 0.00 0.00 0.00 3.02
2332 2461 7.542477 CGATATTCACGGTAATCTAGCATTTCT 59.458 37.037 0.00 0.00 0.00 2.52
2333 2462 7.201444 CCGATATTCACGGTAATCTAGCATTTC 60.201 40.741 0.00 0.00 44.57 2.17
2334 2463 6.590292 CCGATATTCACGGTAATCTAGCATTT 59.410 38.462 0.00 0.00 44.57 2.32
2335 2464 6.100004 CCGATATTCACGGTAATCTAGCATT 58.900 40.000 0.00 0.00 44.57 3.56
2336 2465 5.651530 CCGATATTCACGGTAATCTAGCAT 58.348 41.667 0.00 0.00 44.57 3.79
2337 2466 5.055642 CCGATATTCACGGTAATCTAGCA 57.944 43.478 0.00 0.00 44.57 3.49
2358 2487 5.545588 ACTCTTTAGGAAGTACGGTTTTCC 58.454 41.667 13.31 13.31 42.56 3.13
2359 2488 8.031277 TGATACTCTTTAGGAAGTACGGTTTTC 58.969 37.037 0.00 0.00 34.41 2.29
2360 2489 7.899973 TGATACTCTTTAGGAAGTACGGTTTT 58.100 34.615 0.00 0.00 34.41 2.43
2361 2490 7.472334 TGATACTCTTTAGGAAGTACGGTTT 57.528 36.000 0.00 0.00 34.41 3.27


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

AutoCloner maintained by Alex Coulton.