Multiple sequence alignment - TraesCS5D01G023200

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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 TraesCS5D01G023200 chr5D 100.000 3401 0 0 1 3401 18082678 18086078 0.000000e+00 6281.0
1 TraesCS5D01G023200 chr5D 78.414 1362 229 36 1009 2339 493341765 493343092 0.000000e+00 826.0
2 TraesCS5D01G023200 chr5D 93.277 119 7 1 2330 2448 268274704 268274821 1.250000e-39 174.0
3 TraesCS5D01G023200 chr5B 94.486 2013 83 13 354 2339 13776795 13774784 0.000000e+00 3077.0
4 TraesCS5D01G023200 chr5B 97.810 959 20 1 2443 3401 13774785 13773828 0.000000e+00 1653.0
5 TraesCS5D01G023200 chr5B 78.792 1358 224 34 1001 2327 546075278 546073954 0.000000e+00 854.0
6 TraesCS5D01G023200 chr5B 78.524 1355 237 24 1000 2327 546145903 546144576 0.000000e+00 841.0
7 TraesCS5D01G023200 chr5B 91.793 329 19 5 71 395 13777111 13776787 5.180000e-123 451.0
8 TraesCS5D01G023200 chr5B 82.083 480 60 14 944 1398 545612265 545611787 1.480000e-103 387.0
9 TraesCS5D01G023200 chr5A 94.478 1503 74 1 846 2339 12194369 12192867 0.000000e+00 2307.0
10 TraesCS5D01G023200 chr5A 95.933 959 37 2 2443 3401 12192868 12191912 0.000000e+00 1554.0
11 TraesCS5D01G023200 chr5A 78.764 1375 222 41 1000 2339 616498348 616499687 0.000000e+00 857.0
12 TraesCS5D01G023200 chr5A 95.363 496 22 1 354 848 12195358 12194863 0.000000e+00 787.0
13 TraesCS5D01G023200 chr5A 95.970 397 13 3 1 395 12195745 12195350 2.860000e-180 641.0
14 TraesCS5D01G023200 chr1D 86.807 1516 161 17 841 2339 407672691 407671198 0.000000e+00 1655.0
15 TraesCS5D01G023200 chr1D 85.955 1367 159 20 1000 2339 6714609 6713249 0.000000e+00 1430.0
16 TraesCS5D01G023200 chr1D 90.021 962 92 2 2443 3401 407671199 407670239 0.000000e+00 1242.0
17 TraesCS5D01G023200 chr1D 89.501 962 94 3 2443 3401 6713250 6712293 0.000000e+00 1210.0
18 TraesCS5D01G023200 chr1D 79.824 1363 210 38 1000 2322 6913162 6914499 0.000000e+00 933.0
19 TraesCS5D01G023200 chr1D 79.272 1346 210 39 1020 2329 6721569 6720257 0.000000e+00 876.0
20 TraesCS5D01G023200 chr1D 80.323 371 37 16 1 345 407673628 407673268 7.290000e-62 248.0
21 TraesCS5D01G023200 chr1D 93.571 140 5 3 2326 2462 403331671 403331809 4.450000e-49 206.0
22 TraesCS5D01G023200 chr1D 78.388 273 28 13 626 868 407672979 407672708 7.600000e-32 148.0
23 TraesCS5D01G023200 chr1B 86.675 1516 163 16 841 2339 548193832 548192339 0.000000e+00 1644.0
24 TraesCS5D01G023200 chr1B 83.684 1330 171 35 1025 2339 8855853 8854555 0.000000e+00 1212.0
25 TraesCS5D01G023200 chr1B 89.364 959 89 7 2443 3401 548192340 548191395 0.000000e+00 1194.0
26 TraesCS5D01G023200 chr1B 78.832 1370 216 39 1000 2329 9161800 9163135 0.000000e+00 856.0
27 TraesCS5D01G023200 chr1B 78.717 1372 217 44 1000 2329 8867231 8865893 0.000000e+00 846.0
28 TraesCS5D01G023200 chr1B 80.863 371 35 15 1 345 548194995 548194635 3.370000e-65 259.0
29 TraesCS5D01G023200 chr1B 99.065 107 1 0 2338 2444 492303873 492303979 3.460000e-45 193.0
30 TraesCS5D01G023200 chr1B 93.860 114 6 1 2332 2444 15616942 15616829 1.620000e-38 171.0
31 TraesCS5D01G023200 chr1B 79.512 205 25 8 1017 1207 8820424 8820223 2.750000e-26 130.0
32 TraesCS5D01G023200 chr1B 80.791 177 22 7 697 868 548194018 548193849 9.910000e-26 128.0
33 TraesCS5D01G023200 chr1B 90.476 63 5 1 626 688 548194363 548194302 7.820000e-12 82.4
34 TraesCS5D01G023200 chr1A 84.572 1601 206 20 768 2339 7834444 7836032 0.000000e+00 1550.0
35 TraesCS5D01G023200 chr1A 85.443 1367 166 20 1000 2339 8144501 8143141 0.000000e+00 1391.0
36 TraesCS5D01G023200 chr1A 83.573 1388 190 20 981 2339 8327128 8328506 0.000000e+00 1266.0
37 TraesCS5D01G023200 chr1A 90.135 963 86 5 2443 3401 8143142 8142185 0.000000e+00 1243.0
38 TraesCS5D01G023200 chr1A 88.877 962 103 2 2443 3401 7836031 7836991 0.000000e+00 1181.0
39 TraesCS5D01G023200 chr1A 80.235 1361 202 37 1000 2319 8342046 8343380 0.000000e+00 961.0
40 TraesCS5D01G023200 chr1A 79.869 1376 214 36 1000 2336 8331950 8333301 0.000000e+00 948.0
41 TraesCS5D01G023200 chr1A 80.497 1087 166 26 1253 2319 8364368 8365428 0.000000e+00 791.0
42 TraesCS5D01G023200 chr1A 77.742 620 84 33 623 1207 8339814 8340414 7.030000e-87 331.0
43 TraesCS5D01G023200 chr1A 78.000 350 56 16 1 345 8339322 8339655 2.070000e-47 200.0
44 TraesCS5D01G023200 chr1A 95.763 118 5 0 2335 2452 108071476 108071359 1.250000e-44 191.0
45 TraesCS5D01G023200 chr1A 84.259 108 15 1 6 113 8337341 8337446 1.670000e-18 104.0
46 TraesCS5D01G023200 chr1A 89.024 82 9 0 264 345 7834093 7834174 6.000000e-18 102.0
47 TraesCS5D01G023200 chr1A 100.000 29 0 0 308 336 9375829 9375801 2.000000e-03 54.7
48 TraesCS5D01G023200 chr4B 85.077 1367 162 24 1000 2339 36635850 36634499 0.000000e+00 1356.0
49 TraesCS5D01G023200 chr4B 89.605 962 93 3 2443 3401 36634500 36633543 0.000000e+00 1216.0
50 TraesCS5D01G023200 chr2A 82.634 1382 172 37 1000 2341 611296159 611297512 0.000000e+00 1160.0
51 TraesCS5D01G023200 chr2A 80.470 1362 193 40 1021 2341 733628929 733630258 0.000000e+00 974.0
52 TraesCS5D01G023200 chr2A 79.942 1391 219 32 984 2334 611302813 611304183 0.000000e+00 968.0
53 TraesCS5D01G023200 chr2D 88.290 965 97 10 2443 3401 469985389 469986343 0.000000e+00 1142.0
54 TraesCS5D01G023200 chr2D 80.692 1388 188 46 1000 2341 599926425 599927778 0.000000e+00 1005.0
55 TraesCS5D01G023200 chr2D 79.942 1391 219 34 984 2334 469990572 469991942 0.000000e+00 968.0
56 TraesCS5D01G023200 chr7D 97.196 107 3 0 2338 2444 183211676 183211782 7.500000e-42 182.0
57 TraesCS5D01G023200 chr4D 95.413 109 5 0 2336 2444 261757902 261758010 1.250000e-39 174.0
58 TraesCS5D01G023200 chr3D 93.966 116 6 1 2328 2443 597483307 597483193 1.250000e-39 174.0
59 TraesCS5D01G023200 chr3B 93.103 116 8 0 2337 2452 449159819 449159934 1.620000e-38 171.0


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 TraesCS5D01G023200 chr5D 18082678 18086078 3400 False 6281.000000 6281 100.000000 1 3401 1 chr5D.!!$F1 3400
1 TraesCS5D01G023200 chr5D 493341765 493343092 1327 False 826.000000 826 78.414000 1009 2339 1 chr5D.!!$F3 1330
2 TraesCS5D01G023200 chr5B 13773828 13777111 3283 True 1727.000000 3077 94.696333 71 3401 3 chr5B.!!$R4 3330
3 TraesCS5D01G023200 chr5B 546073954 546075278 1324 True 854.000000 854 78.792000 1001 2327 1 chr5B.!!$R2 1326
4 TraesCS5D01G023200 chr5B 546144576 546145903 1327 True 841.000000 841 78.524000 1000 2327 1 chr5B.!!$R3 1327
5 TraesCS5D01G023200 chr5A 12191912 12195745 3833 True 1322.250000 2307 95.436000 1 3401 4 chr5A.!!$R1 3400
6 TraesCS5D01G023200 chr5A 616498348 616499687 1339 False 857.000000 857 78.764000 1000 2339 1 chr5A.!!$F1 1339
7 TraesCS5D01G023200 chr1D 6712293 6714609 2316 True 1320.000000 1430 87.728000 1000 3401 2 chr1D.!!$R2 2401
8 TraesCS5D01G023200 chr1D 6913162 6914499 1337 False 933.000000 933 79.824000 1000 2322 1 chr1D.!!$F1 1322
9 TraesCS5D01G023200 chr1D 6720257 6721569 1312 True 876.000000 876 79.272000 1020 2329 1 chr1D.!!$R1 1309
10 TraesCS5D01G023200 chr1D 407670239 407673628 3389 True 823.250000 1655 83.884750 1 3401 4 chr1D.!!$R3 3400
11 TraesCS5D01G023200 chr1B 8854555 8855853 1298 True 1212.000000 1212 83.684000 1025 2339 1 chr1B.!!$R2 1314
12 TraesCS5D01G023200 chr1B 9161800 9163135 1335 False 856.000000 856 78.832000 1000 2329 1 chr1B.!!$F1 1329
13 TraesCS5D01G023200 chr1B 8865893 8867231 1338 True 846.000000 846 78.717000 1000 2329 1 chr1B.!!$R3 1329
14 TraesCS5D01G023200 chr1B 548191395 548194995 3600 True 661.480000 1644 85.633800 1 3401 5 chr1B.!!$R5 3400
15 TraesCS5D01G023200 chr1A 8142185 8144501 2316 True 1317.000000 1391 87.789000 1000 3401 2 chr1A.!!$R3 2401
16 TraesCS5D01G023200 chr1A 8327128 8333301 6173 False 1107.000000 1266 81.721000 981 2339 2 chr1A.!!$F3 1358
17 TraesCS5D01G023200 chr1A 7834093 7836991 2898 False 944.333333 1550 87.491000 264 3401 3 chr1A.!!$F2 3137
18 TraesCS5D01G023200 chr1A 8364368 8365428 1060 False 791.000000 791 80.497000 1253 2319 1 chr1A.!!$F1 1066
19 TraesCS5D01G023200 chr1A 8337341 8343380 6039 False 399.000000 961 80.059000 1 2319 4 chr1A.!!$F4 2318
20 TraesCS5D01G023200 chr4B 36633543 36635850 2307 True 1286.000000 1356 87.341000 1000 3401 2 chr4B.!!$R1 2401
21 TraesCS5D01G023200 chr2A 611296159 611297512 1353 False 1160.000000 1160 82.634000 1000 2341 1 chr2A.!!$F1 1341
22 TraesCS5D01G023200 chr2A 733628929 733630258 1329 False 974.000000 974 80.470000 1021 2341 1 chr2A.!!$F3 1320
23 TraesCS5D01G023200 chr2A 611302813 611304183 1370 False 968.000000 968 79.942000 984 2334 1 chr2A.!!$F2 1350
24 TraesCS5D01G023200 chr2D 469985389 469986343 954 False 1142.000000 1142 88.290000 2443 3401 1 chr2D.!!$F1 958
25 TraesCS5D01G023200 chr2D 599926425 599927778 1353 False 1005.000000 1005 80.692000 1000 2341 1 chr2D.!!$F3 1341
26 TraesCS5D01G023200 chr2D 469990572 469991942 1370 False 968.000000 968 79.942000 984 2334 1 chr2D.!!$F2 1350

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
407 2444 0.461961 GTCCTCGCAGACCAGCTAAT 59.538 55.0 0.0 0.0 0.00 1.73 F
914 3932 0.771755 GACCCCAAGTGAACTTCCCT 59.228 55.0 0.0 0.0 33.11 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2348 7366 0.527113 TCGCGACAAGTAATTCCGGA 59.473 50.0 3.71 0.0 0.00 5.14 R
2421 7439 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 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
143 2143 3.830755 ACGTACACTTCCAGTTGTAGGAT 59.169 43.478 8.09 0.00 34.56 3.24
178 2179 3.124806 GCTCCCTCGCTGTTACTTTTTAC 59.875 47.826 0.00 0.00 0.00 2.01
179 2180 4.312443 CTCCCTCGCTGTTACTTTTTACA 58.688 43.478 0.00 0.00 0.00 2.41
407 2444 0.461961 GTCCTCGCAGACCAGCTAAT 59.538 55.000 0.00 0.00 0.00 1.73
431 2477 5.655090 TGTACACTTACCTATTCTGCTAGCA 59.345 40.000 18.22 18.22 0.00 3.49
532 2578 5.045505 ACCACCCCTTTTTGTTAATTTGTGT 60.046 36.000 0.00 0.00 0.00 3.72
584 2632 1.537202 GTTTGCCGACTTCAGCTCAAT 59.463 47.619 0.00 0.00 0.00 2.57
666 2839 6.797995 GCCTTGAATTTGCATTTGTAATGTTG 59.202 34.615 0.00 0.00 0.00 3.33
714 3178 6.687081 TGCGGGTTTAGAAAGGTTATATTG 57.313 37.500 0.00 0.00 0.00 1.90
897 3915 6.206634 TCTGTCCCAATGTGAACTTAATTGAC 59.793 38.462 0.00 0.00 33.96 3.18
898 3916 5.242838 TGTCCCAATGTGAACTTAATTGACC 59.757 40.000 0.00 0.00 33.96 4.02
899 3917 4.770010 TCCCAATGTGAACTTAATTGACCC 59.230 41.667 0.00 0.00 33.96 4.46
900 3918 4.081697 CCCAATGTGAACTTAATTGACCCC 60.082 45.833 0.00 0.00 33.96 4.95
901 3919 4.526262 CCAATGTGAACTTAATTGACCCCA 59.474 41.667 0.00 0.00 33.96 4.96
902 3920 5.011533 CCAATGTGAACTTAATTGACCCCAA 59.988 40.000 0.00 0.00 33.96 4.12
903 3921 5.982890 ATGTGAACTTAATTGACCCCAAG 57.017 39.130 0.00 0.00 35.48 3.61
904 3922 4.798882 TGTGAACTTAATTGACCCCAAGT 58.201 39.130 0.00 0.00 35.48 3.16
905 3923 4.582656 TGTGAACTTAATTGACCCCAAGTG 59.417 41.667 0.00 0.00 35.48 3.16
906 3924 4.825085 GTGAACTTAATTGACCCCAAGTGA 59.175 41.667 0.00 0.00 35.48 3.41
907 3925 5.300792 GTGAACTTAATTGACCCCAAGTGAA 59.699 40.000 0.00 0.00 35.48 3.18
914 3932 0.771755 GACCCCAAGTGAACTTCCCT 59.228 55.000 0.00 0.00 33.11 4.20
917 3935 1.702957 CCCCAAGTGAACTTCCCTGTA 59.297 52.381 0.00 0.00 33.11 2.74
1202 4276 2.094762 AAGTCGTCCTACAATGCCAC 57.905 50.000 0.00 0.00 0.00 5.01
1229 6154 2.851195 CTGGTACCTTGGCATATGGTC 58.149 52.381 14.36 4.14 37.87 4.02
1336 6261 4.823442 TCAAGATATCAAGCGATGGCAATT 59.177 37.500 5.32 0.00 43.41 2.32
1385 6346 2.226330 TGAATCCGTTGTTTGGTCCAG 58.774 47.619 0.00 0.00 0.00 3.86
1398 6359 2.571212 TGGTCCAGTCACATTGTCAAC 58.429 47.619 0.00 0.00 0.00 3.18
1473 6452 2.304761 CAGTGGAAACCTTGCCCTACTA 59.695 50.000 0.00 0.00 0.00 1.82
1502 6493 2.481952 GACAAGAGATGTTGTGGCAGAC 59.518 50.000 0.00 0.00 44.12 3.51
2093 7102 3.341823 GAGGATGCATCAGAAACACACT 58.658 45.455 27.25 12.00 0.00 3.55
2148 7163 6.889301 AACATGACAAGTTCATCAGACATT 57.111 33.333 0.00 0.00 43.68 2.71
2330 7348 7.936496 TTAGTGTAAATCTGAATGATGGCAA 57.064 32.000 0.00 0.00 35.21 4.52
2341 7359 8.557592 TCTGAATGATGGCAATGATAATACTC 57.442 34.615 0.00 0.00 0.00 2.59
2342 7360 7.609146 TCTGAATGATGGCAATGATAATACTCC 59.391 37.037 0.00 0.00 0.00 3.85
2343 7361 6.660521 TGAATGATGGCAATGATAATACTCCC 59.339 38.462 0.00 0.00 0.00 4.30
2344 7362 5.848286 TGATGGCAATGATAATACTCCCT 57.152 39.130 0.00 0.00 0.00 4.20
2345 7363 5.809001 TGATGGCAATGATAATACTCCCTC 58.191 41.667 0.00 0.00 0.00 4.30
2346 7364 4.640771 TGGCAATGATAATACTCCCTCC 57.359 45.455 0.00 0.00 0.00 4.30
2347 7365 3.007940 TGGCAATGATAATACTCCCTCCG 59.992 47.826 0.00 0.00 0.00 4.63
2348 7366 3.008049 GGCAATGATAATACTCCCTCCGT 59.992 47.826 0.00 0.00 0.00 4.69
2349 7367 4.246458 GCAATGATAATACTCCCTCCGTC 58.754 47.826 0.00 0.00 0.00 4.79
2350 7368 4.822026 CAATGATAATACTCCCTCCGTCC 58.178 47.826 0.00 0.00 0.00 4.79
2351 7369 2.511659 TGATAATACTCCCTCCGTCCG 58.488 52.381 0.00 0.00 0.00 4.79
2352 7370 1.817447 GATAATACTCCCTCCGTCCGG 59.183 57.143 0.00 0.00 0.00 5.14
2353 7371 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2354 7372 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2355 7373 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
2356 7374 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
2357 7375 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
2358 7376 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
2359 7377 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
2360 7378 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
2361 7379 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2362 7380 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2363 7381 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2364 7382 1.135315 TCCGTCCGGAATTACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2365 7383 0.643820 CGTCCGGAATTACTTGTCGC 59.356 55.000 5.23 0.00 0.00 5.19
2366 7384 0.643820 GTCCGGAATTACTTGTCGCG 59.356 55.000 5.23 0.00 0.00 5.87
2367 7385 0.527113 TCCGGAATTACTTGTCGCGA 59.473 50.000 3.71 3.71 0.00 5.87
2368 7386 1.067706 TCCGGAATTACTTGTCGCGAA 60.068 47.619 12.06 0.00 0.00 4.70
2369 7387 1.727880 CCGGAATTACTTGTCGCGAAA 59.272 47.619 12.06 0.54 0.00 3.46
2370 7388 2.158058 CCGGAATTACTTGTCGCGAAAA 59.842 45.455 12.06 12.01 0.00 2.29
2371 7389 3.181514 CCGGAATTACTTGTCGCGAAAAT 60.182 43.478 13.05 5.74 0.00 1.82
2372 7390 3.778718 CGGAATTACTTGTCGCGAAAATG 59.221 43.478 13.05 9.32 0.00 2.32
2373 7391 4.095610 GGAATTACTTGTCGCGAAAATGG 58.904 43.478 13.05 4.35 0.00 3.16
2374 7392 4.142773 GGAATTACTTGTCGCGAAAATGGA 60.143 41.667 13.05 0.56 0.00 3.41
2375 7393 5.448632 GGAATTACTTGTCGCGAAAATGGAT 60.449 40.000 13.05 3.91 0.00 3.41
2376 7394 2.900122 ACTTGTCGCGAAAATGGATG 57.100 45.000 13.05 2.76 0.00 3.51
2377 7395 2.151202 ACTTGTCGCGAAAATGGATGT 58.849 42.857 13.05 3.46 0.00 3.06
2378 7396 3.331150 ACTTGTCGCGAAAATGGATGTA 58.669 40.909 13.05 0.00 0.00 2.29
2379 7397 3.938963 ACTTGTCGCGAAAATGGATGTAT 59.061 39.130 13.05 0.00 0.00 2.29
2380 7398 4.034048 ACTTGTCGCGAAAATGGATGTATC 59.966 41.667 13.05 0.00 0.00 2.24
2381 7399 3.792401 TGTCGCGAAAATGGATGTATCT 58.208 40.909 12.06 0.00 0.00 1.98
2382 7400 4.939271 TGTCGCGAAAATGGATGTATCTA 58.061 39.130 12.06 0.00 0.00 1.98
2383 7401 4.982295 TGTCGCGAAAATGGATGTATCTAG 59.018 41.667 12.06 0.00 0.00 2.43
2384 7402 5.220381 GTCGCGAAAATGGATGTATCTAGA 58.780 41.667 12.06 0.00 0.00 2.43
2385 7403 5.690409 GTCGCGAAAATGGATGTATCTAGAA 59.310 40.000 12.06 0.00 0.00 2.10
2386 7404 5.690409 TCGCGAAAATGGATGTATCTAGAAC 59.310 40.000 6.20 0.00 0.00 3.01
2387 7405 5.692204 CGCGAAAATGGATGTATCTAGAACT 59.308 40.000 0.00 0.00 0.00 3.01
2388 7406 6.861572 CGCGAAAATGGATGTATCTAGAACTA 59.138 38.462 0.00 0.00 0.00 2.24
2389 7407 7.381408 CGCGAAAATGGATGTATCTAGAACTAA 59.619 37.037 0.00 0.00 0.00 2.24
2390 7408 9.042008 GCGAAAATGGATGTATCTAGAACTAAA 57.958 33.333 0.00 0.00 0.00 1.85
2397 7415 9.745880 TGGATGTATCTAGAACTAAAATTCGTC 57.254 33.333 0.00 0.00 33.57 4.20
2398 7416 9.968870 GGATGTATCTAGAACTAAAATTCGTCT 57.031 33.333 0.00 0.00 33.57 4.18
2408 7426 9.968870 AGAACTAAAATTCGTCTAGATACATCC 57.031 33.333 0.00 0.00 33.57 3.51
2409 7427 9.745880 GAACTAAAATTCGTCTAGATACATCCA 57.254 33.333 0.00 0.00 0.00 3.41
2414 7432 8.608844 AAATTCGTCTAGATACATCCATTTCC 57.391 34.615 0.00 0.00 0.00 3.13
2415 7433 5.723672 TCGTCTAGATACATCCATTTCCC 57.276 43.478 0.00 0.00 0.00 3.97
2416 7434 4.527038 TCGTCTAGATACATCCATTTCCCC 59.473 45.833 0.00 0.00 0.00 4.81
2417 7435 4.618460 CGTCTAGATACATCCATTTCCCCG 60.618 50.000 0.00 0.00 0.00 5.73
2418 7436 4.527038 GTCTAGATACATCCATTTCCCCGA 59.473 45.833 0.00 0.00 0.00 5.14
2419 7437 3.771577 AGATACATCCATTTCCCCGAC 57.228 47.619 0.00 0.00 0.00 4.79
2420 7438 3.045634 AGATACATCCATTTCCCCGACA 58.954 45.455 0.00 0.00 0.00 4.35
2421 7439 3.458118 AGATACATCCATTTCCCCGACAA 59.542 43.478 0.00 0.00 0.00 3.18
2422 7440 2.128771 ACATCCATTTCCCCGACAAG 57.871 50.000 0.00 0.00 0.00 3.16
2423 7441 1.354368 ACATCCATTTCCCCGACAAGT 59.646 47.619 0.00 0.00 0.00 3.16
2424 7442 2.574369 ACATCCATTTCCCCGACAAGTA 59.426 45.455 0.00 0.00 0.00 2.24
2425 7443 3.202151 ACATCCATTTCCCCGACAAGTAT 59.798 43.478 0.00 0.00 0.00 2.12
2426 7444 4.207165 CATCCATTTCCCCGACAAGTATT 58.793 43.478 0.00 0.00 0.00 1.89
2427 7445 4.310022 TCCATTTCCCCGACAAGTATTT 57.690 40.909 0.00 0.00 0.00 1.40
2428 7446 4.266714 TCCATTTCCCCGACAAGTATTTC 58.733 43.478 0.00 0.00 0.00 2.17
2429 7447 3.380320 CCATTTCCCCGACAAGTATTTCC 59.620 47.826 0.00 0.00 0.00 3.13
2430 7448 2.389962 TTCCCCGACAAGTATTTCCG 57.610 50.000 0.00 0.00 0.00 4.30
2431 7449 0.538118 TCCCCGACAAGTATTTCCGG 59.462 55.000 0.00 0.00 39.85 5.14
2432 7450 0.538118 CCCCGACAAGTATTTCCGGA 59.462 55.000 0.00 0.00 42.49 5.14
2433 7451 1.648504 CCCGACAAGTATTTCCGGAC 58.351 55.000 1.83 0.00 42.49 4.79
2434 7452 1.274596 CCGACAAGTATTTCCGGACG 58.725 55.000 1.83 0.00 42.49 4.79
2435 7453 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2436 7454 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2437 7455 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2438 7456 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2439 7457 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2440 7458 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2441 7459 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2536 7554 1.011333 ACCAAACGTCGGAGTTGTTG 58.989 50.000 10.75 0.00 34.14 3.33
2585 7606 2.082231 ACTGATGCTCATGCTGTTGTC 58.918 47.619 0.00 0.00 40.48 3.18
2593 7615 3.057736 GCTCATGCTGTTGTCACTGATTT 60.058 43.478 0.00 0.00 36.03 2.17
2595 7617 3.253921 TCATGCTGTTGTCACTGATTTGG 59.746 43.478 0.00 0.00 0.00 3.28
2598 7620 2.227388 GCTGTTGTCACTGATTTGGAGG 59.773 50.000 0.00 0.00 0.00 4.30
2599 7621 3.743521 CTGTTGTCACTGATTTGGAGGA 58.256 45.455 0.00 0.00 0.00 3.71
2707 7729 5.763698 AGTTAGTGCCACTAAAAACTTCTCC 59.236 40.000 18.40 3.77 41.80 3.71
3381 8409 2.673775 TTCCCTGTTCAAGCCATCAA 57.326 45.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 41 9.913310 TGAATGATCATGGTATTAACCTAAACA 57.087 29.630 9.46 0.00 46.91 2.83
143 2143 4.017808 GCGAGGGAGCTTCCTTCTATATA 58.982 47.826 16.96 0.00 40.18 0.86
178 2179 7.328249 ACGTAATTTGGCAATGTCAGTAAATTG 59.672 33.333 0.00 0.00 36.95 2.32
179 2180 7.375053 ACGTAATTTGGCAATGTCAGTAAATT 58.625 30.769 0.00 2.24 33.72 1.82
366 2367 2.596346 TGCATGGTCATTGGTCAAGTT 58.404 42.857 0.00 0.00 0.00 2.66
407 2444 5.655090 TGCTAGCAGAATAGGTAAGTGTACA 59.345 40.000 14.93 0.00 31.21 2.90
461 2507 8.173775 CACATCTTTAGTACAGAAATTCAGCTG 58.826 37.037 7.63 7.63 38.10 4.24
584 2632 4.155099 CGCCACCACAGAAATACAACAATA 59.845 41.667 0.00 0.00 0.00 1.90
666 2839 2.747396 TTTGCTTCAATGCATGGTCC 57.253 45.000 0.00 0.00 42.96 4.46
714 3178 9.474313 ACCTCACATATTAGAGAGATATCTTCC 57.526 37.037 6.70 2.09 33.74 3.46
897 3915 0.478507 ACAGGGAAGTTCACTTGGGG 59.521 55.000 4.43 0.00 36.11 4.96
898 3916 3.412386 CTTACAGGGAAGTTCACTTGGG 58.588 50.000 4.43 0.00 36.11 4.12
899 3917 2.814336 GCTTACAGGGAAGTTCACTTGG 59.186 50.000 4.43 0.00 36.11 3.61
900 3918 3.744660 AGCTTACAGGGAAGTTCACTTG 58.255 45.455 4.43 4.05 36.11 3.16
901 3919 4.141482 TGAAGCTTACAGGGAAGTTCACTT 60.141 41.667 4.43 0.06 39.23 3.16
902 3920 3.391296 TGAAGCTTACAGGGAAGTTCACT 59.609 43.478 0.40 0.40 29.46 3.41
903 3921 3.740115 TGAAGCTTACAGGGAAGTTCAC 58.260 45.455 0.00 0.00 29.46 3.18
904 3922 3.807209 GCTGAAGCTTACAGGGAAGTTCA 60.807 47.826 20.36 8.16 38.21 3.18
905 3923 2.744741 GCTGAAGCTTACAGGGAAGTTC 59.255 50.000 20.36 0.00 38.21 3.01
906 3924 2.553247 GGCTGAAGCTTACAGGGAAGTT 60.553 50.000 20.36 0.00 41.70 2.66
907 3925 1.003696 GGCTGAAGCTTACAGGGAAGT 59.996 52.381 20.36 0.00 41.70 3.01
1112 4156 0.610174 TCTTGAGACGAGCTTGCCAT 59.390 50.000 0.00 0.00 0.00 4.40
1202 4276 1.604378 CCAAGGTACCAGCTGGAGG 59.396 63.158 39.19 23.22 38.94 4.30
1229 6154 3.891366 AGTGAAAACTGGGATCTTGTTGG 59.109 43.478 0.00 0.00 0.00 3.77
1336 6261 2.160615 CGGCATGGTTTACGATGACAAA 59.839 45.455 10.68 0.00 39.69 2.83
1385 6346 4.142271 TGGTTTTCCTGTTGACAATGTGAC 60.142 41.667 0.00 0.00 41.38 3.67
1398 6359 4.803613 GTGTTTTTGCTACTGGTTTTCCTG 59.196 41.667 0.00 0.00 43.33 3.86
1473 6452 5.413833 CCACAACATCTCTTGTCTATTTGCT 59.586 40.000 0.00 0.00 37.68 3.91
1482 6461 2.498167 GTCTGCCACAACATCTCTTGT 58.502 47.619 0.00 0.00 41.53 3.16
1502 6493 5.989477 TGATATCTGTTGGGTAGTCAAAGG 58.011 41.667 3.98 0.00 0.00 3.11
1691 6685 2.851263 TTCCGTGGTTGCATAAGTCT 57.149 45.000 0.00 0.00 0.00 3.24
2093 7102 3.073678 CCACTAGTGCTGCAATGTAACA 58.926 45.455 17.86 0.00 0.00 2.41
2148 7163 1.133199 ACTTGAGCAATGGGGTGGAAA 60.133 47.619 0.00 0.00 0.00 3.13
2330 7348 3.090037 CGGACGGAGGGAGTATTATCAT 58.910 50.000 0.00 0.00 0.00 2.45
2341 7359 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2342 7360 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2343 7361 2.537401 GACAAGTAATTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
2344 7362 1.135315 CGACAAGTAATTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
2345 7363 1.274596 CGACAAGTAATTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
2346 7364 0.643820 GCGACAAGTAATTCCGGACG 59.356 55.000 1.83 1.53 0.00 4.79
2347 7365 0.643820 CGCGACAAGTAATTCCGGAC 59.356 55.000 1.83 0.00 0.00 4.79
2348 7366 0.527113 TCGCGACAAGTAATTCCGGA 59.473 50.000 3.71 0.00 0.00 5.14
2349 7367 1.352114 TTCGCGACAAGTAATTCCGG 58.648 50.000 9.15 0.00 0.00 5.14
2350 7368 3.443054 TTTTCGCGACAAGTAATTCCG 57.557 42.857 9.15 0.00 0.00 4.30
2351 7369 4.095610 CCATTTTCGCGACAAGTAATTCC 58.904 43.478 9.15 0.00 0.00 3.01
2352 7370 4.965062 TCCATTTTCGCGACAAGTAATTC 58.035 39.130 9.15 0.00 0.00 2.17
2353 7371 5.106317 ACATCCATTTTCGCGACAAGTAATT 60.106 36.000 9.15 0.00 0.00 1.40
2354 7372 4.394920 ACATCCATTTTCGCGACAAGTAAT 59.605 37.500 9.15 0.42 0.00 1.89
2355 7373 3.749088 ACATCCATTTTCGCGACAAGTAA 59.251 39.130 9.15 0.00 0.00 2.24
2356 7374 3.331150 ACATCCATTTTCGCGACAAGTA 58.669 40.909 9.15 0.00 0.00 2.24
2357 7375 2.151202 ACATCCATTTTCGCGACAAGT 58.849 42.857 9.15 0.00 0.00 3.16
2358 7376 2.900122 ACATCCATTTTCGCGACAAG 57.100 45.000 9.15 2.84 0.00 3.16
2359 7377 4.188462 AGATACATCCATTTTCGCGACAA 58.812 39.130 9.15 9.93 0.00 3.18
2360 7378 3.792401 AGATACATCCATTTTCGCGACA 58.208 40.909 9.15 0.00 0.00 4.35
2361 7379 5.220381 TCTAGATACATCCATTTTCGCGAC 58.780 41.667 9.15 0.00 0.00 5.19
2362 7380 5.447624 TCTAGATACATCCATTTTCGCGA 57.552 39.130 3.71 3.71 0.00 5.87
2363 7381 5.692204 AGTTCTAGATACATCCATTTTCGCG 59.308 40.000 0.00 0.00 0.00 5.87
2364 7382 8.589335 TTAGTTCTAGATACATCCATTTTCGC 57.411 34.615 0.00 0.00 0.00 4.70
2371 7389 9.745880 GACGAATTTTAGTTCTAGATACATCCA 57.254 33.333 0.00 0.00 0.00 3.41
2372 7390 9.968870 AGACGAATTTTAGTTCTAGATACATCC 57.031 33.333 0.00 0.00 0.00 3.51
2382 7400 9.968870 GGATGTATCTAGACGAATTTTAGTTCT 57.031 33.333 0.00 0.00 0.00 3.01
2383 7401 9.745880 TGGATGTATCTAGACGAATTTTAGTTC 57.254 33.333 0.00 0.00 0.00 3.01
2388 7406 9.057089 GGAAATGGATGTATCTAGACGAATTTT 57.943 33.333 0.00 0.00 0.00 1.82
2389 7407 7.661847 GGGAAATGGATGTATCTAGACGAATTT 59.338 37.037 0.00 0.00 0.00 1.82
2390 7408 7.162082 GGGAAATGGATGTATCTAGACGAATT 58.838 38.462 0.00 0.00 0.00 2.17
2391 7409 6.295916 GGGGAAATGGATGTATCTAGACGAAT 60.296 42.308 0.00 0.00 0.00 3.34
2392 7410 5.011738 GGGGAAATGGATGTATCTAGACGAA 59.988 44.000 0.00 0.00 0.00 3.85
2393 7411 4.527038 GGGGAAATGGATGTATCTAGACGA 59.473 45.833 0.00 0.00 0.00 4.20
2394 7412 4.618460 CGGGGAAATGGATGTATCTAGACG 60.618 50.000 0.00 0.00 0.00 4.18
2395 7413 4.527038 TCGGGGAAATGGATGTATCTAGAC 59.473 45.833 0.00 0.00 0.00 2.59
2396 7414 4.527038 GTCGGGGAAATGGATGTATCTAGA 59.473 45.833 0.00 0.00 0.00 2.43
2397 7415 4.283467 TGTCGGGGAAATGGATGTATCTAG 59.717 45.833 0.00 0.00 0.00 2.43
2398 7416 4.228010 TGTCGGGGAAATGGATGTATCTA 58.772 43.478 0.00 0.00 0.00 1.98
2399 7417 3.045634 TGTCGGGGAAATGGATGTATCT 58.954 45.455 0.00 0.00 0.00 1.98
2400 7418 3.485463 TGTCGGGGAAATGGATGTATC 57.515 47.619 0.00 0.00 0.00 2.24
2401 7419 3.202151 ACTTGTCGGGGAAATGGATGTAT 59.798 43.478 0.00 0.00 0.00 2.29
2402 7420 2.574369 ACTTGTCGGGGAAATGGATGTA 59.426 45.455 0.00 0.00 0.00 2.29
2403 7421 1.354368 ACTTGTCGGGGAAATGGATGT 59.646 47.619 0.00 0.00 0.00 3.06
2404 7422 2.128771 ACTTGTCGGGGAAATGGATG 57.871 50.000 0.00 0.00 0.00 3.51
2405 7423 4.519906 AATACTTGTCGGGGAAATGGAT 57.480 40.909 0.00 0.00 0.00 3.41
2406 7424 4.266714 GAAATACTTGTCGGGGAAATGGA 58.733 43.478 0.00 0.00 0.00 3.41
2407 7425 3.380320 GGAAATACTTGTCGGGGAAATGG 59.620 47.826 0.00 0.00 0.00 3.16
2408 7426 3.064820 CGGAAATACTTGTCGGGGAAATG 59.935 47.826 0.00 0.00 0.00 2.32
2409 7427 3.275999 CGGAAATACTTGTCGGGGAAAT 58.724 45.455 0.00 0.00 0.00 2.17
2410 7428 2.616001 CCGGAAATACTTGTCGGGGAAA 60.616 50.000 0.00 0.00 37.35 3.13
2411 7429 1.065998 CCGGAAATACTTGTCGGGGAA 60.066 52.381 0.00 0.00 37.35 3.97
2412 7430 0.538118 CCGGAAATACTTGTCGGGGA 59.462 55.000 0.00 0.00 37.35 4.81
2413 7431 0.538118 TCCGGAAATACTTGTCGGGG 59.462 55.000 0.00 0.00 40.92 5.73
2414 7432 1.648504 GTCCGGAAATACTTGTCGGG 58.351 55.000 5.23 0.00 40.92 5.14
2415 7433 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
2416 7434 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
2417 7435 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2418 7436 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2419 7437 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2420 7438 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2421 7439 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2422 7440 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2423 7441 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2424 7442 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2425 7443 0.251742 TTACTCCCTCCGTCCGGAAA 60.252 55.000 5.23 0.00 44.66 3.13
2426 7444 0.032813 ATTACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2427 7445 0.032813 AATTACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
2428 7446 0.388294 GAATTACTCCCTCCGTCCGG 59.612 60.000 0.00 0.00 0.00 5.14
2429 7447 1.067212 CAGAATTACTCCCTCCGTCCG 59.933 57.143 0.00 0.00 0.00 4.79
2430 7448 2.385803 TCAGAATTACTCCCTCCGTCC 58.614 52.381 0.00 0.00 0.00 4.79
2431 7449 3.700038 TCTTCAGAATTACTCCCTCCGTC 59.300 47.826 0.00 0.00 0.00 4.79
2432 7450 3.709587 TCTTCAGAATTACTCCCTCCGT 58.290 45.455 0.00 0.00 0.00 4.69
2433 7451 4.100189 ACATCTTCAGAATTACTCCCTCCG 59.900 45.833 0.00 0.00 0.00 4.63
2434 7452 5.622346 ACATCTTCAGAATTACTCCCTCC 57.378 43.478 0.00 0.00 0.00 4.30
2435 7453 6.883744 AGAACATCTTCAGAATTACTCCCTC 58.116 40.000 0.00 0.00 0.00 4.30
2436 7454 6.882768 AGAACATCTTCAGAATTACTCCCT 57.117 37.500 0.00 0.00 0.00 4.20
2437 7455 7.929941 AAAGAACATCTTCAGAATTACTCCC 57.070 36.000 0.00 0.00 35.27 4.30
2438 7456 8.884726 GGTAAAGAACATCTTCAGAATTACTCC 58.115 37.037 0.00 0.00 35.27 3.85
2439 7457 9.660180 AGGTAAAGAACATCTTCAGAATTACTC 57.340 33.333 0.00 0.00 35.27 2.59
2536 7554 4.376340 AACCAATAATACTTGCAGCAGC 57.624 40.909 0.00 0.00 42.57 5.25
2585 7606 6.514947 TGAATTTGTTTCCTCCAAATCAGTG 58.485 36.000 0.00 0.00 40.62 3.66
2593 7615 4.099266 CACCACTTGAATTTGTTTCCTCCA 59.901 41.667 0.00 0.00 33.04 3.86
2595 7617 5.043248 CACACCACTTGAATTTGTTTCCTC 58.957 41.667 0.00 0.00 33.04 3.71
2598 7620 4.754322 ACCACACCACTTGAATTTGTTTC 58.246 39.130 0.00 0.00 34.72 2.78
2599 7621 4.817318 ACCACACCACTTGAATTTGTTT 57.183 36.364 0.00 0.00 0.00 2.83
2707 7729 0.593128 CACCACCTCCAAGCTTTTCG 59.407 55.000 0.00 0.00 0.00 3.46
3381 8409 2.172483 ATCTCCGCCGTGAAGCTTGT 62.172 55.000 2.10 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.