Multiple sequence alignment - TraesCS3B01G173200

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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 TraesCS3B01G173200 chr3B 100.000 5468 0 0 1 5468 173376742 173382209 0.000000e+00 10098.0
1 TraesCS3B01G173200 chr3B 97.692 130 3 0 2272 2401 46285116 46285245 1.980000e-54 224.0
2 TraesCS3B01G173200 chr3B 89.362 47 4 1 5422 5468 749148632 749148587 2.130000e-04 58.4
3 TraesCS3B01G173200 chr3D 95.319 2286 79 12 1 2275 121885867 121888135 0.000000e+00 3603.0
4 TraesCS3B01G173200 chr3D 95.048 1878 65 6 2788 4656 121888883 121890741 0.000000e+00 2928.0
5 TraesCS3B01G173200 chr3D 92.784 388 19 6 2399 2786 121888134 121888512 2.230000e-153 553.0
6 TraesCS3B01G173200 chr3D 94.345 336 4 3 4651 4972 121908177 121908511 8.180000e-138 501.0
7 TraesCS3B01G173200 chr3D 94.161 274 11 2 4964 5233 121921830 121922102 3.940000e-111 412.0
8 TraesCS3B01G173200 chr3D 95.906 171 7 0 5271 5441 121922105 121922275 1.500000e-70 278.0
9 TraesCS3B01G173200 chr3D 96.212 132 5 0 2269 2400 11337920 11338051 3.320000e-52 217.0
10 TraesCS3B01G173200 chr3D 92.683 41 3 0 5428 5468 172830728 172830768 5.920000e-05 60.2
11 TraesCS3B01G173200 chr3A 94.134 2199 81 17 116 2275 128149212 128151401 0.000000e+00 3302.0
12 TraesCS3B01G173200 chr3A 95.635 1741 66 5 2788 4521 128152152 128153889 0.000000e+00 2785.0
13 TraesCS3B01G173200 chr3A 93.038 948 53 11 4519 5460 128153927 128154867 0.000000e+00 1373.0
14 TraesCS3B01G173200 chr3A 93.573 389 21 3 2399 2786 128151400 128151785 1.320000e-160 577.0
15 TraesCS3B01G173200 chr5D 99.219 128 1 0 2274 2401 29880185 29880312 1.180000e-56 231.0
16 TraesCS3B01G173200 chr5D 92.000 50 4 0 4032 4081 483063108 483063157 2.730000e-08 71.3
17 TraesCS3B01G173200 chr5D 97.059 34 1 0 9 42 51893678 51893711 2.130000e-04 58.4
18 TraesCS3B01G173200 chr7B 98.425 127 2 0 2274 2400 401136814 401136688 1.980000e-54 224.0
19 TraesCS3B01G173200 chr2B 95.714 140 4 2 2261 2400 134488807 134488670 1.980000e-54 224.0
20 TraesCS3B01G173200 chr2B 92.308 39 3 0 1 39 627326665 627326627 7.650000e-04 56.5
21 TraesCS3B01G173200 chr2B 100.000 29 0 0 1 29 432896808 432896780 3.000000e-03 54.7
22 TraesCS3B01G173200 chr4B 96.296 135 5 0 2274 2408 564161602 564161468 7.130000e-54 222.0
23 TraesCS3B01G173200 chr4B 93.706 143 9 0 2271 2413 413734179 413734321 1.190000e-51 215.0
24 TraesCS3B01G173200 chr4B 100.000 30 0 0 9 38 184302620 184302591 7.650000e-04 56.5
25 TraesCS3B01G173200 chr1B 96.241 133 5 0 2269 2401 54131180 54131312 9.220000e-53 219.0
26 TraesCS3B01G173200 chr1B 88.889 45 5 0 5424 5468 571173328 571173372 7.650000e-04 56.5
27 TraesCS3B01G173200 chr1A 94.891 137 5 2 2265 2400 574666417 574666552 4.290000e-51 213.0
28 TraesCS3B01G173200 chr1A 100.000 35 0 0 5434 5468 111540361 111540395 1.270000e-06 65.8
29 TraesCS3B01G173200 chr7A 97.436 39 0 1 1 38 634877750 634877712 1.270000e-06 65.8
30 TraesCS3B01G173200 chr1D 97.436 39 0 1 1 38 97132508 97132470 1.270000e-06 65.8
31 TraesCS3B01G173200 chr1D 97.222 36 1 0 5433 5468 455658248 455658283 1.640000e-05 62.1
32 TraesCS3B01G173200 chr1D 92.683 41 3 0 5428 5468 473933027 473932987 5.920000e-05 60.2
33 TraesCS3B01G173200 chr2A 94.872 39 1 1 5429 5467 550864907 550864944 5.920000e-05 60.2
34 TraesCS3B01G173200 chr2D 91.111 45 1 3 5427 5468 213059963 213060007 2.130000e-04 58.4
35 TraesCS3B01G173200 chr5B 96.970 33 1 0 6 38 304270712 304270744 7.650000e-04 56.5


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 TraesCS3B01G173200 chr3B 173376742 173382209 5467 False 10098.000000 10098 100.000000 1 5468 1 chr3B.!!$F2 5467
1 TraesCS3B01G173200 chr3D 121885867 121890741 4874 False 2361.333333 3603 94.383667 1 4656 3 chr3D.!!$F4 4655
2 TraesCS3B01G173200 chr3A 128149212 128154867 5655 False 2009.250000 3302 94.095000 116 5460 4 chr3A.!!$F1 5344

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
780 789 0.112412 AAACAGGGTGGGTGGTGATC 59.888 55.0 0.00 0.0 0.00 2.92 F
1496 1511 0.036306 AGAAGGTGGTTAGGGTTGCG 59.964 55.0 0.00 0.0 0.00 4.85 F
2290 2332 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.0 5.23 0.0 44.66 4.30 F
2291 2333 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.0 5.23 0.0 44.66 3.13 F
2295 2337 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.0 5.23 0.0 44.66 2.12 F
4093 4520 0.756294 TCAGCCCTCTGTTTGTCGAA 59.244 50.0 0.00 0.0 41.10 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2276 2318 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 R
2866 3286 0.107654 AATAACTCTGCGTGGCCTCC 60.108 55.000 3.32 0.00 0.00 4.30 R
3777 4204 0.478072 ATCACAGCCCACTTGACCAA 59.522 50.000 0.00 0.00 0.00 3.67 R
4093 4520 2.100989 GGGTAGACCTCATCAACGAGT 58.899 52.381 0.00 0.00 35.85 4.18 R
4159 4586 5.880332 GTGGTCTAGATACTTGAAATTGCCA 59.120 40.000 0.00 0.00 0.00 4.92 R
5355 5841 0.179100 TGCAGATCTTGGCTCTACGC 60.179 55.000 6.60 0.00 38.13 4.42 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
74 75 4.037446 TCCATGTAACACTTTCAGCCAAAC 59.963 41.667 0.00 0.00 0.00 2.93
80 81 5.606348 AACACTTTCAGCCAAACCATTTA 57.394 34.783 0.00 0.00 0.00 1.40
106 107 1.790818 ATCCTTCGGGGTAGGACTTC 58.209 55.000 0.00 0.00 44.25 3.01
166 173 6.098409 AGTGACCGATGGTAGAGAAAATGTAT 59.902 38.462 0.00 0.00 35.25 2.29
194 201 6.207691 TCCATATTTTAACTCTGCTTTGGC 57.792 37.500 0.00 0.00 39.26 4.52
311 318 2.368439 ACGTACGTACCTCCATTGCTA 58.632 47.619 21.41 0.00 0.00 3.49
392 399 1.274167 CACATCAAGCCTGCACCAAAT 59.726 47.619 0.00 0.00 0.00 2.32
429 436 8.893563 TCATTTATTTTTGGATAACCTCACCT 57.106 30.769 0.00 0.00 37.04 4.00
438 445 4.473196 TGGATAACCTCACCTGCAATTCTA 59.527 41.667 0.00 0.00 37.04 2.10
477 484 3.334583 TTGACCACTGTTAGATCCTGC 57.665 47.619 0.00 0.00 0.00 4.85
486 493 4.183865 CTGTTAGATCCTGCGATTTGTGA 58.816 43.478 0.00 0.00 0.00 3.58
508 515 5.300539 TGAGCATGCCAAACTACTTGTTTTA 59.699 36.000 15.66 0.00 45.69 1.52
645 652 8.543774 CAAAAGTTATAATTCTCTAGGCACTCG 58.456 37.037 0.00 0.00 41.75 4.18
713 722 2.639839 AGAGTGACCTTAACATGTGGCT 59.360 45.455 0.00 0.00 0.00 4.75
777 786 0.251165 CCTAAACAGGGTGGGTGGTG 60.251 60.000 0.00 0.00 0.00 4.17
779 788 1.354368 CTAAACAGGGTGGGTGGTGAT 59.646 52.381 0.00 0.00 0.00 3.06
780 789 0.112412 AAACAGGGTGGGTGGTGATC 59.888 55.000 0.00 0.00 0.00 2.92
1030 1044 2.030805 GCACCTCTTAAGTTGCACCTTG 60.031 50.000 6.78 0.00 0.00 3.61
1094 1109 4.758688 CATAATTCTTTGGGGTTCAAGGC 58.241 43.478 0.00 0.00 36.62 4.35
1105 1120 1.528076 TTCAAGGCGCACACATGGT 60.528 52.632 10.83 0.00 0.00 3.55
1193 1208 2.119495 CTAGGCCAGTACCATCACCTT 58.881 52.381 5.01 0.00 0.00 3.50
1241 1256 4.964897 TGTCCTAAGATCATCCAGACATGT 59.035 41.667 0.00 0.00 0.00 3.21
1260 1275 1.804151 GTTTGCGAGTGCCACAAGATA 59.196 47.619 0.00 0.00 41.78 1.98
1379 1394 2.420269 GGCAGGTAGTTTCCTAAGAGGC 60.420 54.545 0.00 0.00 35.87 4.70
1419 1434 0.174162 CCCTTTGCTATGTTGCCTGC 59.826 55.000 0.00 0.00 0.00 4.85
1421 1436 1.180029 CTTTGCTATGTTGCCTGCCT 58.820 50.000 0.00 0.00 0.00 4.75
1451 1466 7.856145 AGTAGAAACAAAGATCATGGTCATC 57.144 36.000 9.06 0.00 0.00 2.92
1496 1511 0.036306 AGAAGGTGGTTAGGGTTGCG 59.964 55.000 0.00 0.00 0.00 4.85
1680 1695 3.970640 GGAGGTGAAGATGATAAGAGGGT 59.029 47.826 0.00 0.00 0.00 4.34
1774 1789 1.039856 GGGTTTGGAAGCAGCTCAAA 58.960 50.000 5.38 5.38 0.00 2.69
1823 1838 0.246635 TCTCTCGGTGCAAGGTTAGC 59.753 55.000 0.00 0.00 0.00 3.09
2093 2114 9.865321 AAGTTATGTATGTTGTACATCGTACTT 57.135 29.630 25.75 22.83 39.88 2.24
2278 2320 8.910351 AATCAAGCACCTAAGAATAATACTCC 57.090 34.615 0.00 0.00 0.00 3.85
2279 2321 6.827727 TCAAGCACCTAAGAATAATACTCCC 58.172 40.000 0.00 0.00 0.00 4.30
2280 2322 6.615726 TCAAGCACCTAAGAATAATACTCCCT 59.384 38.462 0.00 0.00 0.00 4.20
2281 2323 6.673839 AGCACCTAAGAATAATACTCCCTC 57.326 41.667 0.00 0.00 0.00 4.30
2282 2324 5.544562 AGCACCTAAGAATAATACTCCCTCC 59.455 44.000 0.00 0.00 0.00 4.30
2283 2325 5.567025 GCACCTAAGAATAATACTCCCTCCG 60.567 48.000 0.00 0.00 0.00 4.63
2284 2326 5.539193 CACCTAAGAATAATACTCCCTCCGT 59.461 44.000 0.00 0.00 0.00 4.69
2285 2327 5.774184 ACCTAAGAATAATACTCCCTCCGTC 59.226 44.000 0.00 0.00 0.00 4.79
2286 2328 5.185442 CCTAAGAATAATACTCCCTCCGTCC 59.815 48.000 0.00 0.00 0.00 4.79
2287 2329 3.155501 AGAATAATACTCCCTCCGTCCG 58.844 50.000 0.00 0.00 0.00 4.79
2288 2330 1.920610 ATAATACTCCCTCCGTCCGG 58.079 55.000 0.00 0.00 0.00 5.14
2289 2331 0.846015 TAATACTCCCTCCGTCCGGA 59.154 55.000 0.00 0.00 42.90 5.14
2290 2332 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2291 2333 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2292 2334 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2293 2335 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2294 2336 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2295 2337 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2296 2338 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2297 2339 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2298 2340 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2299 2341 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2300 2342 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2301 2343 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2302 2344 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
2303 2345 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
2304 2346 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
2305 2347 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
2306 2348 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
2307 2349 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
2308 2350 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
2309 2351 6.657117 TCCGGAAATACTTGTCATCAAAATGA 59.343 34.615 0.00 0.00 39.63 2.57
2310 2352 7.175816 TCCGGAAATACTTGTCATCAAAATGAA 59.824 33.333 0.00 0.00 43.42 2.57
2311 2353 7.273381 CCGGAAATACTTGTCATCAAAATGAAC 59.727 37.037 0.00 0.00 43.42 3.18
2312 2354 7.807433 CGGAAATACTTGTCATCAAAATGAACA 59.193 33.333 0.00 0.00 43.42 3.18
2313 2355 9.474920 GGAAATACTTGTCATCAAAATGAACAA 57.525 29.630 0.00 0.00 43.42 2.83
2317 2359 7.775397 ACTTGTCATCAAAATGAACAAAAGG 57.225 32.000 0.87 0.00 43.42 3.11
2318 2360 6.762661 ACTTGTCATCAAAATGAACAAAAGGG 59.237 34.615 0.87 0.00 43.42 3.95
2319 2361 5.609423 TGTCATCAAAATGAACAAAAGGGG 58.391 37.500 0.00 0.00 43.42 4.79
2320 2362 5.365025 TGTCATCAAAATGAACAAAAGGGGA 59.635 36.000 0.00 0.00 43.42 4.81
2321 2363 6.043012 TGTCATCAAAATGAACAAAAGGGGAT 59.957 34.615 0.00 0.00 43.42 3.85
2322 2364 6.369615 GTCATCAAAATGAACAAAAGGGGATG 59.630 38.462 0.00 0.00 43.42 3.51
2323 2365 5.885449 TCAAAATGAACAAAAGGGGATGT 57.115 34.783 0.00 0.00 0.00 3.06
2324 2366 6.985653 TCAAAATGAACAAAAGGGGATGTA 57.014 33.333 0.00 0.00 0.00 2.29
2325 2367 7.552050 TCAAAATGAACAAAAGGGGATGTAT 57.448 32.000 0.00 0.00 0.00 2.29
2326 2368 7.610865 TCAAAATGAACAAAAGGGGATGTATC 58.389 34.615 0.00 0.00 0.00 2.24
2327 2369 7.454380 TCAAAATGAACAAAAGGGGATGTATCT 59.546 33.333 0.00 0.00 0.00 1.98
2328 2370 8.748412 CAAAATGAACAAAAGGGGATGTATCTA 58.252 33.333 0.00 0.00 0.00 1.98
2329 2371 8.525290 AAATGAACAAAAGGGGATGTATCTAG 57.475 34.615 0.00 0.00 0.00 2.43
2330 2372 6.884472 TGAACAAAAGGGGATGTATCTAGA 57.116 37.500 0.00 0.00 0.00 2.43
2331 2373 6.650120 TGAACAAAAGGGGATGTATCTAGAC 58.350 40.000 0.00 0.00 0.00 2.59
2332 2374 5.277857 ACAAAAGGGGATGTATCTAGACG 57.722 43.478 0.00 0.00 0.00 4.18
2333 2375 4.715297 ACAAAAGGGGATGTATCTAGACGT 59.285 41.667 0.00 0.00 0.00 4.34
2334 2376 5.895534 ACAAAAGGGGATGTATCTAGACGTA 59.104 40.000 0.00 0.00 0.00 3.57
2335 2377 6.553852 ACAAAAGGGGATGTATCTAGACGTAT 59.446 38.462 0.00 0.00 0.00 3.06
2336 2378 7.070821 ACAAAAGGGGATGTATCTAGACGTATT 59.929 37.037 0.00 0.00 0.00 1.89
2337 2379 7.613551 AAAGGGGATGTATCTAGACGTATTT 57.386 36.000 0.00 0.00 0.00 1.40
2338 2380 7.613551 AAGGGGATGTATCTAGACGTATTTT 57.386 36.000 0.00 0.00 0.00 1.82
2339 2381 8.716674 AAGGGGATGTATCTAGACGTATTTTA 57.283 34.615 0.00 0.00 0.00 1.52
2340 2382 8.350852 AGGGGATGTATCTAGACGTATTTTAG 57.649 38.462 0.00 0.00 0.00 1.85
2341 2383 7.949006 AGGGGATGTATCTAGACGTATTTTAGT 59.051 37.037 0.00 0.00 0.00 2.24
2342 2384 8.583296 GGGGATGTATCTAGACGTATTTTAGTT 58.417 37.037 0.00 0.00 0.00 2.24
2343 2385 9.978044 GGGATGTATCTAGACGTATTTTAGTTT 57.022 33.333 0.00 0.00 0.00 2.66
2387 2429 8.741101 TTCATTTTGATGACAAGTATTTTCGG 57.259 30.769 0.00 0.00 37.32 4.30
2388 2430 8.105097 TCATTTTGATGACAAGTATTTTCGGA 57.895 30.769 0.00 0.00 37.32 4.55
2389 2431 8.020819 TCATTTTGATGACAAGTATTTTCGGAC 58.979 33.333 0.00 0.00 37.32 4.79
2390 2432 5.524511 TTGATGACAAGTATTTTCGGACG 57.475 39.130 0.00 0.00 0.00 4.79
2391 2433 3.930229 TGATGACAAGTATTTTCGGACGG 59.070 43.478 0.00 0.00 0.00 4.79
2392 2434 3.663995 TGACAAGTATTTTCGGACGGA 57.336 42.857 0.00 0.00 0.00 4.69
2393 2435 3.581755 TGACAAGTATTTTCGGACGGAG 58.418 45.455 0.00 0.00 0.00 4.63
2394 2436 2.928116 GACAAGTATTTTCGGACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2395 2437 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2396 2438 1.856629 AGTATTTTCGGACGGAGGGA 58.143 50.000 0.00 0.00 0.00 4.20
2397 2439 1.755380 AGTATTTTCGGACGGAGGGAG 59.245 52.381 0.00 0.00 0.00 4.30
2398 2440 1.479730 GTATTTTCGGACGGAGGGAGT 59.520 52.381 0.00 0.00 0.00 3.85
2399 2441 1.856629 ATTTTCGGACGGAGGGAGTA 58.143 50.000 0.00 0.00 0.00 2.59
2471 2513 4.347360 TGCAGCTAAGCATGACTATCAT 57.653 40.909 0.00 0.00 40.11 2.45
2542 2584 2.338577 AGCTGTGCAGTTCTTGTCTT 57.661 45.000 0.00 0.00 0.00 3.01
2580 2622 4.672251 CCTCCTGGCATCTTTGGG 57.328 61.111 0.00 0.00 0.00 4.12
2618 2660 7.936847 ACACAAGTTAGGTAGACATTTGAATCA 59.063 33.333 0.00 0.00 0.00 2.57
2623 2665 7.604164 AGTTAGGTAGACATTTGAATCACACTG 59.396 37.037 0.00 0.00 0.00 3.66
2636 2678 3.469008 TCACACTGGTGGTAGTTGAAG 57.531 47.619 5.70 0.00 45.32 3.02
2665 2707 7.202093 CCCATGAAAAGGTACAGAGGTATGATA 60.202 40.741 0.00 0.00 0.00 2.15
2681 2723 7.675062 AGGTATGATATGTTGAGATGGAGAAC 58.325 38.462 0.00 0.00 0.00 3.01
2682 2724 7.290948 AGGTATGATATGTTGAGATGGAGAACA 59.709 37.037 0.00 0.00 34.25 3.18
2701 2743 6.681777 AGAACATGTGCTTGGAAATCTTAAC 58.318 36.000 0.00 0.00 0.00 2.01
2704 2751 7.054491 ACATGTGCTTGGAAATCTTAACTTT 57.946 32.000 0.00 0.00 0.00 2.66
2747 2794 5.521735 AGAATACTTCATGCATGTCTCGTTC 59.478 40.000 25.43 21.71 0.00 3.95
2754 2801 4.934602 TCATGCATGTCTCGTTCACAATAA 59.065 37.500 25.43 0.00 0.00 1.40
2758 2805 5.107104 TGCATGTCTCGTTCACAATAACTTC 60.107 40.000 0.00 0.00 0.00 3.01
2786 2833 4.826274 AGCTAAGCTCATGTCAAGGTTA 57.174 40.909 4.93 4.93 30.62 2.85
2866 3286 3.326297 ACCAGGAAGAGAAAGACAGGAAG 59.674 47.826 0.00 0.00 0.00 3.46
2914 3334 9.690913 ATAAATTACTTCACCTTAGTTTACCCC 57.309 33.333 0.00 0.00 0.00 4.95
2953 3373 5.633830 AATGATCACCTTGTGCAAGTTAG 57.366 39.130 0.00 0.00 36.72 2.34
2973 3393 3.956744 AGTTAGAAATGGCTTCCTCACC 58.043 45.455 0.00 0.00 34.21 4.02
3030 3450 9.971922 CTTGTTGTTTGGAAGAAGATAATTCTT 57.028 29.630 2.63 2.63 44.99 2.52
3032 3452 9.965824 TGTTGTTTGGAAGAAGATAATTCTTTC 57.034 29.630 4.49 3.37 42.34 2.62
3056 3476 9.965824 TTCTTCACTTTCAACAGAATTAATTCC 57.034 29.630 21.86 6.98 37.51 3.01
3060 3480 8.141268 TCACTTTCAACAGAATTAATTCCAACC 58.859 33.333 21.86 0.56 37.51 3.77
3070 3490 8.562892 CAGAATTAATTCCAACCAGCTATACAG 58.437 37.037 21.86 0.00 37.51 2.74
3193 3613 4.475016 AGTCTTATGTATGCTCCCTTGGTT 59.525 41.667 0.00 0.00 0.00 3.67
3200 3620 4.721776 TGTATGCTCCCTTGGTTAAGAGAT 59.278 41.667 0.00 0.00 35.92 2.75
3225 3645 9.811995 ATACATAGCTCGTAAAACAGTAAATCA 57.188 29.630 0.00 0.00 0.00 2.57
3291 3711 6.872920 AGATTACCTTCTGTTGTTTGCAAAA 58.127 32.000 14.67 1.61 36.22 2.44
3397 3819 5.201181 CGTTGAGAAAGTTTCTTCAGCTTC 58.799 41.667 18.96 5.80 40.87 3.86
3407 3829 3.297830 TCTTCAGCTTCGTCGATTTGA 57.702 42.857 0.00 0.00 0.00 2.69
3427 3849 8.911247 ATTTGAACTTTGTTGTACTTCAGTTC 57.089 30.769 12.91 12.91 36.10 3.01
3445 3867 5.049398 AGTTCGCAAACTGTTGTTTACAA 57.951 34.783 0.00 0.00 44.13 2.41
3456 3878 5.240844 ACTGTTGTTTACAAGGTGAATAGGC 59.759 40.000 0.00 0.00 36.02 3.93
3727 4154 5.171476 CCATATTCTATCTCCGTCGCAATT 58.829 41.667 0.00 0.00 0.00 2.32
3769 4196 1.447838 CCGGGTCATCAACTCACCG 60.448 63.158 0.00 0.00 40.89 4.94
3777 4204 0.984230 ATCAACTCACCGGTCCACAT 59.016 50.000 2.59 0.00 0.00 3.21
3943 4370 2.287069 CCGTGTAAGTGAGCTCCTATCG 60.287 54.545 12.15 6.96 0.00 2.92
4093 4520 0.756294 TCAGCCCTCTGTTTGTCGAA 59.244 50.000 0.00 0.00 41.10 3.71
4159 4586 1.227853 GTTTCACGGCACCTCCACT 60.228 57.895 0.00 0.00 34.01 4.00
4415 4844 5.062809 GCTGATACAAAGCAGTGAAGTCTAC 59.937 44.000 0.00 0.00 41.33 2.59
4515 4944 9.793252 CTTATAGATTGCTTTTAAGTTGTGCAT 57.207 29.630 0.00 0.00 33.50 3.96
4712 5195 8.911918 TTTAAATAGCCTAAACACAGAGAACA 57.088 30.769 0.00 0.00 0.00 3.18
4713 5196 9.515226 TTTAAATAGCCTAAACACAGAGAACAT 57.485 29.630 0.00 0.00 0.00 2.71
4714 5197 9.515226 TTAAATAGCCTAAACACAGAGAACATT 57.485 29.630 0.00 0.00 0.00 2.71
4715 5198 8.409358 AAATAGCCTAAACACAGAGAACATTT 57.591 30.769 0.00 0.00 0.00 2.32
4716 5199 9.515226 AAATAGCCTAAACACAGAGAACATTTA 57.485 29.630 0.00 0.00 0.00 1.40
4717 5200 6.803154 AGCCTAAACACAGAGAACATTTAC 57.197 37.500 0.00 0.00 0.00 2.01
4718 5201 6.296026 AGCCTAAACACAGAGAACATTTACA 58.704 36.000 0.00 0.00 0.00 2.41
4719 5202 6.942576 AGCCTAAACACAGAGAACATTTACAT 59.057 34.615 0.00 0.00 0.00 2.29
4720 5203 8.100791 AGCCTAAACACAGAGAACATTTACATA 58.899 33.333 0.00 0.00 0.00 2.29
4721 5204 8.893727 GCCTAAACACAGAGAACATTTACATAT 58.106 33.333 0.00 0.00 0.00 1.78
4727 5210 9.330063 ACACAGAGAACATTTACATATGTATGG 57.670 33.333 16.16 10.91 37.76 2.74
4756 5239 7.967890 AATGGGACTTCAAATTCAAAATGTC 57.032 32.000 0.00 0.00 0.00 3.06
4784 5267 5.701290 AGAGCAACCATACTTACTGAACAAC 59.299 40.000 0.00 0.00 0.00 3.32
4795 5278 4.083600 GAACAACGCATCGCCGCA 62.084 61.111 0.00 0.00 0.00 5.69
4873 5356 8.046708 TGCTTTCTTCCAGCTTATACTGATTAA 58.953 33.333 0.00 0.00 40.25 1.40
4932 5415 3.750130 ACAGCTGATATCAATTCCGATGC 59.250 43.478 23.35 4.15 0.00 3.91
5050 5533 3.325716 AGCAAAATGAGAAGGCCAAATGT 59.674 39.130 5.01 0.00 0.00 2.71
5066 5549 4.643387 GTGGACCCCGCTGTGCTT 62.643 66.667 0.00 0.00 0.00 3.91
5131 5614 6.434340 AGGAAACTGTTGACCAATATCTTTCC 59.566 38.462 15.75 14.33 41.13 3.13
5157 5640 5.233476 TGTGTTTCTTACTGTAAGCACTTCG 59.767 40.000 24.24 6.44 37.60 3.79
5188 5671 5.762711 TGCTTAAGCTGAAACATACTTGTGA 59.237 36.000 26.90 0.00 42.66 3.58
5191 5674 8.616076 GCTTAAGCTGAAACATACTTGTGATAT 58.384 33.333 20.38 0.00 35.49 1.63
5194 5677 8.798859 AAGCTGAAACATACTTGTGATATTCT 57.201 30.769 0.00 0.00 35.83 2.40
5195 5678 8.798859 AGCTGAAACATACTTGTGATATTCTT 57.201 30.769 0.00 0.00 35.83 2.52
5229 5715 3.993081 CAGAGTAGCTTGGTTCTGAACAG 59.007 47.826 21.01 12.20 39.46 3.16
5245 5731 8.421784 GTTCTGAACAGGTACTATATCCATCAA 58.578 37.037 15.34 0.00 36.02 2.57
5253 5739 6.792473 AGGTACTATATCCATCAACATCCCAA 59.208 38.462 0.00 0.00 36.02 4.12
5261 5747 3.284617 CATCAACATCCCAATCTCTGCA 58.715 45.455 0.00 0.00 0.00 4.41
5277 5763 2.694628 TCTGCAAGTGTTTTGCTCCAAT 59.305 40.909 12.45 0.00 45.13 3.16
5292 5778 7.421087 TTGCTCCAATTAATGAATCATCCAA 57.579 32.000 0.00 0.00 0.00 3.53
5312 5798 4.568152 AAGCACAACTTGACCATGTAAC 57.432 40.909 0.00 0.00 37.17 2.50
5315 5801 3.058224 GCACAACTTGACCATGTAACTCC 60.058 47.826 0.00 0.00 0.00 3.85
5330 5816 7.415541 CCATGTAACTCCGAAAACATCATGAAT 60.416 37.037 0.00 0.00 34.14 2.57
5344 5830 7.096884 ACATCATGAATGAAATCAGTTCCAG 57.903 36.000 0.00 0.00 40.69 3.86
5355 5841 2.429478 TCAGTTCCAGTGTCATGCATG 58.571 47.619 21.07 21.07 0.00 4.06
5393 5879 2.754552 GCAATACCTCATCTGCCAAACA 59.245 45.455 0.00 0.00 0.00 2.83
5396 5882 5.163513 CAATACCTCATCTGCCAAACAAAC 58.836 41.667 0.00 0.00 0.00 2.93
5400 5886 3.068590 CCTCATCTGCCAAACAAACTTGT 59.931 43.478 0.00 0.00 44.72 3.16
5451 5937 7.609056 TGTGTTAAAGTTATACTCCCTCTGTC 58.391 38.462 0.00 0.00 0.00 3.51
5455 5941 4.561254 AGTTATACTCCCTCTGTCCCAT 57.439 45.455 0.00 0.00 0.00 4.00
5460 5946 8.410623 AGTTATACTCCCTCTGTCCCATAATAT 58.589 37.037 0.00 0.00 0.00 1.28
5461 5947 9.710818 GTTATACTCCCTCTGTCCCATAATATA 57.289 37.037 0.00 0.00 0.00 0.86
5463 5949 8.846423 ATACTCCCTCTGTCCCATAATATAAG 57.154 38.462 0.00 0.00 0.00 1.73
5464 5950 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
5465 5951 7.313731 ACTCCCTCTGTCCCATAATATAAGAA 58.686 38.462 0.00 0.00 0.00 2.52
5466 5952 7.235812 ACTCCCTCTGTCCCATAATATAAGAAC 59.764 40.741 0.00 0.00 0.00 3.01
5467 5953 6.210784 TCCCTCTGTCCCATAATATAAGAACG 59.789 42.308 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 173 7.408756 AAGCAGAGTTAAAATATGGATTGCA 57.591 32.000 0.00 0.00 0.00 4.08
203 210 9.874205 CATGGGTTCATAAAGTAATTTGACAAT 57.126 29.630 0.00 0.00 31.33 2.71
204 211 8.865090 ACATGGGTTCATAAAGTAATTTGACAA 58.135 29.630 0.00 0.00 31.33 3.18
205 212 8.303156 CACATGGGTTCATAAAGTAATTTGACA 58.697 33.333 0.00 0.00 31.33 3.58
304 311 6.426328 CCTCTCACCTAAAAGCTATAGCAATG 59.574 42.308 26.07 12.49 45.16 2.82
311 318 4.024670 ACGACCTCTCACCTAAAAGCTAT 58.975 43.478 0.00 0.00 0.00 2.97
412 419 3.517296 TGCAGGTGAGGTTATCCAAAA 57.483 42.857 0.00 0.00 35.89 2.44
413 420 3.517296 TTGCAGGTGAGGTTATCCAAA 57.483 42.857 0.00 0.00 35.89 3.28
416 423 3.891049 AGAATTGCAGGTGAGGTTATCC 58.109 45.455 0.00 0.00 0.00 2.59
423 430 3.616956 TCTGGTAGAATTGCAGGTGAG 57.383 47.619 0.00 0.00 0.00 3.51
429 436 5.129634 TGTCTTTGTTCTGGTAGAATTGCA 58.870 37.500 0.00 0.00 36.50 4.08
438 445 3.890756 TCAATGCATGTCTTTGTTCTGGT 59.109 39.130 0.00 0.00 33.15 4.00
477 484 1.987770 GTTTGGCATGCTCACAAATCG 59.012 47.619 18.92 0.00 36.60 3.34
529 536 2.438951 TTTGACCTCACGGCCCGTAC 62.439 60.000 9.25 0.00 38.32 3.67
533 540 1.002624 TGATTTGACCTCACGGCCC 60.003 57.895 0.00 0.00 0.00 5.80
549 556 5.392272 GCATGAGTGTTTGCTATTGATGTGA 60.392 40.000 0.00 0.00 35.95 3.58
637 644 9.550406 GTATCTCTATATATACTTCGAGTGCCT 57.450 37.037 6.62 0.00 0.00 4.75
713 722 6.319152 TGTTGACTAAGATTTTTCACCGGAAA 59.681 34.615 9.46 0.00 41.13 3.13
777 786 8.576281 CGATAGTAAGCGTAAATATGTGTGATC 58.424 37.037 0.00 0.00 0.00 2.92
779 788 7.847166 CGATAGTAAGCGTAAATATGTGTGA 57.153 36.000 0.00 0.00 0.00 3.58
1030 1044 6.194796 TCTAGTTTATTTGATGCAGGTTGC 57.805 37.500 0.00 0.00 45.29 4.17
1094 1109 2.058057 GGCTTTAAAACCATGTGTGCG 58.942 47.619 2.65 0.00 0.00 5.34
1105 1120 4.530553 GGGATTTGGAGAAGGGCTTTAAAA 59.469 41.667 0.00 0.00 0.00 1.52
1193 1208 0.104855 ATATGCCGCTCGAGCTTTGA 59.895 50.000 32.88 15.64 39.32 2.69
1241 1256 2.177394 TATCTTGTGGCACTCGCAAA 57.823 45.000 19.83 3.07 44.19 3.68
1379 1394 4.464597 GGGTAGAGGCATAGTAGGATGAAG 59.535 50.000 0.00 0.00 0.00 3.02
1419 1434 7.969536 TGATCTTTGTTTCTACTTCTTGAGG 57.030 36.000 0.00 0.00 0.00 3.86
1421 1436 7.939039 ACCATGATCTTTGTTTCTACTTCTTGA 59.061 33.333 0.00 0.00 0.00 3.02
1451 1466 0.881159 TTAACCCCACGAAGCACACG 60.881 55.000 0.00 0.00 0.00 4.49
1680 1695 6.782988 TCCTTTCCCAATAAACCAACATAACA 59.217 34.615 0.00 0.00 0.00 2.41
1774 1789 7.443575 GCTGGTGATGATCATAGTCAAAATAGT 59.556 37.037 8.54 0.00 0.00 2.12
1912 1929 5.520376 AAAGTTGCAGCAGAAAAGTATGT 57.480 34.783 2.55 0.00 0.00 2.29
2237 2277 7.816031 GGTGCTTGATTTTTATATCATCCATGG 59.184 37.037 4.97 4.97 34.67 3.66
2275 2317 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2276 2318 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2277 2319 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2278 2320 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2279 2321 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2280 2322 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2281 2323 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2282 2324 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
2283 2325 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
2284 2326 6.657117 TCATTTTGATGACAAGTATTTCCGGA 59.343 34.615 0.00 0.00 37.32 5.14
2285 2327 6.851609 TCATTTTGATGACAAGTATTTCCGG 58.148 36.000 0.00 0.00 37.32 5.14
2286 2328 7.807433 TGTTCATTTTGATGACAAGTATTTCCG 59.193 33.333 0.00 0.00 37.32 4.30
2287 2329 9.474920 TTGTTCATTTTGATGACAAGTATTTCC 57.525 29.630 0.00 0.00 37.32 3.13
2291 2333 9.480053 CCTTTTGTTCATTTTGATGACAAGTAT 57.520 29.630 0.00 0.00 37.32 2.12
2292 2334 7.925483 CCCTTTTGTTCATTTTGATGACAAGTA 59.075 33.333 0.00 0.00 37.32 2.24
2293 2335 6.762661 CCCTTTTGTTCATTTTGATGACAAGT 59.237 34.615 0.00 0.00 37.32 3.16
2294 2336 6.203338 CCCCTTTTGTTCATTTTGATGACAAG 59.797 38.462 0.00 0.00 37.32 3.16
2295 2337 6.054295 CCCCTTTTGTTCATTTTGATGACAA 58.946 36.000 0.00 0.00 0.00 3.18
2296 2338 5.365025 TCCCCTTTTGTTCATTTTGATGACA 59.635 36.000 0.00 0.00 0.00 3.58
2297 2339 5.852827 TCCCCTTTTGTTCATTTTGATGAC 58.147 37.500 0.00 0.00 0.00 3.06
2298 2340 6.043012 ACATCCCCTTTTGTTCATTTTGATGA 59.957 34.615 0.00 0.00 32.39 2.92
2299 2341 6.232692 ACATCCCCTTTTGTTCATTTTGATG 58.767 36.000 0.00 0.00 33.80 3.07
2300 2342 6.438186 ACATCCCCTTTTGTTCATTTTGAT 57.562 33.333 0.00 0.00 0.00 2.57
2301 2343 5.885449 ACATCCCCTTTTGTTCATTTTGA 57.115 34.783 0.00 0.00 0.00 2.69
2302 2344 7.614494 AGATACATCCCCTTTTGTTCATTTTG 58.386 34.615 0.00 0.00 0.00 2.44
2303 2345 7.797121 AGATACATCCCCTTTTGTTCATTTT 57.203 32.000 0.00 0.00 0.00 1.82
2304 2346 8.336235 TCTAGATACATCCCCTTTTGTTCATTT 58.664 33.333 0.00 0.00 0.00 2.32
2305 2347 7.775561 GTCTAGATACATCCCCTTTTGTTCATT 59.224 37.037 0.00 0.00 0.00 2.57
2306 2348 7.283329 GTCTAGATACATCCCCTTTTGTTCAT 58.717 38.462 0.00 0.00 0.00 2.57
2307 2349 6.629515 CGTCTAGATACATCCCCTTTTGTTCA 60.630 42.308 0.00 0.00 0.00 3.18
2308 2350 5.753921 CGTCTAGATACATCCCCTTTTGTTC 59.246 44.000 0.00 0.00 0.00 3.18
2309 2351 5.189145 ACGTCTAGATACATCCCCTTTTGTT 59.811 40.000 0.00 0.00 0.00 2.83
2310 2352 4.715297 ACGTCTAGATACATCCCCTTTTGT 59.285 41.667 0.00 0.00 0.00 2.83
2311 2353 5.277857 ACGTCTAGATACATCCCCTTTTG 57.722 43.478 0.00 0.00 0.00 2.44
2312 2354 7.613551 AATACGTCTAGATACATCCCCTTTT 57.386 36.000 0.00 0.00 0.00 2.27
2313 2355 7.613551 AAATACGTCTAGATACATCCCCTTT 57.386 36.000 0.00 0.00 0.00 3.11
2314 2356 7.613551 AAAATACGTCTAGATACATCCCCTT 57.386 36.000 0.00 0.00 0.00 3.95
2315 2357 7.949006 ACTAAAATACGTCTAGATACATCCCCT 59.051 37.037 0.00 0.00 0.00 4.79
2316 2358 8.120140 ACTAAAATACGTCTAGATACATCCCC 57.880 38.462 0.00 0.00 0.00 4.81
2317 2359 9.978044 AAACTAAAATACGTCTAGATACATCCC 57.022 33.333 0.00 0.00 0.00 3.85
2361 2403 9.357652 CCGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
2362 2404 8.572185 TCCGAAAATACTTGTCATCAAAATGAA 58.428 29.630 0.00 0.00 43.42 2.57
2363 2405 8.020819 GTCCGAAAATACTTGTCATCAAAATGA 58.979 33.333 0.00 0.00 39.63 2.57
2364 2406 7.007367 CGTCCGAAAATACTTGTCATCAAAATG 59.993 37.037 0.00 0.00 32.87 2.32
2365 2407 7.021196 CGTCCGAAAATACTTGTCATCAAAAT 58.979 34.615 0.00 0.00 32.87 1.82
2366 2408 6.367421 CGTCCGAAAATACTTGTCATCAAAA 58.633 36.000 0.00 0.00 32.87 2.44
2367 2409 5.106869 CCGTCCGAAAATACTTGTCATCAAA 60.107 40.000 0.00 0.00 32.87 2.69
2368 2410 4.390603 CCGTCCGAAAATACTTGTCATCAA 59.609 41.667 0.00 0.00 0.00 2.57
2369 2411 3.930229 CCGTCCGAAAATACTTGTCATCA 59.070 43.478 0.00 0.00 0.00 3.07
2370 2412 4.178540 TCCGTCCGAAAATACTTGTCATC 58.821 43.478 0.00 0.00 0.00 2.92
2371 2413 4.181578 CTCCGTCCGAAAATACTTGTCAT 58.818 43.478 0.00 0.00 0.00 3.06
2372 2414 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
2373 2415 2.928116 CCTCCGTCCGAAAATACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2374 2416 2.354403 CCCTCCGTCCGAAAATACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2375 2417 2.093869 TCCCTCCGTCCGAAAATACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2376 2418 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
2377 2419 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
2378 2420 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
2379 2421 1.856629 ACTCCCTCCGTCCGAAAATA 58.143 50.000 0.00 0.00 0.00 1.40
2380 2422 1.856629 TACTCCCTCCGTCCGAAAAT 58.143 50.000 0.00 0.00 0.00 1.82
2381 2423 1.479323 CATACTCCCTCCGTCCGAAAA 59.521 52.381 0.00 0.00 0.00 2.29
2382 2424 1.108776 CATACTCCCTCCGTCCGAAA 58.891 55.000 0.00 0.00 0.00 3.46
2383 2425 0.256752 TCATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
2384 2426 0.179026 CTCATACTCCCTCCGTCCGA 60.179 60.000 0.00 0.00 0.00 4.55
2385 2427 1.797211 GCTCATACTCCCTCCGTCCG 61.797 65.000 0.00 0.00 0.00 4.79
2386 2428 1.465200 GGCTCATACTCCCTCCGTCC 61.465 65.000 0.00 0.00 0.00 4.79
2387 2429 0.755698 TGGCTCATACTCCCTCCGTC 60.756 60.000 0.00 0.00 0.00 4.79
2388 2430 0.325296 TTGGCTCATACTCCCTCCGT 60.325 55.000 0.00 0.00 0.00 4.69
2389 2431 0.830648 TTTGGCTCATACTCCCTCCG 59.169 55.000 0.00 0.00 0.00 4.63
2390 2432 1.141858 CCTTTGGCTCATACTCCCTCC 59.858 57.143 0.00 0.00 0.00 4.30
2391 2433 1.840635 ACCTTTGGCTCATACTCCCTC 59.159 52.381 0.00 0.00 0.00 4.30
2392 2434 1.972588 ACCTTTGGCTCATACTCCCT 58.027 50.000 0.00 0.00 0.00 4.20
2393 2435 2.808906 AACCTTTGGCTCATACTCCC 57.191 50.000 0.00 0.00 0.00 4.30
2394 2436 4.443621 GACTAACCTTTGGCTCATACTCC 58.556 47.826 0.00 0.00 0.00 3.85
2395 2437 4.113354 CGACTAACCTTTGGCTCATACTC 58.887 47.826 0.00 0.00 0.00 2.59
2396 2438 3.514309 ACGACTAACCTTTGGCTCATACT 59.486 43.478 0.00 0.00 0.00 2.12
2397 2439 3.858247 ACGACTAACCTTTGGCTCATAC 58.142 45.455 0.00 0.00 0.00 2.39
2398 2440 4.020928 TGAACGACTAACCTTTGGCTCATA 60.021 41.667 0.00 0.00 0.00 2.15
2399 2441 3.244422 TGAACGACTAACCTTTGGCTCAT 60.244 43.478 0.00 0.00 0.00 2.90
2494 2536 6.995686 TGGAGTTAAATAAGACAAGAACTGCA 59.004 34.615 3.12 3.12 41.16 4.41
2542 2584 6.072064 GGAGGCTAGCTACATCGAGTTAAATA 60.072 42.308 15.72 0.00 0.00 1.40
2580 2622 6.456501 ACCTAACTTGTGTGAGTAAGATGTC 58.543 40.000 0.00 0.00 0.00 3.06
2618 2660 1.202770 GCCTTCAACTACCACCAGTGT 60.203 52.381 0.00 0.00 0.00 3.55
2623 2665 1.001269 GGGGCCTTCAACTACCACC 60.001 63.158 0.84 0.00 0.00 4.61
2636 2678 1.005450 TCTGTACCTTTTCATGGGGCC 59.995 52.381 0.00 0.00 0.00 5.80
2665 2707 3.693085 GCACATGTTCTCCATCTCAACAT 59.307 43.478 0.00 0.00 40.61 2.71
2681 2723 9.474920 TTTAAAGTTAAGATTTCCAAGCACATG 57.525 29.630 0.00 0.00 0.00 3.21
2731 2778 2.453983 TGTGAACGAGACATGCATGA 57.546 45.000 32.75 4.93 0.00 3.07
2732 2779 3.752412 ATTGTGAACGAGACATGCATG 57.248 42.857 25.09 25.09 0.00 4.06
2747 2794 7.883073 CTTAGCTAATTGCGAAGTTATTGTG 57.117 36.000 6.64 0.00 45.32 3.33
2786 2833 4.334759 GCATACATTGTCTTGTGATGAGCT 59.665 41.667 0.00 0.00 0.00 4.09
2866 3286 0.107654 AATAACTCTGCGTGGCCTCC 60.108 55.000 3.32 0.00 0.00 4.30
2899 3319 4.721132 TCAAGTTGGGGTAAACTAAGGTG 58.279 43.478 2.34 0.00 39.48 4.00
2953 3373 3.686016 TGGTGAGGAAGCCATTTCTAAC 58.314 45.455 0.00 0.00 36.03 2.34
3030 3450 9.965824 GGAATTAATTCTGTTGAAAGTGAAGAA 57.034 29.630 23.85 0.00 37.00 2.52
3032 3452 9.748708 TTGGAATTAATTCTGTTGAAAGTGAAG 57.251 29.630 23.85 0.00 37.00 3.02
3042 3462 7.961326 ATAGCTGGTTGGAATTAATTCTGTT 57.039 32.000 23.85 10.44 37.00 3.16
3044 3464 8.450578 TGTATAGCTGGTTGGAATTAATTCTG 57.549 34.615 23.85 10.93 37.00 3.02
3056 3476 5.174395 GCATATCTCCTGTATAGCTGGTTG 58.826 45.833 0.00 0.00 37.45 3.77
3060 3480 7.734924 TTTTTGCATATCTCCTGTATAGCTG 57.265 36.000 0.00 0.00 0.00 4.24
3116 3536 5.010617 TGCCCCTAAATTTTGACAGAAGTTC 59.989 40.000 0.00 0.00 0.00 3.01
3124 3544 7.875327 TCTAATACTGCCCCTAAATTTTGAC 57.125 36.000 0.00 0.00 0.00 3.18
3152 3572 9.270640 CATAAGACTAATCCTTTCATCCTGAAG 57.729 37.037 0.00 0.00 37.70 3.02
3154 3574 8.324191 ACATAAGACTAATCCTTTCATCCTGA 57.676 34.615 0.00 0.00 0.00 3.86
3158 3578 9.717942 AGCATACATAAGACTAATCCTTTCATC 57.282 33.333 0.00 0.00 0.00 2.92
3193 3613 8.900781 ACTGTTTTACGAGCTATGTATCTCTTA 58.099 33.333 0.00 0.00 0.00 2.10
3200 3620 9.811995 ATGATTTACTGTTTTACGAGCTATGTA 57.188 29.630 0.00 0.00 0.00 2.29
3291 3711 8.928448 TGTAGAGTCCAGAATTCTATAAGCAAT 58.072 33.333 7.86 0.00 0.00 3.56
3360 3782 7.222161 ACTTTCTCAACGTAGGAGGTAAATTT 58.778 34.615 14.90 0.00 33.18 1.82
3370 3792 5.333416 GCTGAAGAAACTTTCTCAACGTAGG 60.333 44.000 4.46 0.00 39.61 3.18
3375 3797 5.201181 CGAAGCTGAAGAAACTTTCTCAAC 58.799 41.667 4.46 1.72 39.61 3.18
3397 3819 5.734311 AGTACAACAAAGTTCAAATCGACG 58.266 37.500 0.00 0.00 0.00 5.12
3407 3829 4.393680 TGCGAACTGAAGTACAACAAAGTT 59.606 37.500 0.00 0.00 0.00 2.66
3427 3849 3.545873 CACCTTGTAAACAACAGTTTGCG 59.454 43.478 4.02 0.00 39.67 4.85
3445 3867 2.027561 TGTACGCTTTGCCTATTCACCT 60.028 45.455 0.00 0.00 0.00 4.00
3456 3878 1.402720 CCCAATGGCTTGTACGCTTTG 60.403 52.381 0.00 0.00 0.00 2.77
3727 4154 2.696707 CGTTACTCCTATTACAGCCCCA 59.303 50.000 0.00 0.00 0.00 4.96
3777 4204 0.478072 ATCACAGCCCACTTGACCAA 59.522 50.000 0.00 0.00 0.00 3.67
4093 4520 2.100989 GGGTAGACCTCATCAACGAGT 58.899 52.381 0.00 0.00 35.85 4.18
4159 4586 5.880332 GTGGTCTAGATACTTGAAATTGCCA 59.120 40.000 0.00 0.00 0.00 4.92
4415 4844 3.120546 CCAGCAACGTCTTATGTTCACAG 60.121 47.826 0.00 0.00 0.00 3.66
4515 4944 7.608761 GGTCCAACAAAGGTAGTCATAACATTA 59.391 37.037 0.00 0.00 0.00 1.90
4589 5058 9.762062 CTGACTAATACATAACGAGCATACTAG 57.238 37.037 0.00 0.00 0.00 2.57
4756 5239 4.045104 CAGTAAGTATGGTTGCTCTAGCG 58.955 47.826 0.00 0.00 45.83 4.26
4784 5267 3.406361 GGATACTGCGGCGATGCG 61.406 66.667 12.98 0.00 37.81 4.73
4795 5278 0.465705 CTGGTGGTCGCATGGATACT 59.534 55.000 0.00 0.00 37.61 2.12
5050 5533 2.925706 TAAGCACAGCGGGGTCCA 60.926 61.111 0.00 0.00 0.00 4.02
5066 5549 0.403655 TCATTTGCACCTGGGCAGTA 59.596 50.000 9.31 4.09 45.88 2.74
5106 5589 6.434340 GGAAAGATATTGGTCAACAGTTTCCT 59.566 38.462 14.72 0.00 38.15 3.36
5119 5602 8.960591 AGTAAGAAACACATGGAAAGATATTGG 58.039 33.333 0.00 0.00 0.00 3.16
5131 5614 6.545504 AGTGCTTACAGTAAGAAACACATG 57.454 37.500 22.50 0.00 38.02 3.21
5191 5674 9.561069 AAGCTACTCTGAACTCAATTTAAAGAA 57.439 29.630 0.00 0.00 0.00 2.52
5192 5675 8.993121 CAAGCTACTCTGAACTCAATTTAAAGA 58.007 33.333 0.00 0.00 0.00 2.52
5193 5676 8.233190 CCAAGCTACTCTGAACTCAATTTAAAG 58.767 37.037 0.00 0.00 0.00 1.85
5194 5677 7.719633 ACCAAGCTACTCTGAACTCAATTTAAA 59.280 33.333 0.00 0.00 0.00 1.52
5195 5678 7.224297 ACCAAGCTACTCTGAACTCAATTTAA 58.776 34.615 0.00 0.00 0.00 1.52
5197 5680 5.625150 ACCAAGCTACTCTGAACTCAATTT 58.375 37.500 0.00 0.00 0.00 1.82
5229 5715 6.620877 TGGGATGTTGATGGATATAGTACC 57.379 41.667 0.00 0.00 0.00 3.34
5245 5731 2.040813 ACACTTGCAGAGATTGGGATGT 59.959 45.455 3.37 0.00 0.00 3.06
5261 5747 8.149647 TGATTCATTAATTGGAGCAAAACACTT 58.850 29.630 0.00 0.00 0.00 3.16
5277 5763 6.839124 AGTTGTGCTTGGATGATTCATTAA 57.161 33.333 0.00 0.00 0.00 1.40
5292 5778 3.815401 GAGTTACATGGTCAAGTTGTGCT 59.185 43.478 2.11 0.00 0.00 4.40
5312 5798 7.252708 TGATTTCATTCATGATGTTTTCGGAG 58.747 34.615 0.00 0.00 36.56 4.63
5315 5801 8.456904 AACTGATTTCATTCATGATGTTTTCG 57.543 30.769 0.00 0.00 36.56 3.46
5330 5816 3.503363 GCATGACACTGGAACTGATTTCA 59.497 43.478 0.00 0.00 35.70 2.69
5344 5830 0.302890 GCTCTACGCATGCATGACAC 59.697 55.000 30.64 11.65 38.92 3.67
5355 5841 0.179100 TGCAGATCTTGGCTCTACGC 60.179 55.000 6.60 0.00 38.13 4.42
5372 5858 2.754552 TGTTTGGCAGATGAGGTATTGC 59.245 45.455 0.00 0.00 35.87 3.56
5393 5879 0.681175 GCCATCAGCCCAACAAGTTT 59.319 50.000 0.00 0.00 34.35 2.66
5396 5882 1.888018 CAGCCATCAGCCCAACAAG 59.112 57.895 0.00 0.00 45.47 3.16
5400 5886 1.077501 GTAGCAGCCATCAGCCCAA 60.078 57.895 0.00 0.00 45.47 4.12


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

AutoCloner maintained by Alex Coulton.