Multiple sequence alignment - TraesCS1B01G345700

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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 TraesCS1B01G345700 chr1B 100.000 2525 0 0 1 2525 573936351 573938875 0.000000e+00 4663.0
1 TraesCS1B01G345700 chr1B 80.071 281 39 11 1894 2158 573944458 573944737 2.560000e-45 193.0
2 TraesCS1B01G345700 chr1D 89.197 1657 84 36 432 2043 424867339 424868945 0.000000e+00 1980.0
3 TraesCS1B01G345700 chr1D 91.304 414 21 7 1 411 424866949 424867350 3.670000e-153 551.0
4 TraesCS1B01G345700 chr1D 84.270 267 25 5 2028 2284 424924958 424925217 6.980000e-61 244.0
5 TraesCS1B01G345700 chr1D 92.941 85 6 0 1814 1898 424927138 424927222 9.480000e-25 124.0
6 TraesCS1B01G345700 chr1D 85.106 94 8 4 2067 2158 424927398 424927487 9.620000e-15 91.6
7 TraesCS1B01G345700 chr1A 86.169 1352 97 52 968 2277 520763184 520764487 0.000000e+00 1378.0
8 TraesCS1B01G345700 chr1A 91.633 490 27 8 432 912 520762685 520763169 0.000000e+00 665.0
9 TraesCS1B01G345700 chr1A 90.443 429 28 7 1 418 520762276 520762702 1.020000e-153 553.0
10 TraesCS1B01G345700 chr1A 87.139 381 27 12 1924 2284 520772583 520772961 1.810000e-111 412.0
11 TraesCS1B01G345700 chr1A 88.800 125 13 1 1804 1927 520770575 520770699 4.350000e-33 152.0
12 TraesCS1B01G345700 chr5D 84.840 376 33 12 432 799 115700146 115700505 8.590000e-95 357.0
13 TraesCS1B01G345700 chr5D 86.458 192 25 1 2332 2523 46603840 46603650 2.550000e-50 209.0
14 TraesCS1B01G345700 chr4B 84.896 192 29 0 2332 2523 603512164 603512355 7.130000e-46 195.0
15 TraesCS1B01G345700 chr7D 84.737 190 29 0 2334 2523 46789622 46789811 9.220000e-45 191.0
16 TraesCS1B01G345700 chr4D 84.021 194 27 3 2332 2523 442648994 442648803 1.540000e-42 183.0
17 TraesCS1B01G345700 chr6B 82.812 192 32 1 2332 2523 506273095 506272905 1.200000e-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 TraesCS1B01G345700 chr1B 573936351 573938875 2524 False 4663.000000 4663 100.0000 1 2525 1 chr1B.!!$F1 2524
1 TraesCS1B01G345700 chr1D 424866949 424868945 1996 False 1265.500000 1980 90.2505 1 2043 2 chr1D.!!$F1 2042
2 TraesCS1B01G345700 chr1A 520762276 520764487 2211 False 865.333333 1378 89.4150 1 2277 3 chr1A.!!$F1 2276
3 TraesCS1B01G345700 chr1A 520770575 520772961 2386 False 282.000000 412 87.9695 1804 2284 2 chr1A.!!$F2 480

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
242 264 0.246635 TAAAGCGCTCGAGAAAGGCT 59.753 50.0 18.75 15.12 35.01 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1802 0.393132 GCTAACTGCTTCCAGGTCCC 60.393 60.0 0.0 0.0 43.53 4.46 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
67 69 4.610456 GCATCACGTTTCTCAATCGAACAA 60.610 41.667 0.00 0.00 0.00 2.83
72 74 4.209288 ACGTTTCTCAATCGAACAACTCTG 59.791 41.667 0.00 0.00 0.00 3.35
100 102 1.243342 CCTCAAATCACGCCCTTGCA 61.243 55.000 0.00 0.00 37.32 4.08
142 144 7.582667 AATTTCCCCTAAAAATACTCCGATG 57.417 36.000 0.00 0.00 0.00 3.84
234 256 1.999735 CAATCCAGTTAAAGCGCTCGA 59.000 47.619 12.06 0.00 0.00 4.04
235 257 1.927895 ATCCAGTTAAAGCGCTCGAG 58.072 50.000 12.06 8.45 0.00 4.04
236 258 0.885879 TCCAGTTAAAGCGCTCGAGA 59.114 50.000 18.75 0.00 0.00 4.04
237 259 1.271379 TCCAGTTAAAGCGCTCGAGAA 59.729 47.619 18.75 0.00 0.00 2.87
238 260 2.066262 CCAGTTAAAGCGCTCGAGAAA 58.934 47.619 18.75 0.00 0.00 2.52
239 261 2.092838 CCAGTTAAAGCGCTCGAGAAAG 59.907 50.000 18.75 7.64 0.00 2.62
240 262 2.092838 CAGTTAAAGCGCTCGAGAAAGG 59.907 50.000 18.75 2.59 0.00 3.11
241 263 1.076332 TTAAAGCGCTCGAGAAAGGC 58.924 50.000 18.75 13.01 0.00 4.35
242 264 0.246635 TAAAGCGCTCGAGAAAGGCT 59.753 50.000 18.75 15.12 35.01 4.58
243 265 1.294659 AAAGCGCTCGAGAAAGGCTG 61.295 55.000 18.75 0.00 33.58 4.85
244 266 3.191539 GCGCTCGAGAAAGGCTGG 61.192 66.667 18.75 0.00 0.00 4.85
245 267 2.510238 CGCTCGAGAAAGGCTGGG 60.510 66.667 18.75 0.00 0.00 4.45
254 276 1.220493 AGAAAGGCTGGGAAAAAGGGT 59.780 47.619 0.00 0.00 0.00 4.34
418 441 3.610911 GCCACAGATTAACCTAAGCACT 58.389 45.455 0.00 0.00 0.00 4.40
419 442 4.010349 GCCACAGATTAACCTAAGCACTT 58.990 43.478 0.00 0.00 0.00 3.16
420 443 4.459337 GCCACAGATTAACCTAAGCACTTT 59.541 41.667 0.00 0.00 0.00 2.66
421 444 5.619981 GCCACAGATTAACCTAAGCACTTTG 60.620 44.000 0.00 0.00 0.00 2.77
422 445 5.393962 CACAGATTAACCTAAGCACTTTGC 58.606 41.667 0.00 0.00 45.46 3.68
450 473 4.680171 AAACAGATTAACCTAAGCACGC 57.320 40.909 0.00 0.00 0.00 5.34
451 474 3.328382 ACAGATTAACCTAAGCACGCA 57.672 42.857 0.00 0.00 0.00 5.24
452 475 3.873910 ACAGATTAACCTAAGCACGCAT 58.126 40.909 0.00 0.00 0.00 4.73
453 476 3.623060 ACAGATTAACCTAAGCACGCATG 59.377 43.478 0.00 0.00 0.00 4.06
454 477 3.623060 CAGATTAACCTAAGCACGCATGT 59.377 43.478 0.00 0.00 0.00 3.21
485 510 7.278424 TGTTAAACGTTTGAGTGTTAAGCTAGT 59.722 33.333 23.46 0.00 0.00 2.57
494 519 5.919141 TGAGTGTTAAGCTAGTTCTCGTTTC 59.081 40.000 0.00 0.00 0.00 2.78
526 551 7.446931 TCATTTTTACACAGTTCAAGCCAGATA 59.553 33.333 0.00 0.00 0.00 1.98
538 563 5.962433 TCAAGCCAGATACAACACTACTAC 58.038 41.667 0.00 0.00 0.00 2.73
540 565 4.267536 AGCCAGATACAACACTACTACGA 58.732 43.478 0.00 0.00 0.00 3.43
541 566 4.096081 AGCCAGATACAACACTACTACGAC 59.904 45.833 0.00 0.00 0.00 4.34
543 568 4.397103 CCAGATACAACACTACTACGACCA 59.603 45.833 0.00 0.00 0.00 4.02
544 569 5.067413 CCAGATACAACACTACTACGACCAT 59.933 44.000 0.00 0.00 0.00 3.55
545 570 6.405508 CCAGATACAACACTACTACGACCATT 60.406 42.308 0.00 0.00 0.00 3.16
546 571 7.201758 CCAGATACAACACTACTACGACCATTA 60.202 40.741 0.00 0.00 0.00 1.90
547 572 7.642978 CAGATACAACACTACTACGACCATTAC 59.357 40.741 0.00 0.00 0.00 1.89
549 574 4.523943 ACAACACTACTACGACCATTACCA 59.476 41.667 0.00 0.00 0.00 3.25
551 576 5.927281 ACACTACTACGACCATTACCAAT 57.073 39.130 0.00 0.00 0.00 3.16
552 577 6.290294 ACACTACTACGACCATTACCAATT 57.710 37.500 0.00 0.00 0.00 2.32
554 579 5.522460 CACTACTACGACCATTACCAATTGG 59.478 44.000 23.31 23.31 42.17 3.16
673 698 6.662414 TTGACGAATTCCATTCATACTCAC 57.338 37.500 0.00 0.00 39.22 3.51
721 748 2.298163 CCCAGCTGCTGAACATTTCTTT 59.702 45.455 30.10 0.00 32.44 2.52
745 772 4.912586 TCCAATTTGATTTGACTACGGGA 58.087 39.130 0.00 0.00 0.00 5.14
754 781 2.125673 ACTACGGGATGTGTGCGC 60.126 61.111 0.00 0.00 0.00 6.09
817 847 3.513515 TGCTGGTTCAAAGTTTCAAACCT 59.486 39.130 21.59 0.00 41.41 3.50
894 925 5.759506 AGAATCAATCATCGTCGTCTACT 57.240 39.130 0.00 0.00 0.00 2.57
895 926 5.753744 AGAATCAATCATCGTCGTCTACTC 58.246 41.667 0.00 0.00 0.00 2.59
896 927 3.587403 TCAATCATCGTCGTCTACTCG 57.413 47.619 0.00 0.00 0.00 4.18
897 928 3.192466 TCAATCATCGTCGTCTACTCGA 58.808 45.455 0.00 0.00 37.96 4.04
905 936 2.685850 TCGTCTACTCGACTCATCCA 57.314 50.000 0.00 0.00 40.59 3.41
906 937 3.195471 TCGTCTACTCGACTCATCCAT 57.805 47.619 0.00 0.00 40.59 3.41
907 938 3.132160 TCGTCTACTCGACTCATCCATC 58.868 50.000 0.00 0.00 40.59 3.51
908 939 2.224549 CGTCTACTCGACTCATCCATCC 59.775 54.545 0.00 0.00 40.59 3.51
909 940 3.215151 GTCTACTCGACTCATCCATCCA 58.785 50.000 0.00 0.00 39.61 3.41
950 990 2.435693 CGTCTCCCTCCCACCCATC 61.436 68.421 0.00 0.00 0.00 3.51
958 998 3.849951 CCCACCCATCGACTCCCG 61.850 72.222 0.00 0.00 40.25 5.14
1493 1536 1.153823 CCGCGACGATCAAGAAGGT 60.154 57.895 8.23 0.00 0.00 3.50
1500 1549 1.908483 GATCAAGAAGGTCCCCGCT 59.092 57.895 0.00 0.00 0.00 5.52
1674 1741 1.338105 GCAGGATGGTTTTGGCCTTTC 60.338 52.381 3.32 0.00 35.86 2.62
1679 1746 4.065088 GGATGGTTTTGGCCTTTCTTTTC 58.935 43.478 3.32 0.00 0.00 2.29
1692 1766 1.104577 TCTTTTCCCCGTGTGGTTGC 61.105 55.000 0.00 0.00 0.00 4.17
1726 1802 9.537848 GTACATTTTAGTGGTTAGATTTTGTCG 57.462 33.333 0.00 0.00 0.00 4.35
1778 1854 2.216046 CATACTGCATACACAGCCCAG 58.784 52.381 0.00 0.00 41.60 4.45
1782 1858 0.179076 TGCATACACAGCCCAGATCG 60.179 55.000 0.00 0.00 0.00 3.69
1786 1863 0.104855 TACACAGCCCAGATCGATGC 59.895 55.000 0.54 0.00 0.00 3.91
1810 1887 6.258068 GCTGTTAATTGGTAGAGTACACATCC 59.742 42.308 0.00 0.00 0.00 3.51
1876 1957 2.862140 GCAATCCAAACAAGTTCGGTGG 60.862 50.000 0.00 0.00 0.00 4.61
1915 1996 6.307800 GCATACACACGCTGACATTTTAAAAT 59.692 34.615 7.64 7.64 0.00 1.82
1918 1999 7.160633 ACACACGCTGACATTTTAAAATTTC 57.839 32.000 16.71 16.71 0.00 2.17
1919 2000 6.075099 ACACACGCTGACATTTTAAAATTTCG 60.075 34.615 17.81 14.30 29.81 3.46
1920 2001 5.974751 ACACGCTGACATTTTAAAATTTCGT 59.025 32.000 17.81 15.04 29.81 3.85
1937 3906 2.765122 TCGTGAACATGACATGCTGAA 58.235 42.857 15.49 0.00 0.00 3.02
2017 3993 1.790387 GAGTCAGTGCGGTGCATTC 59.210 57.895 0.00 0.00 41.91 2.67
2117 4101 4.721037 CGTACGTACATTGACTCGTCTAAC 59.279 45.833 24.50 0.00 37.66 2.34
2241 4251 1.338020 GGACAGCTCAGGTTTGTTTGG 59.662 52.381 0.00 0.00 0.00 3.28
2255 4265 2.083774 TGTTTGGGAGCGATGATTGAC 58.916 47.619 0.00 0.00 0.00 3.18
2284 4294 2.052590 CGTGTGCCGTTCGTTTGG 60.053 61.111 0.00 0.00 0.00 3.28
2285 4295 2.526993 CGTGTGCCGTTCGTTTGGA 61.527 57.895 0.00 0.00 0.00 3.53
2286 4296 1.837538 CGTGTGCCGTTCGTTTGGAT 61.838 55.000 0.00 0.00 0.00 3.41
2287 4297 0.385473 GTGTGCCGTTCGTTTGGATG 60.385 55.000 0.00 0.00 0.00 3.51
2288 4298 0.816018 TGTGCCGTTCGTTTGGATGT 60.816 50.000 0.00 0.00 0.00 3.06
2289 4299 1.149987 GTGCCGTTCGTTTGGATGTA 58.850 50.000 0.00 0.00 0.00 2.29
2290 4300 1.735571 GTGCCGTTCGTTTGGATGTAT 59.264 47.619 0.00 0.00 0.00 2.29
2291 4301 2.931325 GTGCCGTTCGTTTGGATGTATA 59.069 45.455 0.00 0.00 0.00 1.47
2292 4302 3.558418 GTGCCGTTCGTTTGGATGTATAT 59.442 43.478 0.00 0.00 0.00 0.86
2293 4303 3.558006 TGCCGTTCGTTTGGATGTATATG 59.442 43.478 0.00 0.00 0.00 1.78
2294 4304 3.059188 GCCGTTCGTTTGGATGTATATGG 60.059 47.826 0.00 0.00 0.00 2.74
2295 4305 4.373527 CCGTTCGTTTGGATGTATATGGA 58.626 43.478 0.00 0.00 0.00 3.41
2296 4306 4.447724 CCGTTCGTTTGGATGTATATGGAG 59.552 45.833 0.00 0.00 0.00 3.86
2297 4307 5.286438 CGTTCGTTTGGATGTATATGGAGA 58.714 41.667 0.00 0.00 0.00 3.71
2298 4308 5.926542 CGTTCGTTTGGATGTATATGGAGAT 59.073 40.000 0.00 0.00 0.00 2.75
2299 4309 6.423905 CGTTCGTTTGGATGTATATGGAGATT 59.576 38.462 0.00 0.00 0.00 2.40
2300 4310 7.042051 CGTTCGTTTGGATGTATATGGAGATTT 60.042 37.037 0.00 0.00 0.00 2.17
2301 4311 8.621286 GTTCGTTTGGATGTATATGGAGATTTT 58.379 33.333 0.00 0.00 0.00 1.82
2302 4312 8.746052 TCGTTTGGATGTATATGGAGATTTTT 57.254 30.769 0.00 0.00 0.00 1.94
2303 4313 8.836413 TCGTTTGGATGTATATGGAGATTTTTC 58.164 33.333 0.00 0.00 0.00 2.29
2304 4314 8.840321 CGTTTGGATGTATATGGAGATTTTTCT 58.160 33.333 0.00 0.00 0.00 2.52
2307 4317 9.565090 TTGGATGTATATGGAGATTTTTCTCTG 57.435 33.333 3.26 0.00 36.97 3.35
2308 4318 8.159447 TGGATGTATATGGAGATTTTTCTCTGG 58.841 37.037 3.26 0.00 36.97 3.86
2309 4319 8.160106 GGATGTATATGGAGATTTTTCTCTGGT 58.840 37.037 3.26 0.00 36.97 4.00
2317 4327 9.790344 ATGGAGATTTTTCTCTGGTATATCTTG 57.210 33.333 3.26 0.00 36.97 3.02
2318 4328 8.772250 TGGAGATTTTTCTCTGGTATATCTTGT 58.228 33.333 3.26 0.00 36.97 3.16
2319 4329 9.267084 GGAGATTTTTCTCTGGTATATCTTGTC 57.733 37.037 3.26 0.00 36.97 3.18
2320 4330 9.823647 GAGATTTTTCTCTGGTATATCTTGTCA 57.176 33.333 0.00 0.00 34.12 3.58
2324 4334 7.792374 TTTCTCTGGTATATCTTGTCAATGC 57.208 36.000 0.00 0.00 0.00 3.56
2325 4335 6.484364 TCTCTGGTATATCTTGTCAATGCA 57.516 37.500 0.00 0.00 0.00 3.96
2326 4336 6.283694 TCTCTGGTATATCTTGTCAATGCAC 58.716 40.000 0.00 0.00 0.00 4.57
2327 4337 5.368145 TCTGGTATATCTTGTCAATGCACC 58.632 41.667 0.00 0.00 0.00 5.01
2328 4338 5.130975 TCTGGTATATCTTGTCAATGCACCT 59.869 40.000 0.00 0.00 0.00 4.00
2329 4339 5.754782 TGGTATATCTTGTCAATGCACCTT 58.245 37.500 0.00 0.00 0.00 3.50
2330 4340 6.894682 TGGTATATCTTGTCAATGCACCTTA 58.105 36.000 0.00 0.00 0.00 2.69
2331 4341 7.517320 TGGTATATCTTGTCAATGCACCTTAT 58.483 34.615 0.00 0.00 0.00 1.73
2332 4342 7.998383 TGGTATATCTTGTCAATGCACCTTATT 59.002 33.333 0.00 0.00 0.00 1.40
2333 4343 9.502091 GGTATATCTTGTCAATGCACCTTATTA 57.498 33.333 0.00 0.00 0.00 0.98
2336 4346 7.798596 ATCTTGTCAATGCACCTTATTAGAG 57.201 36.000 0.00 0.00 0.00 2.43
2337 4347 5.586243 TCTTGTCAATGCACCTTATTAGAGC 59.414 40.000 0.00 0.00 0.00 4.09
2338 4348 4.842574 TGTCAATGCACCTTATTAGAGCA 58.157 39.130 0.00 0.00 36.90 4.26
2339 4349 5.439721 TGTCAATGCACCTTATTAGAGCAT 58.560 37.500 0.00 5.99 41.53 3.79
2340 4350 5.528690 TGTCAATGCACCTTATTAGAGCATC 59.471 40.000 10.57 2.55 40.01 3.91
2351 4361 4.740235 GAGCATCTACAGCCGGAC 57.260 61.111 5.05 0.00 0.00 4.79
2352 4362 1.816537 GAGCATCTACAGCCGGACA 59.183 57.895 5.05 0.00 0.00 4.02
2353 4363 0.390860 GAGCATCTACAGCCGGACAT 59.609 55.000 5.05 0.00 0.00 3.06
2354 4364 1.613925 GAGCATCTACAGCCGGACATA 59.386 52.381 5.05 0.00 0.00 2.29
2355 4365 2.035961 GAGCATCTACAGCCGGACATAA 59.964 50.000 5.05 0.00 0.00 1.90
2356 4366 2.135933 GCATCTACAGCCGGACATAAC 58.864 52.381 5.05 0.00 0.00 1.89
2357 4367 2.483013 GCATCTACAGCCGGACATAACA 60.483 50.000 5.05 0.00 0.00 2.41
2358 4368 3.792401 CATCTACAGCCGGACATAACAA 58.208 45.455 5.05 0.00 0.00 2.83
2359 4369 3.965379 TCTACAGCCGGACATAACAAA 57.035 42.857 5.05 0.00 0.00 2.83
2360 4370 4.481368 TCTACAGCCGGACATAACAAAT 57.519 40.909 5.05 0.00 0.00 2.32
2361 4371 5.601583 TCTACAGCCGGACATAACAAATA 57.398 39.130 5.05 0.00 0.00 1.40
2362 4372 6.169557 TCTACAGCCGGACATAACAAATAT 57.830 37.500 5.05 0.00 0.00 1.28
2363 4373 5.989168 TCTACAGCCGGACATAACAAATATG 59.011 40.000 5.05 0.00 45.80 1.78
2364 4374 4.776349 ACAGCCGGACATAACAAATATGA 58.224 39.130 5.05 0.00 43.52 2.15
2365 4375 4.574828 ACAGCCGGACATAACAAATATGAC 59.425 41.667 5.05 0.00 43.52 3.06
2366 4376 4.024048 CAGCCGGACATAACAAATATGACC 60.024 45.833 5.05 4.98 46.79 4.02
2376 4386 9.816354 ACATAACAAATATGACCCTTTAAATGC 57.184 29.630 2.67 0.00 43.52 3.56
2377 4387 9.260002 CATAACAAATATGACCCTTTAAATGCC 57.740 33.333 0.00 0.00 43.52 4.40
2378 4388 6.865834 ACAAATATGACCCTTTAAATGCCA 57.134 33.333 0.00 0.00 0.00 4.92
2379 4389 6.877236 ACAAATATGACCCTTTAAATGCCAG 58.123 36.000 0.00 0.00 0.00 4.85
2380 4390 5.535753 AATATGACCCTTTAAATGCCAGC 57.464 39.130 0.00 0.00 0.00 4.85
2381 4391 1.173043 TGACCCTTTAAATGCCAGCG 58.827 50.000 0.00 0.00 0.00 5.18
2382 4392 0.455815 GACCCTTTAAATGCCAGCGG 59.544 55.000 0.00 0.00 0.00 5.52
2383 4393 0.039035 ACCCTTTAAATGCCAGCGGA 59.961 50.000 0.00 0.00 0.00 5.54
2384 4394 0.455815 CCCTTTAAATGCCAGCGGAC 59.544 55.000 0.00 0.00 0.00 4.79
2385 4395 1.173043 CCTTTAAATGCCAGCGGACA 58.827 50.000 0.00 0.00 0.00 4.02
2386 4396 1.135402 CCTTTAAATGCCAGCGGACAC 60.135 52.381 0.00 0.00 0.00 3.67
2387 4397 0.519519 TTTAAATGCCAGCGGACACG 59.480 50.000 0.00 0.00 44.63 4.49
2398 4408 3.294908 CGGACACGCATGTTCAATG 57.705 52.632 0.00 0.00 39.95 2.82
2399 4409 0.795698 CGGACACGCATGTTCAATGA 59.204 50.000 0.00 0.00 39.95 2.57
2400 4410 1.464023 CGGACACGCATGTTCAATGAC 60.464 52.381 0.00 0.00 39.95 3.06
2401 4411 1.135689 GGACACGCATGTTCAATGACC 60.136 52.381 0.00 0.00 39.95 4.02
2402 4412 0.516877 ACACGCATGTTCAATGACCG 59.483 50.000 0.00 0.00 34.46 4.79
2403 4413 0.179192 CACGCATGTTCAATGACCGG 60.179 55.000 0.00 0.00 0.00 5.28
2404 4414 1.305219 ACGCATGTTCAATGACCGGG 61.305 55.000 6.32 0.00 0.00 5.73
2405 4415 1.139520 GCATGTTCAATGACCGGGC 59.860 57.895 6.32 1.57 0.00 6.13
2406 4416 1.429021 CATGTTCAATGACCGGGCG 59.571 57.895 6.32 0.00 0.00 6.13
2407 4417 1.002624 ATGTTCAATGACCGGGCGT 60.003 52.632 6.32 0.00 0.00 5.68
2408 4418 1.305219 ATGTTCAATGACCGGGCGTG 61.305 55.000 0.47 2.84 0.00 5.34
2409 4419 3.053291 TTCAATGACCGGGCGTGC 61.053 61.111 0.47 0.00 0.00 5.34
2422 4432 4.054825 CGTGCCCATTTTGCGCCT 62.055 61.111 4.18 0.00 35.87 5.52
2423 4433 2.125952 GTGCCCATTTTGCGCCTC 60.126 61.111 4.18 0.00 33.19 4.70
2424 4434 2.283101 TGCCCATTTTGCGCCTCT 60.283 55.556 4.18 0.00 0.00 3.69
2425 4435 2.182537 GCCCATTTTGCGCCTCTG 59.817 61.111 4.18 0.00 0.00 3.35
2426 4436 2.639327 GCCCATTTTGCGCCTCTGT 61.639 57.895 4.18 0.00 0.00 3.41
2427 4437 1.966762 CCCATTTTGCGCCTCTGTT 59.033 52.632 4.18 0.00 0.00 3.16
2428 4438 0.318120 CCCATTTTGCGCCTCTGTTT 59.682 50.000 4.18 0.00 0.00 2.83
2429 4439 1.543802 CCCATTTTGCGCCTCTGTTTA 59.456 47.619 4.18 0.00 0.00 2.01
2430 4440 2.166254 CCCATTTTGCGCCTCTGTTTAT 59.834 45.455 4.18 0.00 0.00 1.40
2431 4441 3.438360 CCATTTTGCGCCTCTGTTTATC 58.562 45.455 4.18 0.00 0.00 1.75
2432 4442 3.438360 CATTTTGCGCCTCTGTTTATCC 58.562 45.455 4.18 0.00 0.00 2.59
2433 4443 1.083489 TTTGCGCCTCTGTTTATCCG 58.917 50.000 4.18 0.00 0.00 4.18
2434 4444 0.036765 TTGCGCCTCTGTTTATCCGT 60.037 50.000 4.18 0.00 0.00 4.69
2435 4445 0.459585 TGCGCCTCTGTTTATCCGTC 60.460 55.000 4.18 0.00 0.00 4.79
2436 4446 1.152383 GCGCCTCTGTTTATCCGTCC 61.152 60.000 0.00 0.00 0.00 4.79
2437 4447 0.870307 CGCCTCTGTTTATCCGTCCG 60.870 60.000 0.00 0.00 0.00 4.79
2438 4448 1.152383 GCCTCTGTTTATCCGTCCGC 61.152 60.000 0.00 0.00 0.00 5.54
2439 4449 0.870307 CCTCTGTTTATCCGTCCGCG 60.870 60.000 0.00 0.00 37.95 6.46
2440 4450 1.480219 CTCTGTTTATCCGTCCGCGC 61.480 60.000 0.00 0.00 36.67 6.86
2441 4451 1.807981 CTGTTTATCCGTCCGCGCA 60.808 57.895 8.75 0.00 36.67 6.09
2442 4452 1.355796 CTGTTTATCCGTCCGCGCAA 61.356 55.000 8.75 0.00 36.67 4.85
2443 4453 1.059838 GTTTATCCGTCCGCGCAAC 59.940 57.895 8.75 3.68 36.67 4.17
2444 4454 2.101835 TTTATCCGTCCGCGCAACC 61.102 57.895 8.75 0.00 36.67 3.77
2445 4455 2.783241 TTTATCCGTCCGCGCAACCA 62.783 55.000 8.75 0.00 36.67 3.67
2446 4456 3.993376 TATCCGTCCGCGCAACCAC 62.993 63.158 8.75 0.00 36.67 4.16
2450 4460 3.712881 GTCCGCGCAACCACACTC 61.713 66.667 8.75 0.00 0.00 3.51
2451 4461 4.980805 TCCGCGCAACCACACTCC 62.981 66.667 8.75 0.00 0.00 3.85
2452 4462 4.988598 CCGCGCAACCACACTCCT 62.989 66.667 8.75 0.00 0.00 3.69
2453 4463 3.414700 CGCGCAACCACACTCCTC 61.415 66.667 8.75 0.00 0.00 3.71
2454 4464 2.031163 GCGCAACCACACTCCTCT 59.969 61.111 0.30 0.00 0.00 3.69
2455 4465 1.598130 GCGCAACCACACTCCTCTT 60.598 57.895 0.30 0.00 0.00 2.85
2456 4466 1.166531 GCGCAACCACACTCCTCTTT 61.167 55.000 0.30 0.00 0.00 2.52
2457 4467 1.308998 CGCAACCACACTCCTCTTTT 58.691 50.000 0.00 0.00 0.00 2.27
2458 4468 1.676006 CGCAACCACACTCCTCTTTTT 59.324 47.619 0.00 0.00 0.00 1.94
2479 4489 4.436242 TTCTTCTCATATATCCGGTCGC 57.564 45.455 0.00 0.00 0.00 5.19
2480 4490 3.687125 TCTTCTCATATATCCGGTCGCT 58.313 45.455 0.00 0.00 0.00 4.93
2481 4491 4.079970 TCTTCTCATATATCCGGTCGCTT 58.920 43.478 0.00 0.00 0.00 4.68
2482 4492 3.850122 TCTCATATATCCGGTCGCTTG 57.150 47.619 0.00 0.00 0.00 4.01
2483 4493 2.094700 TCTCATATATCCGGTCGCTTGC 60.095 50.000 0.00 0.00 0.00 4.01
2484 4494 1.616374 TCATATATCCGGTCGCTTGCA 59.384 47.619 0.00 0.00 0.00 4.08
2485 4495 1.726791 CATATATCCGGTCGCTTGCAC 59.273 52.381 0.00 0.00 0.00 4.57
2486 4496 0.318360 TATATCCGGTCGCTTGCACG 60.318 55.000 0.00 0.00 0.00 5.34
2487 4497 2.292794 ATATCCGGTCGCTTGCACGT 62.293 55.000 0.00 0.00 0.00 4.49
2488 4498 1.655885 TATCCGGTCGCTTGCACGTA 61.656 55.000 0.00 0.00 0.00 3.57
2489 4499 2.495366 ATCCGGTCGCTTGCACGTAA 62.495 55.000 0.00 0.00 0.00 3.18
2490 4500 2.098233 CCGGTCGCTTGCACGTAAT 61.098 57.895 0.00 0.00 0.00 1.89
2491 4501 1.632046 CCGGTCGCTTGCACGTAATT 61.632 55.000 0.00 0.00 0.00 1.40
2492 4502 0.518355 CGGTCGCTTGCACGTAATTG 60.518 55.000 0.00 0.00 0.00 2.32
2493 4503 0.179200 GGTCGCTTGCACGTAATTGG 60.179 55.000 0.00 0.00 0.00 3.16
2494 4504 0.515564 GTCGCTTGCACGTAATTGGT 59.484 50.000 0.00 0.00 0.00 3.67
2495 4505 0.515127 TCGCTTGCACGTAATTGGTG 59.485 50.000 7.01 7.01 38.42 4.17
2496 4506 0.454285 CGCTTGCACGTAATTGGTGG 60.454 55.000 11.83 0.00 35.94 4.61
2497 4507 0.878416 GCTTGCACGTAATTGGTGGA 59.122 50.000 11.83 7.39 35.94 4.02
2498 4508 1.135689 GCTTGCACGTAATTGGTGGAG 60.136 52.381 11.83 6.09 37.06 3.86
2499 4509 2.422597 CTTGCACGTAATTGGTGGAGA 58.577 47.619 11.83 2.53 37.06 3.71
2500 4510 2.779755 TGCACGTAATTGGTGGAGAT 57.220 45.000 11.83 0.00 35.94 2.75
2501 4511 3.897141 TGCACGTAATTGGTGGAGATA 57.103 42.857 11.83 0.00 35.94 1.98
2502 4512 4.209307 TGCACGTAATTGGTGGAGATAA 57.791 40.909 11.83 0.00 35.94 1.75
2503 4513 4.580868 TGCACGTAATTGGTGGAGATAAA 58.419 39.130 11.83 0.00 35.94 1.40
2504 4514 4.634004 TGCACGTAATTGGTGGAGATAAAG 59.366 41.667 11.83 0.00 35.94 1.85
2505 4515 4.873827 GCACGTAATTGGTGGAGATAAAGA 59.126 41.667 11.83 0.00 35.94 2.52
2506 4516 5.006746 GCACGTAATTGGTGGAGATAAAGAG 59.993 44.000 11.83 0.00 35.94 2.85
2507 4517 6.338146 CACGTAATTGGTGGAGATAAAGAGA 58.662 40.000 0.00 0.00 0.00 3.10
2508 4518 6.477033 CACGTAATTGGTGGAGATAAAGAGAG 59.523 42.308 0.00 0.00 0.00 3.20
2509 4519 6.380274 ACGTAATTGGTGGAGATAAAGAGAGA 59.620 38.462 0.00 0.00 0.00 3.10
2510 4520 6.920758 CGTAATTGGTGGAGATAAAGAGAGAG 59.079 42.308 0.00 0.00 0.00 3.20
2511 4521 7.201830 CGTAATTGGTGGAGATAAAGAGAGAGA 60.202 40.741 0.00 0.00 0.00 3.10
2512 4522 7.502060 AATTGGTGGAGATAAAGAGAGAGAA 57.498 36.000 0.00 0.00 0.00 2.87
2513 4523 6.935240 TTGGTGGAGATAAAGAGAGAGAAA 57.065 37.500 0.00 0.00 0.00 2.52
2514 4524 7.502060 TTGGTGGAGATAAAGAGAGAGAAAT 57.498 36.000 0.00 0.00 0.00 2.17
2515 4525 8.609617 TTGGTGGAGATAAAGAGAGAGAAATA 57.390 34.615 0.00 0.00 0.00 1.40
2516 4526 8.609617 TGGTGGAGATAAAGAGAGAGAAATAA 57.390 34.615 0.00 0.00 0.00 1.40
2517 4527 9.046846 TGGTGGAGATAAAGAGAGAGAAATAAA 57.953 33.333 0.00 0.00 0.00 1.40
2518 4528 9.892130 GGTGGAGATAAAGAGAGAGAAATAAAA 57.108 33.333 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 59 3.070018 AGAAGGCAGAGTTGTTCGATTG 58.930 45.455 0.00 0.00 0.00 2.67
67 69 3.864789 TTTGAGGAAAGAAGGCAGAGT 57.135 42.857 0.00 0.00 0.00 3.24
72 74 2.414691 GCGTGATTTGAGGAAAGAAGGC 60.415 50.000 0.00 0.00 0.00 4.35
100 102 9.686683 GGGGAAATTATATAGAAGTGCATGTAT 57.313 33.333 0.00 0.00 0.00 2.29
234 256 1.220493 ACCCTTTTTCCCAGCCTTTCT 59.780 47.619 0.00 0.00 0.00 2.52
235 257 1.717032 ACCCTTTTTCCCAGCCTTTC 58.283 50.000 0.00 0.00 0.00 2.62
236 258 2.190398 AACCCTTTTTCCCAGCCTTT 57.810 45.000 0.00 0.00 0.00 3.11
237 259 3.239449 CTTAACCCTTTTTCCCAGCCTT 58.761 45.455 0.00 0.00 0.00 4.35
238 260 2.492753 CCTTAACCCTTTTTCCCAGCCT 60.493 50.000 0.00 0.00 0.00 4.58
239 261 1.899814 CCTTAACCCTTTTTCCCAGCC 59.100 52.381 0.00 0.00 0.00 4.85
240 262 1.275291 GCCTTAACCCTTTTTCCCAGC 59.725 52.381 0.00 0.00 0.00 4.85
241 263 2.826128 GAGCCTTAACCCTTTTTCCCAG 59.174 50.000 0.00 0.00 0.00 4.45
242 264 2.178106 TGAGCCTTAACCCTTTTTCCCA 59.822 45.455 0.00 0.00 0.00 4.37
243 265 2.561419 GTGAGCCTTAACCCTTTTTCCC 59.439 50.000 0.00 0.00 0.00 3.97
244 266 2.561419 GGTGAGCCTTAACCCTTTTTCC 59.439 50.000 0.00 0.00 0.00 3.13
245 267 3.255888 CAGGTGAGCCTTAACCCTTTTTC 59.744 47.826 0.00 0.00 44.18 2.29
254 276 1.071699 ACGAAAGCAGGTGAGCCTTAA 59.928 47.619 0.00 0.00 44.18 1.85
266 288 3.380004 AGACATGGAAAAACACGAAAGCA 59.620 39.130 0.00 0.00 0.00 3.91
301 323 1.374947 TGGCTGACCAGTTACCTGC 59.625 57.895 0.00 0.00 42.67 4.85
427 450 5.009210 TGCGTGCTTAGGTTAATCTGTTTTT 59.991 36.000 0.00 0.00 0.00 1.94
428 451 4.517453 TGCGTGCTTAGGTTAATCTGTTTT 59.483 37.500 0.00 0.00 0.00 2.43
429 452 4.069304 TGCGTGCTTAGGTTAATCTGTTT 58.931 39.130 0.00 0.00 0.00 2.83
430 453 3.670625 TGCGTGCTTAGGTTAATCTGTT 58.329 40.909 0.00 0.00 0.00 3.16
431 454 3.328382 TGCGTGCTTAGGTTAATCTGT 57.672 42.857 0.00 0.00 0.00 3.41
432 455 3.623060 ACATGCGTGCTTAGGTTAATCTG 59.377 43.478 5.64 0.00 0.00 2.90
433 456 3.873910 ACATGCGTGCTTAGGTTAATCT 58.126 40.909 5.64 0.00 0.00 2.40
434 457 5.064198 TGTTACATGCGTGCTTAGGTTAATC 59.936 40.000 5.64 0.00 0.00 1.75
435 458 4.938832 TGTTACATGCGTGCTTAGGTTAAT 59.061 37.500 5.64 0.00 0.00 1.40
436 459 4.316645 TGTTACATGCGTGCTTAGGTTAA 58.683 39.130 5.64 0.00 0.00 2.01
437 460 3.927854 TGTTACATGCGTGCTTAGGTTA 58.072 40.909 5.64 0.00 0.00 2.85
438 461 2.773487 TGTTACATGCGTGCTTAGGTT 58.227 42.857 5.64 0.00 0.00 3.50
439 462 2.465860 TGTTACATGCGTGCTTAGGT 57.534 45.000 5.64 0.00 0.00 3.08
440 463 2.677836 ACATGTTACATGCGTGCTTAGG 59.322 45.455 23.43 0.00 0.00 2.69
441 464 4.340894 AACATGTTACATGCGTGCTTAG 57.659 40.909 23.43 0.00 0.00 2.18
442 465 5.864628 TTAACATGTTACATGCGTGCTTA 57.135 34.783 23.43 12.08 0.00 3.09
443 466 4.757799 TTAACATGTTACATGCGTGCTT 57.242 36.364 23.43 12.99 0.00 3.91
444 467 4.472286 GTTTAACATGTTACATGCGTGCT 58.528 39.130 23.43 2.52 0.00 4.40
445 468 3.296943 CGTTTAACATGTTACATGCGTGC 59.703 43.478 23.43 10.37 0.00 5.34
446 469 4.459606 ACGTTTAACATGTTACATGCGTG 58.540 39.130 23.43 3.82 0.00 5.34
447 470 4.735662 ACGTTTAACATGTTACATGCGT 57.264 36.364 23.43 20.06 0.00 5.24
448 471 5.621634 TCAAACGTTTAACATGTTACATGCG 59.378 36.000 23.43 19.48 33.04 4.73
449 472 6.635239 ACTCAAACGTTTAACATGTTACATGC 59.365 34.615 23.43 7.43 33.04 4.06
450 473 7.642194 ACACTCAAACGTTTAACATGTTACATG 59.358 33.333 22.12 22.12 33.04 3.21
451 474 7.699566 ACACTCAAACGTTTAACATGTTACAT 58.300 30.769 17.85 0.00 33.04 2.29
452 475 7.074507 ACACTCAAACGTTTAACATGTTACA 57.925 32.000 17.85 9.11 33.04 2.41
453 476 7.958112 AACACTCAAACGTTTAACATGTTAC 57.042 32.000 17.85 9.45 33.04 2.50
454 477 9.705471 CTTAACACTCAAACGTTTAACATGTTA 57.295 29.630 22.39 22.39 33.04 2.41
494 519 9.760660 GCTTGAACTGTGTAAAAATGAGTATAG 57.239 33.333 0.00 0.00 0.00 1.31
526 551 4.523943 TGGTAATGGTCGTAGTAGTGTTGT 59.476 41.667 0.00 0.00 0.00 3.32
538 563 4.766375 ACTCTACCAATTGGTAATGGTCG 58.234 43.478 31.85 21.30 46.94 4.79
547 572 5.511545 GGGCAGATAGTACTCTACCAATTGG 60.512 48.000 23.31 23.31 42.17 3.16
549 574 5.216622 TGGGCAGATAGTACTCTACCAATT 58.783 41.667 0.00 0.00 31.21 2.32
551 576 4.259933 TGGGCAGATAGTACTCTACCAA 57.740 45.455 0.00 0.00 31.21 3.67
552 577 3.965470 TGGGCAGATAGTACTCTACCA 57.035 47.619 0.00 1.32 31.21 3.25
554 579 3.892588 AGCTTGGGCAGATAGTACTCTAC 59.107 47.826 0.00 0.00 41.70 2.59
555 580 4.186077 AGCTTGGGCAGATAGTACTCTA 57.814 45.455 0.00 0.00 41.70 2.43
556 581 3.039252 AGCTTGGGCAGATAGTACTCT 57.961 47.619 0.00 0.00 41.70 3.24
563 588 2.837591 TCTGTTGTAGCTTGGGCAGATA 59.162 45.455 0.00 0.00 41.70 1.98
565 590 1.055849 TCTGTTGTAGCTTGGGCAGA 58.944 50.000 0.00 0.00 41.70 4.26
705 732 5.443185 TTGGAGAAAGAAATGTTCAGCAG 57.557 39.130 0.00 0.00 0.00 4.24
721 748 4.941263 CCCGTAGTCAAATCAAATTGGAGA 59.059 41.667 0.00 0.00 0.00 3.71
859 890 1.375523 GATTCTTGGACGCGGTGGT 60.376 57.895 12.47 0.00 0.00 4.16
894 925 2.564504 GGATGATGGATGGATGAGTCGA 59.435 50.000 0.00 0.00 0.00 4.20
895 926 2.301009 TGGATGATGGATGGATGAGTCG 59.699 50.000 0.00 0.00 0.00 4.18
896 927 4.515361 GATGGATGATGGATGGATGAGTC 58.485 47.826 0.00 0.00 0.00 3.36
897 928 3.055312 CGATGGATGATGGATGGATGAGT 60.055 47.826 0.00 0.00 0.00 3.41
898 929 3.532542 CGATGGATGATGGATGGATGAG 58.467 50.000 0.00 0.00 0.00 2.90
899 930 2.355412 GCGATGGATGATGGATGGATGA 60.355 50.000 0.00 0.00 0.00 2.92
900 931 2.014857 GCGATGGATGATGGATGGATG 58.985 52.381 0.00 0.00 0.00 3.51
901 932 1.064906 GGCGATGGATGATGGATGGAT 60.065 52.381 0.00 0.00 0.00 3.41
902 933 0.325933 GGCGATGGATGATGGATGGA 59.674 55.000 0.00 0.00 0.00 3.41
903 934 0.679002 GGGCGATGGATGATGGATGG 60.679 60.000 0.00 0.00 0.00 3.51
904 935 1.022982 CGGGCGATGGATGATGGATG 61.023 60.000 0.00 0.00 0.00 3.51
905 936 1.194121 TCGGGCGATGGATGATGGAT 61.194 55.000 0.00 0.00 0.00 3.41
906 937 1.406860 TTCGGGCGATGGATGATGGA 61.407 55.000 0.00 0.00 0.00 3.41
907 938 0.321919 ATTCGGGCGATGGATGATGG 60.322 55.000 0.00 0.00 0.00 3.51
908 939 1.466167 GAATTCGGGCGATGGATGATG 59.534 52.381 0.00 0.00 0.00 3.07
909 940 1.611673 GGAATTCGGGCGATGGATGAT 60.612 52.381 0.00 0.00 0.00 2.45
971 1011 1.341606 GTCGACGCCTTTCTCTTCTG 58.658 55.000 0.00 0.00 0.00 3.02
1674 1741 1.362355 GCAACCACACGGGGAAAAG 59.638 57.895 0.00 0.00 42.91 2.27
1679 1746 4.920112 TCACGCAACCACACGGGG 62.920 66.667 0.00 0.00 42.91 5.73
1692 1766 8.714179 TCTAACCACTAAAATGTACAATTCACG 58.286 33.333 0.00 0.00 0.00 4.35
1726 1802 0.393132 GCTAACTGCTTCCAGGTCCC 60.393 60.000 0.00 0.00 43.53 4.46
1778 1854 5.986135 ACTCTACCAATTAACAGCATCGATC 59.014 40.000 0.00 0.00 0.00 3.69
1782 1858 6.816640 TGTGTACTCTACCAATTAACAGCATC 59.183 38.462 0.00 0.00 0.00 3.91
1786 1863 6.761714 GGGATGTGTACTCTACCAATTAACAG 59.238 42.308 0.00 0.00 0.00 3.16
1810 1887 1.499056 GCACGTCACATGCTTCTGG 59.501 57.895 0.00 0.00 40.08 3.86
1876 1957 3.128415 TGTGTATGCATTGCACATGTACC 59.872 43.478 23.92 7.38 43.04 3.34
1915 1996 3.137533 TCAGCATGTCATGTTCACGAAA 58.862 40.909 14.26 0.00 37.40 3.46
1918 1999 3.541071 TTTCAGCATGTCATGTTCACG 57.459 42.857 14.26 0.00 37.40 4.35
1919 2000 8.400947 AGTATAATTTCAGCATGTCATGTTCAC 58.599 33.333 14.26 0.00 37.40 3.18
1920 2001 8.510243 AGTATAATTTCAGCATGTCATGTTCA 57.490 30.769 14.26 0.00 37.40 3.18
2017 3993 2.997315 TCCCAGTCCCAGAGCACG 60.997 66.667 0.00 0.00 0.00 5.34
2071 4053 5.350365 CGTACGGGATTGGGTTATGATTATG 59.650 44.000 7.57 0.00 0.00 1.90
2241 4251 1.202417 TCTTCCGTCAATCATCGCTCC 60.202 52.381 0.00 0.00 0.00 4.70
2291 4301 9.790344 CAAGATATACCAGAGAAAAATCTCCAT 57.210 33.333 2.35 0.00 37.46 3.41
2292 4302 8.772250 ACAAGATATACCAGAGAAAAATCTCCA 58.228 33.333 2.35 0.00 37.46 3.86
2293 4303 9.267084 GACAAGATATACCAGAGAAAAATCTCC 57.733 37.037 2.35 0.00 37.46 3.71
2294 4304 9.823647 TGACAAGATATACCAGAGAAAAATCTC 57.176 33.333 0.00 0.00 37.03 2.75
2298 4308 8.677300 GCATTGACAAGATATACCAGAGAAAAA 58.323 33.333 0.00 0.00 0.00 1.94
2299 4309 7.828717 TGCATTGACAAGATATACCAGAGAAAA 59.171 33.333 0.00 0.00 0.00 2.29
2300 4310 7.280876 GTGCATTGACAAGATATACCAGAGAAA 59.719 37.037 0.00 0.00 0.00 2.52
2301 4311 6.763135 GTGCATTGACAAGATATACCAGAGAA 59.237 38.462 0.00 0.00 0.00 2.87
2302 4312 6.283694 GTGCATTGACAAGATATACCAGAGA 58.716 40.000 0.00 0.00 0.00 3.10
2303 4313 5.468072 GGTGCATTGACAAGATATACCAGAG 59.532 44.000 0.00 0.00 0.00 3.35
2304 4314 5.130975 AGGTGCATTGACAAGATATACCAGA 59.869 40.000 0.00 0.00 0.00 3.86
2305 4315 5.371526 AGGTGCATTGACAAGATATACCAG 58.628 41.667 0.00 0.00 0.00 4.00
2306 4316 5.372343 AGGTGCATTGACAAGATATACCA 57.628 39.130 0.00 0.00 0.00 3.25
2307 4317 7.986085 ATAAGGTGCATTGACAAGATATACC 57.014 36.000 0.00 0.00 0.00 2.73
2310 4320 9.499479 CTCTAATAAGGTGCATTGACAAGATAT 57.501 33.333 0.00 0.00 0.00 1.63
2311 4321 7.442364 GCTCTAATAAGGTGCATTGACAAGATA 59.558 37.037 0.00 0.00 0.00 1.98
2312 4322 6.261826 GCTCTAATAAGGTGCATTGACAAGAT 59.738 38.462 0.00 0.00 0.00 2.40
2313 4323 5.586243 GCTCTAATAAGGTGCATTGACAAGA 59.414 40.000 0.00 0.00 0.00 3.02
2314 4324 5.355071 TGCTCTAATAAGGTGCATTGACAAG 59.645 40.000 0.00 0.00 31.18 3.16
2315 4325 5.252547 TGCTCTAATAAGGTGCATTGACAA 58.747 37.500 0.00 0.00 31.18 3.18
2316 4326 4.842574 TGCTCTAATAAGGTGCATTGACA 58.157 39.130 0.00 0.00 31.18 3.58
2317 4327 5.762218 AGATGCTCTAATAAGGTGCATTGAC 59.238 40.000 0.00 0.00 40.65 3.18
2318 4328 5.933617 AGATGCTCTAATAAGGTGCATTGA 58.066 37.500 0.00 0.00 40.65 2.57
2319 4329 6.707608 TGTAGATGCTCTAATAAGGTGCATTG 59.292 38.462 0.00 0.00 40.65 2.82
2320 4330 6.830912 TGTAGATGCTCTAATAAGGTGCATT 58.169 36.000 0.00 0.00 40.65 3.56
2321 4331 6.425210 TGTAGATGCTCTAATAAGGTGCAT 57.575 37.500 0.00 0.00 42.06 3.96
2322 4332 5.740224 GCTGTAGATGCTCTAATAAGGTGCA 60.740 44.000 0.00 0.00 37.15 4.57
2323 4333 4.688413 GCTGTAGATGCTCTAATAAGGTGC 59.312 45.833 0.00 0.00 29.58 5.01
2324 4334 5.233988 GGCTGTAGATGCTCTAATAAGGTG 58.766 45.833 0.00 0.00 29.58 4.00
2325 4335 4.021894 CGGCTGTAGATGCTCTAATAAGGT 60.022 45.833 0.00 0.00 29.58 3.50
2326 4336 4.489810 CGGCTGTAGATGCTCTAATAAGG 58.510 47.826 0.00 0.00 29.58 2.69
2327 4337 4.218635 TCCGGCTGTAGATGCTCTAATAAG 59.781 45.833 0.00 0.00 29.58 1.73
2328 4338 4.022242 GTCCGGCTGTAGATGCTCTAATAA 60.022 45.833 0.00 0.00 29.58 1.40
2329 4339 3.506455 GTCCGGCTGTAGATGCTCTAATA 59.494 47.826 0.00 0.00 29.58 0.98
2330 4340 2.297597 GTCCGGCTGTAGATGCTCTAAT 59.702 50.000 0.00 0.00 29.58 1.73
2331 4341 1.681793 GTCCGGCTGTAGATGCTCTAA 59.318 52.381 0.00 0.00 29.58 2.10
2332 4342 1.319541 GTCCGGCTGTAGATGCTCTA 58.680 55.000 0.00 0.00 0.00 2.43
2333 4343 0.684479 TGTCCGGCTGTAGATGCTCT 60.684 55.000 0.00 0.00 0.00 4.09
2334 4344 0.390860 ATGTCCGGCTGTAGATGCTC 59.609 55.000 0.00 0.00 0.00 4.26
2335 4345 1.704641 TATGTCCGGCTGTAGATGCT 58.295 50.000 0.00 0.00 0.00 3.79
2336 4346 2.135933 GTTATGTCCGGCTGTAGATGC 58.864 52.381 0.00 0.00 0.00 3.91
2337 4347 3.452755 TGTTATGTCCGGCTGTAGATG 57.547 47.619 0.00 0.00 0.00 2.90
2338 4348 4.481368 TTTGTTATGTCCGGCTGTAGAT 57.519 40.909 0.00 0.00 0.00 1.98
2339 4349 3.965379 TTTGTTATGTCCGGCTGTAGA 57.035 42.857 0.00 0.00 0.00 2.59
2340 4350 5.989168 TCATATTTGTTATGTCCGGCTGTAG 59.011 40.000 0.00 0.00 39.06 2.74
2341 4351 5.756347 GTCATATTTGTTATGTCCGGCTGTA 59.244 40.000 0.00 0.00 39.06 2.74
2342 4352 4.574828 GTCATATTTGTTATGTCCGGCTGT 59.425 41.667 0.00 0.00 39.06 4.40
2343 4353 4.024048 GGTCATATTTGTTATGTCCGGCTG 60.024 45.833 0.00 0.00 36.96 4.85
2344 4354 4.134563 GGTCATATTTGTTATGTCCGGCT 58.865 43.478 0.00 0.00 36.96 5.52
2345 4355 3.252458 GGGTCATATTTGTTATGTCCGGC 59.748 47.826 0.00 0.00 43.48 6.13
2346 4356 4.714632 AGGGTCATATTTGTTATGTCCGG 58.285 43.478 0.00 0.00 43.48 5.14
2347 4357 6.693315 AAAGGGTCATATTTGTTATGTCCG 57.307 37.500 0.00 0.00 43.48 4.79
2350 4360 9.816354 GCATTTAAAGGGTCATATTTGTTATGT 57.184 29.630 1.57 0.00 39.06 2.29
2351 4361 9.260002 GGCATTTAAAGGGTCATATTTGTTATG 57.740 33.333 1.57 0.00 39.31 1.90
2352 4362 8.986991 TGGCATTTAAAGGGTCATATTTGTTAT 58.013 29.630 1.57 0.00 0.00 1.89
2353 4363 8.367660 TGGCATTTAAAGGGTCATATTTGTTA 57.632 30.769 1.57 0.00 0.00 2.41
2354 4364 7.251321 TGGCATTTAAAGGGTCATATTTGTT 57.749 32.000 1.57 0.00 0.00 2.83
2355 4365 6.630188 GCTGGCATTTAAAGGGTCATATTTGT 60.630 38.462 1.57 0.00 0.00 2.83
2356 4366 5.754890 GCTGGCATTTAAAGGGTCATATTTG 59.245 40.000 1.57 0.00 0.00 2.32
2357 4367 5.451798 CGCTGGCATTTAAAGGGTCATATTT 60.452 40.000 1.57 0.00 0.00 1.40
2358 4368 4.037923 CGCTGGCATTTAAAGGGTCATATT 59.962 41.667 1.57 0.00 0.00 1.28
2359 4369 3.569701 CGCTGGCATTTAAAGGGTCATAT 59.430 43.478 1.57 0.00 0.00 1.78
2360 4370 2.948979 CGCTGGCATTTAAAGGGTCATA 59.051 45.455 1.57 0.00 0.00 2.15
2361 4371 1.750778 CGCTGGCATTTAAAGGGTCAT 59.249 47.619 1.57 0.00 0.00 3.06
2362 4372 1.173043 CGCTGGCATTTAAAGGGTCA 58.827 50.000 1.57 0.00 0.00 4.02
2363 4373 0.455815 CCGCTGGCATTTAAAGGGTC 59.544 55.000 1.57 0.00 0.00 4.46
2364 4374 0.039035 TCCGCTGGCATTTAAAGGGT 59.961 50.000 1.57 0.00 0.00 4.34
2365 4375 0.455815 GTCCGCTGGCATTTAAAGGG 59.544 55.000 1.57 0.00 0.00 3.95
2366 4376 1.135402 GTGTCCGCTGGCATTTAAAGG 60.135 52.381 0.00 0.00 0.00 3.11
2367 4377 1.465689 CGTGTCCGCTGGCATTTAAAG 60.466 52.381 0.00 0.00 0.00 1.85
2368 4378 0.519519 CGTGTCCGCTGGCATTTAAA 59.480 50.000 0.00 0.00 0.00 1.52
2369 4379 2.167161 CGTGTCCGCTGGCATTTAA 58.833 52.632 0.00 0.00 0.00 1.52
2370 4380 3.883462 CGTGTCCGCTGGCATTTA 58.117 55.556 0.00 0.00 0.00 1.40
2380 4390 0.795698 TCATTGAACATGCGTGTCCG 59.204 50.000 12.96 0.00 37.67 4.79
2381 4391 1.135689 GGTCATTGAACATGCGTGTCC 60.136 52.381 12.96 0.00 37.67 4.02
2382 4392 1.464023 CGGTCATTGAACATGCGTGTC 60.464 52.381 12.96 6.78 37.67 3.67
2383 4393 0.516877 CGGTCATTGAACATGCGTGT 59.483 50.000 5.51 5.51 41.28 4.49
2384 4394 0.179192 CCGGTCATTGAACATGCGTG 60.179 55.000 3.82 3.82 0.00 5.34
2385 4395 1.305219 CCCGGTCATTGAACATGCGT 61.305 55.000 0.00 0.00 0.00 5.24
2386 4396 1.429021 CCCGGTCATTGAACATGCG 59.571 57.895 0.00 0.00 0.00 4.73
2387 4397 1.139520 GCCCGGTCATTGAACATGC 59.860 57.895 0.00 0.00 0.00 4.06
2388 4398 1.305219 ACGCCCGGTCATTGAACATG 61.305 55.000 0.00 0.00 0.00 3.21
2389 4399 1.002624 ACGCCCGGTCATTGAACAT 60.003 52.632 0.00 0.00 0.00 2.71
2390 4400 1.963855 CACGCCCGGTCATTGAACA 60.964 57.895 0.00 0.00 0.00 3.18
2391 4401 2.867472 CACGCCCGGTCATTGAAC 59.133 61.111 0.00 0.00 0.00 3.18
2392 4402 3.053291 GCACGCCCGGTCATTGAA 61.053 61.111 0.00 0.00 0.00 2.69
2409 4419 0.318120 AAACAGAGGCGCAAAATGGG 59.682 50.000 10.83 0.00 0.00 4.00
2410 4420 3.438360 GATAAACAGAGGCGCAAAATGG 58.562 45.455 10.83 0.00 0.00 3.16
2411 4421 3.438360 GGATAAACAGAGGCGCAAAATG 58.562 45.455 10.83 4.52 0.00 2.32
2412 4422 2.097466 CGGATAAACAGAGGCGCAAAAT 59.903 45.455 10.83 0.00 0.00 1.82
2413 4423 1.466950 CGGATAAACAGAGGCGCAAAA 59.533 47.619 10.83 0.00 0.00 2.44
2414 4424 1.083489 CGGATAAACAGAGGCGCAAA 58.917 50.000 10.83 0.00 0.00 3.68
2415 4425 0.036765 ACGGATAAACAGAGGCGCAA 60.037 50.000 10.83 0.00 0.00 4.85
2416 4426 0.459585 GACGGATAAACAGAGGCGCA 60.460 55.000 10.83 0.00 0.00 6.09
2417 4427 1.152383 GGACGGATAAACAGAGGCGC 61.152 60.000 0.00 0.00 0.00 6.53
2418 4428 0.870307 CGGACGGATAAACAGAGGCG 60.870 60.000 0.00 0.00 0.00 5.52
2419 4429 1.152383 GCGGACGGATAAACAGAGGC 61.152 60.000 0.00 0.00 0.00 4.70
2420 4430 0.870307 CGCGGACGGATAAACAGAGG 60.870 60.000 0.00 0.00 34.97 3.69
2421 4431 1.480219 GCGCGGACGGATAAACAGAG 61.480 60.000 8.83 0.00 40.57 3.35
2422 4432 1.517694 GCGCGGACGGATAAACAGA 60.518 57.895 8.83 0.00 40.57 3.41
2423 4433 1.355796 TTGCGCGGACGGATAAACAG 61.356 55.000 8.83 0.00 40.25 3.16
2424 4434 1.374378 TTGCGCGGACGGATAAACA 60.374 52.632 8.83 0.00 40.25 2.83
2425 4435 1.059838 GTTGCGCGGACGGATAAAC 59.940 57.895 8.83 0.00 40.25 2.01
2426 4436 2.101835 GGTTGCGCGGACGGATAAA 61.102 57.895 8.83 0.00 40.25 1.40
2427 4437 2.509786 GGTTGCGCGGACGGATAA 60.510 61.111 8.83 0.00 40.25 1.75
2428 4438 3.761140 TGGTTGCGCGGACGGATA 61.761 61.111 8.83 0.00 40.25 2.59
2433 4443 3.712881 GAGTGTGGTTGCGCGGAC 61.713 66.667 8.83 3.71 0.00 4.79
2434 4444 4.980805 GGAGTGTGGTTGCGCGGA 62.981 66.667 8.83 0.00 0.00 5.54
2435 4445 4.988598 AGGAGTGTGGTTGCGCGG 62.989 66.667 8.83 0.00 0.00 6.46
2436 4446 3.414700 GAGGAGTGTGGTTGCGCG 61.415 66.667 0.00 0.00 0.00 6.86
2437 4447 1.166531 AAAGAGGAGTGTGGTTGCGC 61.167 55.000 0.00 0.00 0.00 6.09
2438 4448 1.308998 AAAAGAGGAGTGTGGTTGCG 58.691 50.000 0.00 0.00 0.00 4.85
2455 4465 5.694910 GCGACCGGATATATGAGAAGAAAAA 59.305 40.000 9.46 0.00 0.00 1.94
2456 4466 5.010719 AGCGACCGGATATATGAGAAGAAAA 59.989 40.000 9.46 0.00 0.00 2.29
2457 4467 4.523173 AGCGACCGGATATATGAGAAGAAA 59.477 41.667 9.46 0.00 0.00 2.52
2458 4468 4.079970 AGCGACCGGATATATGAGAAGAA 58.920 43.478 9.46 0.00 0.00 2.52
2459 4469 3.687125 AGCGACCGGATATATGAGAAGA 58.313 45.455 9.46 0.00 0.00 2.87
2460 4470 4.169508 CAAGCGACCGGATATATGAGAAG 58.830 47.826 9.46 0.00 0.00 2.85
2461 4471 3.614150 GCAAGCGACCGGATATATGAGAA 60.614 47.826 9.46 0.00 0.00 2.87
2462 4472 2.094700 GCAAGCGACCGGATATATGAGA 60.095 50.000 9.46 0.00 0.00 3.27
2463 4473 2.263077 GCAAGCGACCGGATATATGAG 58.737 52.381 9.46 0.00 0.00 2.90
2464 4474 1.616374 TGCAAGCGACCGGATATATGA 59.384 47.619 9.46 0.00 0.00 2.15
2465 4475 1.726791 GTGCAAGCGACCGGATATATG 59.273 52.381 9.46 2.34 0.00 1.78
2466 4476 1.668919 CGTGCAAGCGACCGGATATAT 60.669 52.381 9.46 0.00 0.00 0.86
2467 4477 0.318360 CGTGCAAGCGACCGGATATA 60.318 55.000 9.46 0.00 0.00 0.86
2468 4478 1.591594 CGTGCAAGCGACCGGATAT 60.592 57.895 9.46 0.00 0.00 1.63
2469 4479 1.655885 TACGTGCAAGCGACCGGATA 61.656 55.000 9.46 0.00 35.59 2.59
2470 4480 2.495366 TTACGTGCAAGCGACCGGAT 62.495 55.000 9.46 0.00 35.59 4.18
2471 4481 2.495366 ATTACGTGCAAGCGACCGGA 62.495 55.000 9.46 0.00 35.59 5.14
2472 4482 1.632046 AATTACGTGCAAGCGACCGG 61.632 55.000 0.00 0.00 35.59 5.28
2473 4483 0.518355 CAATTACGTGCAAGCGACCG 60.518 55.000 3.48 0.00 35.59 4.79
2474 4484 0.179200 CCAATTACGTGCAAGCGACC 60.179 55.000 3.48 0.00 35.59 4.79
2475 4485 0.515564 ACCAATTACGTGCAAGCGAC 59.484 50.000 3.48 0.00 35.59 5.19
2476 4486 0.515127 CACCAATTACGTGCAAGCGA 59.485 50.000 3.48 0.00 35.59 4.93
2477 4487 0.454285 CCACCAATTACGTGCAAGCG 60.454 55.000 0.00 0.00 37.94 4.68
2478 4488 0.878416 TCCACCAATTACGTGCAAGC 59.122 50.000 0.00 0.00 0.00 4.01
2479 4489 2.422597 TCTCCACCAATTACGTGCAAG 58.577 47.619 0.00 0.00 0.00 4.01
2480 4490 2.552599 TCTCCACCAATTACGTGCAA 57.447 45.000 0.00 0.00 0.00 4.08
2481 4491 2.779755 ATCTCCACCAATTACGTGCA 57.220 45.000 0.00 0.00 0.00 4.57
2482 4492 4.873827 TCTTTATCTCCACCAATTACGTGC 59.126 41.667 0.00 0.00 0.00 5.34
2483 4493 6.338146 TCTCTTTATCTCCACCAATTACGTG 58.662 40.000 0.00 0.00 0.00 4.49
2484 4494 6.380274 TCTCTCTTTATCTCCACCAATTACGT 59.620 38.462 0.00 0.00 0.00 3.57
2485 4495 6.806751 TCTCTCTTTATCTCCACCAATTACG 58.193 40.000 0.00 0.00 0.00 3.18
2486 4496 8.012957 TCTCTCTCTTTATCTCCACCAATTAC 57.987 38.462 0.00 0.00 0.00 1.89
2487 4497 8.609617 TTCTCTCTCTTTATCTCCACCAATTA 57.390 34.615 0.00 0.00 0.00 1.40
2488 4498 7.502060 TTCTCTCTCTTTATCTCCACCAATT 57.498 36.000 0.00 0.00 0.00 2.32
2489 4499 7.502060 TTTCTCTCTCTTTATCTCCACCAAT 57.498 36.000 0.00 0.00 0.00 3.16
2490 4500 6.935240 TTTCTCTCTCTTTATCTCCACCAA 57.065 37.500 0.00 0.00 0.00 3.67
2491 4501 8.609617 TTATTTCTCTCTCTTTATCTCCACCA 57.390 34.615 0.00 0.00 0.00 4.17
2492 4502 9.892130 TTTTATTTCTCTCTCTTTATCTCCACC 57.108 33.333 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.