Multiple sequence alignment - TraesCS3A01G397400

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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 TraesCS3A01G397400 chr3A 100.000 2654 0 0 1 2654 644779110 644781763 0.000000e+00 4902.0
1 TraesCS3A01G397400 chr3A 93.612 407 23 3 2251 2654 698531520 698531926 2.920000e-169 604.0
2 TraesCS3A01G397400 chr3A 77.138 608 102 19 1066 1667 644697725 644698301 4.260000e-83 318.0
3 TraesCS3A01G397400 chr3A 77.067 375 54 21 152 505 88197824 88198187 1.250000e-43 187.0
4 TraesCS3A01G397400 chr3A 86.842 114 15 0 966 1079 644696511 644696624 7.710000e-26 128.0
5 TraesCS3A01G397400 chr3D 93.352 1399 54 14 838 2217 506160884 506162262 0.000000e+00 2032.0
6 TraesCS3A01G397400 chr3D 86.740 724 54 19 1 710 506159902 506160597 0.000000e+00 767.0
7 TraesCS3A01G397400 chr3B 94.358 1223 57 7 839 2055 667855796 667857012 0.000000e+00 1866.0
8 TraesCS3A01G397400 chr3B 81.408 710 84 34 26 710 667853996 667854682 1.080000e-148 536.0
9 TraesCS3A01G397400 chr3B 91.121 214 11 2 2046 2251 667859520 667859733 1.560000e-72 283.0
10 TraesCS3A01G397400 chr3B 77.297 370 43 25 163 515 120398199 120398544 2.100000e-41 180.0
11 TraesCS3A01G397400 chr2A 97.767 403 8 1 2252 2654 42477032 42477433 0.000000e+00 693.0
12 TraesCS3A01G397400 chr5A 94.335 406 19 3 2251 2654 76199719 76199316 1.040000e-173 619.0
13 TraesCS3A01G397400 chr5A 85.396 404 38 9 2251 2654 81225146 81225528 1.480000e-107 399.0
14 TraesCS3A01G397400 chr6D 90.370 405 26 6 2251 2654 280908686 280908294 1.090000e-143 520.0
15 TraesCS3A01G397400 chr7D 89.901 406 26 7 2250 2654 44731563 44731954 2.360000e-140 508.0
16 TraesCS3A01G397400 chr7D 94.569 313 14 3 2247 2557 19699700 19700011 5.140000e-132 481.0
17 TraesCS3A01G397400 chr7D 84.861 251 17 9 2245 2493 393942153 393941922 1.590000e-57 233.0
18 TraesCS3A01G397400 chr5D 95.146 309 13 2 2251 2557 290387855 290387547 1.100000e-133 486.0
19 TraesCS3A01G397400 chr7A 94.805 308 13 3 2253 2557 735957780 735957473 6.650000e-131 477.0
20 TraesCS3A01G397400 chr6A 86.453 406 31 11 2251 2654 574223103 574223486 8.780000e-115 424.0
21 TraesCS3A01G397400 chr5B 85.714 406 36 9 2251 2654 562449859 562450244 2.460000e-110 409.0
22 TraesCS3A01G397400 chr4D 80.602 299 34 17 236 515 503521248 503521541 2.680000e-50 209.0
23 TraesCS3A01G397400 chr2B 80.195 308 37 14 153 437 94253350 94253044 2.680000e-50 209.0
24 TraesCS3A01G397400 chr4B 77.657 367 49 22 176 515 649252096 649252456 2.700000e-45 193.0
25 TraesCS3A01G397400 chr4B 78.523 298 40 19 236 515 649249514 649249805 9.770000e-40 174.0
26 TraesCS3A01G397400 chr1D 100.000 29 0 0 373 401 63540612 63540640 1.000000e-03 54.7
27 TraesCS3A01G397400 chr1B 100.000 29 0 0 373 401 101470469 101470497 1.000000e-03 54.7


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 TraesCS3A01G397400 chr3A 644779110 644781763 2653 False 4902.0 4902 100.000000 1 2654 1 chr3A.!!$F2 2653
1 TraesCS3A01G397400 chr3A 644696511 644698301 1790 False 223.0 318 81.990000 966 1667 2 chr3A.!!$F4 701
2 TraesCS3A01G397400 chr3D 506159902 506162262 2360 False 1399.5 2032 90.046000 1 2217 2 chr3D.!!$F1 2216
3 TraesCS3A01G397400 chr3B 667853996 667859733 5737 False 895.0 1866 88.962333 26 2251 3 chr3B.!!$F2 2225

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
805 1862 0.397254 GCTGAGCCCCACCTCTAGTA 60.397 60.0 0.0 0.0 33.02 1.82 F
972 2164 0.531200 GATCGGTTTCGGTGGTCTCT 59.469 55.0 0.0 0.0 36.95 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1649 3975 0.179006 GATGGATCCCTGGCTTCACC 60.179 60.0 9.90 0.00 39.84 4.02 R
2477 7339 0.243095 GAAAAGGCTGCAGCTGAAGG 59.757 55.0 35.82 9.95 41.70 3.46 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
56 61 4.580580 GGAGGTTTCTTCTTCTTCTTTGCA 59.419 41.667 0.00 0.00 0.00 4.08
82 88 6.269077 GGAAACCGGGGGATTATTTCATTATT 59.731 38.462 6.32 0.00 32.13 1.40
86 92 4.380444 CGGGGGATTATTTCATTATTGCCG 60.380 45.833 0.00 0.00 0.00 5.69
109 117 5.003804 GCCACTATAATTGTCCTACCATGG 58.996 45.833 11.19 11.19 0.00 3.66
123 131 5.188163 TCCTACCATGGAAATTTAGACGACA 59.812 40.000 21.47 0.00 32.39 4.35
125 133 6.542370 CCTACCATGGAAATTTAGACGACAAT 59.458 38.462 21.47 0.00 0.00 2.71
135 143 5.733620 TTTAGACGACAATAACTCCCACT 57.266 39.130 0.00 0.00 0.00 4.00
171 179 2.229792 GGACATGAAGTTTCTGCACCA 58.770 47.619 0.00 0.00 0.00 4.17
172 180 2.622942 GGACATGAAGTTTCTGCACCAA 59.377 45.455 0.00 0.00 0.00 3.67
174 182 4.262164 GGACATGAAGTTTCTGCACCAAAT 60.262 41.667 0.00 0.00 0.00 2.32
343 358 6.652900 GCTCTGAGAAATAGACTTTTTGGAGT 59.347 38.462 9.28 0.00 0.00 3.85
350 365 9.793259 AGAAATAGACTTTTTGGAGTGTCAATA 57.207 29.630 0.00 0.00 32.41 1.90
355 370 8.237811 AGACTTTTTGGAGTGTCAATATTGTT 57.762 30.769 14.97 0.50 32.41 2.83
356 371 8.695456 AGACTTTTTGGAGTGTCAATATTGTTT 58.305 29.630 14.97 0.16 32.41 2.83
357 372 9.313118 GACTTTTTGGAGTGTCAATATTGTTTT 57.687 29.630 14.97 0.49 0.00 2.43
358 373 9.665719 ACTTTTTGGAGTGTCAATATTGTTTTT 57.334 25.926 14.97 0.83 0.00 1.94
403 435 2.979151 TCTTCATGAAATTTTGCACGCG 59.021 40.909 9.88 3.53 0.00 6.01
409 441 1.849219 GAAATTTTGCACGCGTGTTCA 59.151 42.857 36.80 25.62 0.00 3.18
415 447 0.660488 TGCACGCGTGTTCAGAATTT 59.340 45.000 36.80 0.00 0.00 1.82
422 454 3.358700 CGCGTGTTCAGAATTTGTCAATG 59.641 43.478 0.00 0.00 0.00 2.82
427 459 6.253298 CGTGTTCAGAATTTGTCAATGTTTGT 59.747 34.615 0.00 0.00 0.00 2.83
430 462 8.441608 TGTTCAGAATTTGTCAATGTTTGTTTG 58.558 29.630 0.00 0.00 0.00 2.93
495 528 3.965379 TTTACTATTCACGAGGGTGCA 57.035 42.857 0.00 0.00 44.03 4.57
505 538 0.665670 CGAGGGTGCATATGAGCTCG 60.666 60.000 9.64 8.65 34.99 5.03
509 542 0.679505 GGTGCATATGAGCTCGGGTA 59.320 55.000 9.64 2.49 34.99 3.69
614 649 3.753797 CCAAACTTTGAGAGAAGGTAGGC 59.246 47.826 2.87 0.00 0.00 3.93
638 673 8.303876 GGCATTGTATTTTCCTCAAACTTTAGA 58.696 33.333 0.00 0.00 0.00 2.10
753 788 7.933215 TTTCATCATAGATGGATATTGGCAG 57.067 36.000 7.11 0.00 0.00 4.85
754 789 5.434408 TCATCATAGATGGATATTGGCAGC 58.566 41.667 7.11 0.00 0.00 5.25
783 1840 2.997315 CCAGGCCCGTCTCACTGA 60.997 66.667 0.00 0.00 32.86 3.41
795 1852 2.046507 CACTGACAGCTGAGCCCC 60.047 66.667 23.35 4.40 0.00 5.80
796 1853 2.527624 ACTGACAGCTGAGCCCCA 60.528 61.111 23.35 8.79 0.00 4.96
798 1855 3.618780 CTGACAGCTGAGCCCCACC 62.619 68.421 23.35 0.00 0.00 4.61
799 1856 3.325753 GACAGCTGAGCCCCACCT 61.326 66.667 23.35 0.00 0.00 4.00
800 1857 3.322318 GACAGCTGAGCCCCACCTC 62.322 68.421 23.35 0.00 0.00 3.85
801 1858 3.007920 CAGCTGAGCCCCACCTCT 61.008 66.667 8.42 0.00 33.02 3.69
802 1859 1.687146 CAGCTGAGCCCCACCTCTA 60.687 63.158 8.42 0.00 33.02 2.43
803 1860 1.382420 AGCTGAGCCCCACCTCTAG 60.382 63.158 0.00 0.00 33.02 2.43
804 1861 1.687493 GCTGAGCCCCACCTCTAGT 60.687 63.158 0.00 0.00 33.02 2.57
805 1862 0.397254 GCTGAGCCCCACCTCTAGTA 60.397 60.000 0.00 0.00 33.02 1.82
806 1863 1.404843 CTGAGCCCCACCTCTAGTAC 58.595 60.000 0.00 0.00 33.02 2.73
812 1978 2.892215 GCCCCACCTCTAGTACTACATC 59.108 54.545 0.00 0.00 0.00 3.06
830 1996 1.863267 TCGCAATTTGCAAACCCAAG 58.137 45.000 15.41 5.65 45.36 3.61
945 2137 4.840005 CCCGCGCTTCCCTCTTCC 62.840 72.222 5.56 0.00 0.00 3.46
963 2155 1.878522 CTGCTCCCGATCGGTTTCG 60.879 63.158 31.22 16.86 38.83 3.46
972 2164 0.531200 GATCGGTTTCGGTGGTCTCT 59.469 55.000 0.00 0.00 36.95 3.10
982 2174 3.362797 TGGTCTCTTCTCGCGCGT 61.363 61.111 30.98 0.00 0.00 6.01
1089 3394 1.224592 GTCCTCCACCATCCGCATT 59.775 57.895 0.00 0.00 0.00 3.56
1422 3742 3.373565 CGGCTTGCCAAGAACCCC 61.374 66.667 9.04 0.00 0.00 4.95
1521 3847 2.900838 GCTGCTGCCGATGCTGAT 60.901 61.111 3.85 0.00 38.61 2.90
1649 3975 2.303549 GATCCCCAGGACGTGCTCAG 62.304 65.000 6.61 1.04 32.98 3.35
1706 4036 3.057946 CGATGAACAGAGCAGGATCGATA 60.058 47.826 0.00 0.00 35.79 2.92
1881 4214 9.038072 TGGGAAGTACTGTAATACATTAGTTGA 57.962 33.333 13.34 0.00 30.26 3.18
1918 4251 7.572523 TTCAGAGACAAAGTTTGATGATGTT 57.427 32.000 22.23 0.00 0.00 2.71
2029 4364 7.178712 AGAAATCTAACACTTGTGAAGAACG 57.821 36.000 7.83 0.00 0.00 3.95
2110 6965 3.409026 TTGTGGCTTTTCTCCTCTCTC 57.591 47.619 0.00 0.00 0.00 3.20
2111 6966 2.614259 TGTGGCTTTTCTCCTCTCTCT 58.386 47.619 0.00 0.00 0.00 3.10
2132 6987 3.799281 TTTTTCTGCTTTGGACTGGTG 57.201 42.857 0.00 0.00 0.00 4.17
2198 7060 3.074538 ACAACTGTCTAATTTGAGCCCCT 59.925 43.478 0.00 0.00 0.00 4.79
2251 7113 0.539438 GACAACATGGGGTCAAGCCA 60.539 55.000 12.51 0.00 39.65 4.75
2252 7114 0.540365 ACAACATGGGGTCAAGCCAG 60.540 55.000 0.00 0.00 39.65 4.85
2253 7115 0.540365 CAACATGGGGTCAAGCCAGT 60.540 55.000 0.00 0.00 39.65 4.00
2254 7116 0.540365 AACATGGGGTCAAGCCAGTG 60.540 55.000 0.00 1.13 39.65 3.66
2255 7117 1.679977 CATGGGGTCAAGCCAGTGG 60.680 63.158 4.20 4.20 39.65 4.00
2256 7118 2.162906 ATGGGGTCAAGCCAGTGGT 61.163 57.895 11.74 0.00 39.65 4.16
2257 7119 2.282462 GGGGTCAAGCCAGTGGTG 60.282 66.667 11.74 1.78 39.65 4.17
2268 7130 3.819245 CAGTGGTGGACCCAGAAAA 57.181 52.632 0.00 0.00 46.45 2.29
2269 7131 2.065899 CAGTGGTGGACCCAGAAAAA 57.934 50.000 0.00 0.00 46.45 1.94
2294 7156 9.995003 AAAAATGAAGGATATGCACACTTTAAA 57.005 25.926 0.00 0.00 0.00 1.52
2295 7157 9.995003 AAAATGAAGGATATGCACACTTTAAAA 57.005 25.926 0.00 0.00 0.00 1.52
2296 7158 9.995003 AAATGAAGGATATGCACACTTTAAAAA 57.005 25.926 0.00 0.00 0.00 1.94
2351 7213 5.288804 TGGCAAAAGAATAACACAAAGAGC 58.711 37.500 0.00 0.00 0.00 4.09
2352 7214 5.068987 TGGCAAAAGAATAACACAAAGAGCT 59.931 36.000 0.00 0.00 0.00 4.09
2353 7215 5.631096 GGCAAAAGAATAACACAAAGAGCTC 59.369 40.000 5.27 5.27 0.00 4.09
2354 7216 6.208644 GCAAAAGAATAACACAAAGAGCTCA 58.791 36.000 17.77 0.00 0.00 4.26
2355 7217 6.697019 GCAAAAGAATAACACAAAGAGCTCAA 59.303 34.615 17.77 0.00 0.00 3.02
2356 7218 7.383300 GCAAAAGAATAACACAAAGAGCTCAAT 59.617 33.333 17.77 0.59 0.00 2.57
2357 7219 8.909671 CAAAAGAATAACACAAAGAGCTCAATC 58.090 33.333 17.77 0.00 0.00 2.67
2358 7220 7.750229 AAGAATAACACAAAGAGCTCAATCA 57.250 32.000 17.77 0.00 0.00 2.57
2359 7221 7.750229 AGAATAACACAAAGAGCTCAATCAA 57.250 32.000 17.77 0.00 0.00 2.57
2360 7222 8.345724 AGAATAACACAAAGAGCTCAATCAAT 57.654 30.769 17.77 0.00 0.00 2.57
2361 7223 8.800332 AGAATAACACAAAGAGCTCAATCAATT 58.200 29.630 17.77 6.02 0.00 2.32
2366 7228 9.598517 AACACAAAGAGCTCAATCAATTAAAAA 57.401 25.926 17.77 0.00 0.00 1.94
2386 7248 3.988379 AAAGCTCAATCAAGTTTCGCA 57.012 38.095 0.00 0.00 0.00 5.10
2387 7249 4.510038 AAAGCTCAATCAAGTTTCGCAT 57.490 36.364 0.00 0.00 0.00 4.73
2388 7250 5.627499 AAAGCTCAATCAAGTTTCGCATA 57.373 34.783 0.00 0.00 0.00 3.14
2389 7251 5.824904 AAGCTCAATCAAGTTTCGCATAT 57.175 34.783 0.00 0.00 0.00 1.78
2390 7252 5.824904 AGCTCAATCAAGTTTCGCATATT 57.175 34.783 0.00 0.00 0.00 1.28
2391 7253 6.925610 AGCTCAATCAAGTTTCGCATATTA 57.074 33.333 0.00 0.00 0.00 0.98
2392 7254 7.502120 AGCTCAATCAAGTTTCGCATATTAT 57.498 32.000 0.00 0.00 0.00 1.28
2393 7255 7.358066 AGCTCAATCAAGTTTCGCATATTATG 58.642 34.615 0.00 0.00 0.00 1.90
2394 7256 7.012704 AGCTCAATCAAGTTTCGCATATTATGT 59.987 33.333 5.60 0.00 0.00 2.29
2395 7257 7.645340 GCTCAATCAAGTTTCGCATATTATGTT 59.355 33.333 5.60 0.00 0.00 2.71
2396 7258 9.507280 CTCAATCAAGTTTCGCATATTATGTTT 57.493 29.630 5.60 0.00 0.00 2.83
2397 7259 9.502145 TCAATCAAGTTTCGCATATTATGTTTC 57.498 29.630 5.60 0.00 0.00 2.78
2398 7260 9.288124 CAATCAAGTTTCGCATATTATGTTTCA 57.712 29.630 5.60 0.00 0.00 2.69
2399 7261 9.507280 AATCAAGTTTCGCATATTATGTTTCAG 57.493 29.630 5.60 0.00 0.00 3.02
2400 7262 8.262715 TCAAGTTTCGCATATTATGTTTCAGA 57.737 30.769 5.60 0.00 0.00 3.27
2401 7263 8.726068 TCAAGTTTCGCATATTATGTTTCAGAA 58.274 29.630 5.60 2.42 0.00 3.02
2402 7264 9.340695 CAAGTTTCGCATATTATGTTTCAGAAA 57.659 29.630 5.60 0.00 0.00 2.52
2403 7265 9.906660 AAGTTTCGCATATTATGTTTCAGAAAA 57.093 25.926 0.00 0.00 0.00 2.29
2404 7266 9.906660 AGTTTCGCATATTATGTTTCAGAAAAA 57.093 25.926 0.00 0.00 0.00 1.94
2452 7314 9.647797 ACAATACAAATAGTCGTACATGAAAGA 57.352 29.630 0.00 0.00 0.00 2.52
2457 7319 9.084164 ACAAATAGTCGTACATGAAAGATACAC 57.916 33.333 0.00 0.00 0.00 2.90
2458 7320 9.083080 CAAATAGTCGTACATGAAAGATACACA 57.917 33.333 0.00 0.00 0.00 3.72
2459 7321 9.647797 AAATAGTCGTACATGAAAGATACACAA 57.352 29.630 0.00 0.00 0.00 3.33
2460 7322 8.858003 ATAGTCGTACATGAAAGATACACAAG 57.142 34.615 0.00 0.00 0.00 3.16
2461 7323 6.920817 AGTCGTACATGAAAGATACACAAGA 58.079 36.000 0.00 0.00 0.00 3.02
2462 7324 7.375834 AGTCGTACATGAAAGATACACAAGAA 58.624 34.615 0.00 0.00 0.00 2.52
2463 7325 8.035394 AGTCGTACATGAAAGATACACAAGAAT 58.965 33.333 0.00 0.00 0.00 2.40
2464 7326 9.297586 GTCGTACATGAAAGATACACAAGAATA 57.702 33.333 0.00 0.00 0.00 1.75
2465 7327 9.863845 TCGTACATGAAAGATACACAAGAATAA 57.136 29.630 0.00 0.00 0.00 1.40
2466 7328 9.901724 CGTACATGAAAGATACACAAGAATAAC 57.098 33.333 0.00 0.00 0.00 1.89
2470 7332 9.694520 CATGAAAGATACACAAGAATAACTTCG 57.305 33.333 0.00 0.00 36.61 3.79
2471 7333 8.251750 TGAAAGATACACAAGAATAACTTCGG 57.748 34.615 0.00 0.00 36.61 4.30
2472 7334 7.876068 TGAAAGATACACAAGAATAACTTCGGT 59.124 33.333 0.00 0.00 36.61 4.69
2473 7335 8.617290 AAAGATACACAAGAATAACTTCGGTT 57.383 30.769 0.00 0.00 41.52 4.44
2474 7336 8.617290 AAGATACACAAGAATAACTTCGGTTT 57.383 30.769 0.00 0.00 39.17 3.27
2475 7337 8.029642 AGATACACAAGAATAACTTCGGTTTG 57.970 34.615 0.00 0.00 39.17 2.93
2476 7338 4.855531 ACACAAGAATAACTTCGGTTTGC 58.144 39.130 0.00 0.00 39.17 3.68
2477 7339 4.226761 CACAAGAATAACTTCGGTTTGCC 58.773 43.478 0.00 0.00 39.17 4.52
2478 7340 3.254903 ACAAGAATAACTTCGGTTTGCCC 59.745 43.478 0.00 0.00 39.17 5.36
2479 7341 3.434940 AGAATAACTTCGGTTTGCCCT 57.565 42.857 0.00 0.00 39.17 5.19
2480 7342 3.763057 AGAATAACTTCGGTTTGCCCTT 58.237 40.909 0.00 0.00 39.17 3.95
2481 7343 3.756963 AGAATAACTTCGGTTTGCCCTTC 59.243 43.478 0.00 0.00 39.17 3.46
2482 7344 2.642154 TAACTTCGGTTTGCCCTTCA 57.358 45.000 0.00 0.00 39.17 3.02
2483 7345 1.318576 AACTTCGGTTTGCCCTTCAG 58.681 50.000 0.00 0.00 33.96 3.02
2484 7346 1.172812 ACTTCGGTTTGCCCTTCAGC 61.173 55.000 0.00 0.00 0.00 4.26
2485 7347 0.890996 CTTCGGTTTGCCCTTCAGCT 60.891 55.000 0.00 0.00 0.00 4.24
2486 7348 1.172180 TTCGGTTTGCCCTTCAGCTG 61.172 55.000 7.63 7.63 0.00 4.24
2487 7349 2.653115 GGTTTGCCCTTCAGCTGC 59.347 61.111 9.47 0.00 0.00 5.25
2488 7350 2.202395 GGTTTGCCCTTCAGCTGCA 61.202 57.895 9.47 0.00 0.00 4.41
2489 7351 1.288127 GTTTGCCCTTCAGCTGCAG 59.712 57.895 10.11 10.11 36.21 4.41
2490 7352 2.567497 TTTGCCCTTCAGCTGCAGC 61.567 57.895 31.53 31.53 42.49 5.25
2492 7354 4.737177 GCCCTTCAGCTGCAGCCT 62.737 66.667 34.39 19.10 43.38 4.58
2493 7355 2.035312 CCCTTCAGCTGCAGCCTT 59.965 61.111 34.39 15.43 43.38 4.35
2494 7356 1.605738 CCCTTCAGCTGCAGCCTTT 60.606 57.895 34.39 14.59 43.38 3.11
2495 7357 1.183676 CCCTTCAGCTGCAGCCTTTT 61.184 55.000 34.39 14.18 43.38 2.27
2496 7358 0.243095 CCTTCAGCTGCAGCCTTTTC 59.757 55.000 34.39 6.88 43.38 2.29
2497 7359 1.245732 CTTCAGCTGCAGCCTTTTCT 58.754 50.000 34.39 12.93 43.38 2.52
2498 7360 2.430465 CTTCAGCTGCAGCCTTTTCTA 58.570 47.619 34.39 12.35 43.38 2.10
2499 7361 2.795231 TCAGCTGCAGCCTTTTCTAT 57.205 45.000 34.39 11.28 43.38 1.98
2500 7362 3.077484 TCAGCTGCAGCCTTTTCTATT 57.923 42.857 34.39 10.47 43.38 1.73
2501 7363 3.424703 TCAGCTGCAGCCTTTTCTATTT 58.575 40.909 34.39 9.65 43.38 1.40
2502 7364 3.828451 TCAGCTGCAGCCTTTTCTATTTT 59.172 39.130 34.39 9.07 43.38 1.82
2503 7365 3.924686 CAGCTGCAGCCTTTTCTATTTTG 59.075 43.478 34.39 17.51 43.38 2.44
2504 7366 3.828451 AGCTGCAGCCTTTTCTATTTTGA 59.172 39.130 34.39 0.00 43.38 2.69
2505 7367 3.922850 GCTGCAGCCTTTTCTATTTTGAC 59.077 43.478 28.76 0.00 34.31 3.18
2506 7368 4.488879 CTGCAGCCTTTTCTATTTTGACC 58.511 43.478 0.00 0.00 0.00 4.02
2507 7369 4.151883 TGCAGCCTTTTCTATTTTGACCT 58.848 39.130 0.00 0.00 0.00 3.85
2508 7370 4.218417 TGCAGCCTTTTCTATTTTGACCTC 59.782 41.667 0.00 0.00 0.00 3.85
2509 7371 4.218417 GCAGCCTTTTCTATTTTGACCTCA 59.782 41.667 0.00 0.00 0.00 3.86
2510 7372 5.105595 GCAGCCTTTTCTATTTTGACCTCAT 60.106 40.000 0.00 0.00 0.00 2.90
2511 7373 6.327934 CAGCCTTTTCTATTTTGACCTCATG 58.672 40.000 0.00 0.00 0.00 3.07
2512 7374 6.012745 AGCCTTTTCTATTTTGACCTCATGT 58.987 36.000 0.00 0.00 0.00 3.21
2513 7375 6.494835 AGCCTTTTCTATTTTGACCTCATGTT 59.505 34.615 0.00 0.00 0.00 2.71
2514 7376 7.015584 AGCCTTTTCTATTTTGACCTCATGTTT 59.984 33.333 0.00 0.00 0.00 2.83
2515 7377 7.657354 GCCTTTTCTATTTTGACCTCATGTTTT 59.343 33.333 0.00 0.00 0.00 2.43
2516 7378 9.196552 CCTTTTCTATTTTGACCTCATGTTTTC 57.803 33.333 0.00 0.00 0.00 2.29
2517 7379 9.748708 CTTTTCTATTTTGACCTCATGTTTTCA 57.251 29.630 0.00 0.00 0.00 2.69
2519 7381 9.528018 TTTCTATTTTGACCTCATGTTTTCAAC 57.472 29.630 0.00 0.00 0.00 3.18
2520 7382 8.231692 TCTATTTTGACCTCATGTTTTCAACA 57.768 30.769 0.00 0.00 46.94 3.33
2521 7383 8.690884 TCTATTTTGACCTCATGTTTTCAACAA 58.309 29.630 0.00 0.00 45.86 2.83
2522 7384 9.311916 CTATTTTGACCTCATGTTTTCAACAAA 57.688 29.630 0.00 0.00 45.86 2.83
2523 7385 7.969536 TTTTGACCTCATGTTTTCAACAAAA 57.030 28.000 0.00 0.00 45.86 2.44
2524 7386 8.558973 TTTTGACCTCATGTTTTCAACAAAAT 57.441 26.923 0.00 0.00 45.86 1.82
2525 7387 7.536895 TTGACCTCATGTTTTCAACAAAATG 57.463 32.000 0.00 0.00 45.86 2.32
2526 7388 6.047870 TGACCTCATGTTTTCAACAAAATGG 58.952 36.000 0.00 0.00 45.86 3.16
2527 7389 6.127225 TGACCTCATGTTTTCAACAAAATGGA 60.127 34.615 0.00 0.00 45.86 3.41
2528 7390 6.048509 ACCTCATGTTTTCAACAAAATGGAC 58.951 36.000 0.00 0.00 45.86 4.02
2529 7391 6.047870 CCTCATGTTTTCAACAAAATGGACA 58.952 36.000 0.00 0.00 45.86 4.02
2530 7392 6.707161 CCTCATGTTTTCAACAAAATGGACAT 59.293 34.615 0.00 0.00 45.86 3.06
2531 7393 7.871973 CCTCATGTTTTCAACAAAATGGACATA 59.128 33.333 0.00 0.00 45.86 2.29
2532 7394 9.258826 CTCATGTTTTCAACAAAATGGACATAA 57.741 29.630 0.00 0.00 45.86 1.90
2533 7395 9.775854 TCATGTTTTCAACAAAATGGACATAAT 57.224 25.926 0.00 0.00 45.86 1.28
2563 7425 7.984617 ACTAATCCTCTTTATCTTGAGTTCTGC 59.015 37.037 0.00 0.00 0.00 4.26
2564 7426 5.745312 TCCTCTTTATCTTGAGTTCTGCA 57.255 39.130 0.00 0.00 0.00 4.41
2565 7427 6.114187 TCCTCTTTATCTTGAGTTCTGCAA 57.886 37.500 0.00 0.00 0.00 4.08
2566 7428 6.169094 TCCTCTTTATCTTGAGTTCTGCAAG 58.831 40.000 0.00 0.00 43.09 4.01
2567 7429 5.936956 CCTCTTTATCTTGAGTTCTGCAAGT 59.063 40.000 0.00 0.00 42.49 3.16
2568 7430 7.039011 TCCTCTTTATCTTGAGTTCTGCAAGTA 60.039 37.037 0.00 0.00 42.49 2.24
2569 7431 7.064016 CCTCTTTATCTTGAGTTCTGCAAGTAC 59.936 40.741 0.00 0.00 42.49 2.73
2570 7432 7.441836 TCTTTATCTTGAGTTCTGCAAGTACA 58.558 34.615 0.00 0.00 42.49 2.90
2571 7433 7.931407 TCTTTATCTTGAGTTCTGCAAGTACAA 59.069 33.333 0.00 0.00 42.49 2.41
2572 7434 5.931441 ATCTTGAGTTCTGCAAGTACAAC 57.069 39.130 0.00 0.00 42.49 3.32
2573 7435 4.765273 TCTTGAGTTCTGCAAGTACAACA 58.235 39.130 0.00 0.00 42.49 3.33
2574 7436 5.182487 TCTTGAGTTCTGCAAGTACAACAA 58.818 37.500 0.00 0.00 42.49 2.83
2575 7437 5.645929 TCTTGAGTTCTGCAAGTACAACAAA 59.354 36.000 0.00 0.00 42.49 2.83
2576 7438 5.888691 TGAGTTCTGCAAGTACAACAAAA 57.111 34.783 0.00 0.00 36.61 2.44
2577 7439 5.636837 TGAGTTCTGCAAGTACAACAAAAC 58.363 37.500 0.00 0.00 36.61 2.43
2578 7440 5.182190 TGAGTTCTGCAAGTACAACAAAACA 59.818 36.000 0.00 0.00 36.61 2.83
2579 7441 6.019779 AGTTCTGCAAGTACAACAAAACAA 57.980 33.333 0.00 0.00 36.61 2.83
2580 7442 6.092748 AGTTCTGCAAGTACAACAAAACAAG 58.907 36.000 0.00 0.00 36.61 3.16
2581 7443 5.888691 TCTGCAAGTACAACAAAACAAGA 57.111 34.783 0.00 0.00 33.76 3.02
2582 7444 6.260870 TCTGCAAGTACAACAAAACAAGAA 57.739 33.333 0.00 0.00 33.76 2.52
2583 7445 6.321717 TCTGCAAGTACAACAAAACAAGAAG 58.678 36.000 0.00 0.00 33.76 2.85
2584 7446 6.019779 TGCAAGTACAACAAAACAAGAAGT 57.980 33.333 0.00 0.00 0.00 3.01
2585 7447 7.119992 TCTGCAAGTACAACAAAACAAGAAGTA 59.880 33.333 0.00 0.00 33.76 2.24
2586 7448 7.594714 TGCAAGTACAACAAAACAAGAAGTAA 58.405 30.769 0.00 0.00 0.00 2.24
2587 7449 7.753132 TGCAAGTACAACAAAACAAGAAGTAAG 59.247 33.333 0.00 0.00 0.00 2.34
2588 7450 7.966204 GCAAGTACAACAAAACAAGAAGTAAGA 59.034 33.333 0.00 0.00 0.00 2.10
2589 7451 9.490663 CAAGTACAACAAAACAAGAAGTAAGAG 57.509 33.333 0.00 0.00 0.00 2.85
2590 7452 8.788325 AGTACAACAAAACAAGAAGTAAGAGT 57.212 30.769 0.00 0.00 0.00 3.24
2591 7453 8.880750 AGTACAACAAAACAAGAAGTAAGAGTC 58.119 33.333 0.00 0.00 0.00 3.36
2592 7454 7.085052 ACAACAAAACAAGAAGTAAGAGTCC 57.915 36.000 0.00 0.00 0.00 3.85
2593 7455 6.884836 ACAACAAAACAAGAAGTAAGAGTCCT 59.115 34.615 0.00 0.00 0.00 3.85
2594 7456 8.044908 ACAACAAAACAAGAAGTAAGAGTCCTA 58.955 33.333 0.00 0.00 0.00 2.94
2595 7457 8.336080 CAACAAAACAAGAAGTAAGAGTCCTAC 58.664 37.037 0.00 0.00 0.00 3.18
2596 7458 7.562135 ACAAAACAAGAAGTAAGAGTCCTACA 58.438 34.615 1.83 0.00 0.00 2.74
2597 7459 8.044908 ACAAAACAAGAAGTAAGAGTCCTACAA 58.955 33.333 1.83 0.00 0.00 2.41
2598 7460 9.057089 CAAAACAAGAAGTAAGAGTCCTACAAT 57.943 33.333 1.83 0.00 0.00 2.71
2599 7461 9.628500 AAAACAAGAAGTAAGAGTCCTACAATT 57.372 29.630 1.83 0.00 0.00 2.32
2601 7463 9.708092 AACAAGAAGTAAGAGTCCTACAATTAC 57.292 33.333 1.83 0.00 0.00 1.89
2602 7464 8.867097 ACAAGAAGTAAGAGTCCTACAATTACA 58.133 33.333 1.83 0.00 0.00 2.41
2603 7465 9.706691 CAAGAAGTAAGAGTCCTACAATTACAA 57.293 33.333 1.83 0.00 0.00 2.41
2604 7466 9.708092 AAGAAGTAAGAGTCCTACAATTACAAC 57.292 33.333 1.83 0.00 0.00 3.32
2605 7467 8.867097 AGAAGTAAGAGTCCTACAATTACAACA 58.133 33.333 1.83 0.00 0.00 3.33
2606 7468 9.485206 GAAGTAAGAGTCCTACAATTACAACAA 57.515 33.333 1.83 0.00 0.00 2.83
2607 7469 9.841295 AAGTAAGAGTCCTACAATTACAACAAA 57.159 29.630 1.83 0.00 0.00 2.83
2608 7470 9.841295 AGTAAGAGTCCTACAATTACAACAAAA 57.159 29.630 1.83 0.00 0.00 2.44
2609 7471 9.874215 GTAAGAGTCCTACAATTACAACAAAAC 57.126 33.333 0.00 0.00 0.00 2.43
2610 7472 7.186021 AGAGTCCTACAATTACAACAAAACG 57.814 36.000 0.00 0.00 0.00 3.60
2611 7473 6.987992 AGAGTCCTACAATTACAACAAAACGA 59.012 34.615 0.00 0.00 0.00 3.85
2612 7474 7.660208 AGAGTCCTACAATTACAACAAAACGAT 59.340 33.333 0.00 0.00 0.00 3.73
2613 7475 7.581476 AGTCCTACAATTACAACAAAACGATG 58.419 34.615 0.00 0.00 0.00 3.84
2614 7476 7.442969 AGTCCTACAATTACAACAAAACGATGA 59.557 33.333 0.00 0.00 0.00 2.92
2615 7477 7.532884 GTCCTACAATTACAACAAAACGATGAC 59.467 37.037 0.00 0.00 0.00 3.06
2616 7478 6.518395 CCTACAATTACAACAAAACGATGACG 59.482 38.462 0.00 0.00 45.75 4.35
2617 7479 6.050454 ACAATTACAACAAAACGATGACGA 57.950 33.333 0.00 0.00 42.66 4.20
2618 7480 6.664515 ACAATTACAACAAAACGATGACGAT 58.335 32.000 0.00 0.00 42.66 3.73
2619 7481 7.136119 ACAATTACAACAAAACGATGACGATT 58.864 30.769 0.00 0.00 42.66 3.34
2620 7482 7.112844 ACAATTACAACAAAACGATGACGATTG 59.887 33.333 0.00 0.00 42.66 2.67
2621 7483 4.545823 ACAACAAAACGATGACGATTGT 57.454 36.364 0.00 0.00 45.86 2.71
2627 7489 3.896648 AACGATGACGATTGTTTTGCT 57.103 38.095 0.00 0.00 42.66 3.91
2628 7490 3.455619 ACGATGACGATTGTTTTGCTC 57.544 42.857 0.00 0.00 42.66 4.26
2629 7491 2.805671 ACGATGACGATTGTTTTGCTCA 59.194 40.909 0.00 0.00 42.66 4.26
2630 7492 3.249799 ACGATGACGATTGTTTTGCTCAA 59.750 39.130 0.00 0.00 42.66 3.02
2631 7493 4.218265 CGATGACGATTGTTTTGCTCAAA 58.782 39.130 0.00 0.00 42.66 2.69
2632 7494 4.319115 CGATGACGATTGTTTTGCTCAAAG 59.681 41.667 0.00 0.00 42.66 2.77
2633 7495 3.963665 TGACGATTGTTTTGCTCAAAGG 58.036 40.909 0.00 0.00 0.00 3.11
2634 7496 3.629855 TGACGATTGTTTTGCTCAAAGGA 59.370 39.130 0.00 0.00 0.00 3.36
2635 7497 4.278170 TGACGATTGTTTTGCTCAAAGGAT 59.722 37.500 0.00 0.00 0.00 3.24
2636 7498 5.471797 TGACGATTGTTTTGCTCAAAGGATA 59.528 36.000 0.00 0.00 0.00 2.59
2637 7499 6.016693 TGACGATTGTTTTGCTCAAAGGATAA 60.017 34.615 0.00 0.00 0.00 1.75
2638 7500 6.744112 ACGATTGTTTTGCTCAAAGGATAAA 58.256 32.000 0.00 0.00 0.00 1.40
2639 7501 7.378181 ACGATTGTTTTGCTCAAAGGATAAAT 58.622 30.769 0.00 0.00 0.00 1.40
2640 7502 8.519526 ACGATTGTTTTGCTCAAAGGATAAATA 58.480 29.630 0.00 0.00 0.00 1.40
2641 7503 9.013490 CGATTGTTTTGCTCAAAGGATAAATAG 57.987 33.333 0.00 0.00 0.00 1.73
2642 7504 9.860898 GATTGTTTTGCTCAAAGGATAAATAGT 57.139 29.630 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.552350 ACTTGGACCAACTAGTGAGTTAGTTA 59.448 38.462 1.69 0.00 44.39 2.24
22 23 1.850345 AGAAACCTCCACTTGGACCAA 59.150 47.619 6.76 6.76 39.78 3.67
56 61 2.583566 TGAAATAATCCCCCGGTTTCCT 59.416 45.455 0.00 0.00 0.00 3.36
82 88 1.488812 AGGACAATTATAGTGGCGGCA 59.511 47.619 7.97 7.97 0.00 5.69
86 92 5.003804 CCATGGTAGGACAATTATAGTGGC 58.996 45.833 2.57 0.00 0.00 5.01
109 117 7.333672 AGTGGGAGTTATTGTCGTCTAAATTTC 59.666 37.037 0.00 0.00 0.00 2.17
123 131 6.070653 TGGTATTCGTGTTAGTGGGAGTTATT 60.071 38.462 0.00 0.00 0.00 1.40
125 133 4.771577 TGGTATTCGTGTTAGTGGGAGTTA 59.228 41.667 0.00 0.00 0.00 2.24
135 143 4.223255 TCATGTCCCTTGGTATTCGTGTTA 59.777 41.667 0.00 0.00 0.00 2.41
171 179 5.187381 TGTTCATGTGGGTGCATATGAATTT 59.813 36.000 6.97 0.00 42.00 1.82
172 180 4.710865 TGTTCATGTGGGTGCATATGAATT 59.289 37.500 6.97 0.00 42.00 2.17
174 182 3.694926 TGTTCATGTGGGTGCATATGAA 58.305 40.909 6.97 0.00 39.32 2.57
254 264 4.510711 TCATGAAATTTTGCACGCATGTTT 59.489 33.333 12.42 0.00 35.75 2.83
322 337 7.279615 TGACACTCCAAAAAGTCTATTTCTCA 58.720 34.615 0.00 0.00 32.41 3.27
329 344 8.918202 ACAATATTGACACTCCAAAAAGTCTA 57.082 30.769 22.16 0.00 32.41 2.59
403 435 7.524294 ACAAACATTGACAAATTCTGAACAC 57.476 32.000 0.00 0.00 0.00 3.32
409 441 6.981762 TGCAAACAAACATTGACAAATTCT 57.018 29.167 0.00 0.00 0.00 2.40
472 505 5.979993 TGCACCCTCGTGAATAGTAAAATA 58.020 37.500 0.00 0.00 43.14 1.40
473 506 4.839121 TGCACCCTCGTGAATAGTAAAAT 58.161 39.130 0.00 0.00 43.14 1.82
495 528 2.894126 CCTTCTGTACCCGAGCTCATAT 59.106 50.000 15.40 0.00 0.00 1.78
505 538 2.676176 GCGAAAGTACCCTTCTGTACCC 60.676 54.545 0.00 0.00 41.63 3.69
509 542 3.139077 CAAAGCGAAAGTACCCTTCTGT 58.861 45.455 0.00 0.00 0.00 3.41
552 585 4.086457 CACTTACCAAACCCTTTATGCCT 58.914 43.478 0.00 0.00 0.00 4.75
638 673 6.625267 AGTAGGGACAACTGAGTATGGATAT 58.375 40.000 0.00 0.00 0.00 1.63
727 762 8.709272 TGCCAATATCCATCTATGATGAAAAA 57.291 30.769 8.91 0.00 0.00 1.94
728 763 7.094075 GCTGCCAATATCCATCTATGATGAAAA 60.094 37.037 8.91 0.00 0.00 2.29
729 764 6.376299 GCTGCCAATATCCATCTATGATGAAA 59.624 38.462 8.91 0.00 0.00 2.69
730 765 5.884232 GCTGCCAATATCCATCTATGATGAA 59.116 40.000 8.91 0.00 0.00 2.57
731 766 5.434408 GCTGCCAATATCCATCTATGATGA 58.566 41.667 8.91 0.00 0.00 2.92
732 767 4.579340 GGCTGCCAATATCCATCTATGATG 59.421 45.833 15.17 0.92 0.00 3.07
753 788 2.043953 CCTGGGCTTGGTAAGGGC 60.044 66.667 0.00 0.00 0.00 5.19
754 789 2.043953 GCCTGGGCTTGGTAAGGG 60.044 66.667 4.12 0.00 38.26 3.95
781 1838 3.640407 GGTGGGGCTCAGCTGTCA 61.640 66.667 14.67 3.23 40.48 3.58
795 1852 4.895224 TTGCGATGTAGTACTAGAGGTG 57.105 45.455 1.87 0.00 0.00 4.00
796 1853 6.273825 CAAATTGCGATGTAGTACTAGAGGT 58.726 40.000 1.87 0.00 0.00 3.85
798 1855 6.204075 GCAAATTGCGATGTAGTACTAGAG 57.796 41.667 0.90 0.00 31.71 2.43
830 1996 2.108362 CGCGAGGGATTGGGGTAC 59.892 66.667 0.00 0.00 0.00 3.34
908 2100 0.617820 CGGGGAAAGAGGGGAGAAGA 60.618 60.000 0.00 0.00 0.00 2.87
909 2101 1.908483 CGGGGAAAGAGGGGAGAAG 59.092 63.158 0.00 0.00 0.00 2.85
910 2102 2.298661 GCGGGGAAAGAGGGGAGAA 61.299 63.158 0.00 0.00 0.00 2.87
945 2137 1.878522 CGAAACCGATCGGGAGCAG 60.879 63.158 35.87 19.50 39.12 4.24
963 2155 2.507324 GCGCGAGAAGAGACCACC 60.507 66.667 12.10 0.00 0.00 4.61
1581 3907 2.202236 GAACCATCTGCCCCAGCTCA 62.202 60.000 0.00 0.00 40.80 4.26
1589 3915 2.511600 CCGTCCGAACCATCTGCC 60.512 66.667 0.00 0.00 0.00 4.85
1621 3947 0.397941 TCCTGGGGATCGATGAATGC 59.602 55.000 0.54 0.00 0.00 3.56
1649 3975 0.179006 GATGGATCCCTGGCTTCACC 60.179 60.000 9.90 0.00 39.84 4.02
1747 4078 6.564709 CATACATATGGCACTTGTATGCTT 57.435 37.500 25.95 7.37 43.44 3.91
1881 4214 9.512588 ACTTTGTCTCTGAATTAATCAAGTGAT 57.487 29.630 0.00 0.00 37.67 3.06
1896 4229 6.732154 ACAACATCATCAAACTTTGTCTCTG 58.268 36.000 1.44 0.08 0.00 3.35
1918 4251 8.918961 AGACAAACGAAACAATAATTTGAACA 57.081 26.923 2.27 0.00 36.64 3.18
1931 4264 4.527564 CATGGACTGAAGACAAACGAAAC 58.472 43.478 0.00 0.00 0.00 2.78
2029 4364 2.945668 GGAATTGCTCACTGATGTACCC 59.054 50.000 0.00 0.00 0.00 3.69
2132 6987 5.182001 ACACAAGATCAGTTGCCACTTAATC 59.818 40.000 0.00 0.00 0.00 1.75
2229 7091 1.892329 GCTTGACCCCATGTTGTCCAT 60.892 52.381 8.80 0.00 0.00 3.41
2239 7101 2.776526 ACCACTGGCTTGACCCCA 60.777 61.111 0.00 0.00 37.83 4.96
2246 7108 2.776526 TGGGTCCACCACTGGCTT 60.777 61.111 0.00 0.00 46.80 4.35
2268 7130 9.995003 TTTAAAGTGTGCATATCCTTCATTTTT 57.005 25.926 0.00 0.00 0.00 1.94
2269 7131 9.995003 TTTTAAAGTGTGCATATCCTTCATTTT 57.005 25.926 0.00 0.00 0.00 1.82
2270 7132 9.995003 TTTTTAAAGTGTGCATATCCTTCATTT 57.005 25.926 0.00 0.00 0.00 2.32
2325 7187 7.761249 GCTCTTTGTGTTATTCTTTTGCCATAT 59.239 33.333 0.00 0.00 0.00 1.78
2326 7188 7.039784 AGCTCTTTGTGTTATTCTTTTGCCATA 60.040 33.333 0.00 0.00 0.00 2.74
2327 7189 5.928264 GCTCTTTGTGTTATTCTTTTGCCAT 59.072 36.000 0.00 0.00 0.00 4.40
2328 7190 5.068987 AGCTCTTTGTGTTATTCTTTTGCCA 59.931 36.000 0.00 0.00 0.00 4.92
2329 7191 5.532557 AGCTCTTTGTGTTATTCTTTTGCC 58.467 37.500 0.00 0.00 0.00 4.52
2330 7192 6.208644 TGAGCTCTTTGTGTTATTCTTTTGC 58.791 36.000 16.19 0.00 0.00 3.68
2331 7193 8.807667 ATTGAGCTCTTTGTGTTATTCTTTTG 57.192 30.769 16.19 0.00 0.00 2.44
2332 7194 8.632679 TGATTGAGCTCTTTGTGTTATTCTTTT 58.367 29.630 16.19 0.00 0.00 2.27
2333 7195 8.169977 TGATTGAGCTCTTTGTGTTATTCTTT 57.830 30.769 16.19 0.00 0.00 2.52
2334 7196 7.750229 TGATTGAGCTCTTTGTGTTATTCTT 57.250 32.000 16.19 0.00 0.00 2.52
2335 7197 7.750229 TTGATTGAGCTCTTTGTGTTATTCT 57.250 32.000 16.19 0.00 0.00 2.40
2336 7198 8.976986 AATTGATTGAGCTCTTTGTGTTATTC 57.023 30.769 16.19 0.00 0.00 1.75
2340 7202 9.598517 TTTTTAATTGATTGAGCTCTTTGTGTT 57.401 25.926 16.19 6.26 0.00 3.32
2364 7226 4.681744 TGCGAAACTTGATTGAGCTTTTT 58.318 34.783 0.00 0.00 0.00 1.94
2365 7227 4.305989 TGCGAAACTTGATTGAGCTTTT 57.694 36.364 0.00 0.00 0.00 2.27
2366 7228 3.988379 TGCGAAACTTGATTGAGCTTT 57.012 38.095 0.00 0.00 0.00 3.51
2367 7229 5.824904 ATATGCGAAACTTGATTGAGCTT 57.175 34.783 0.00 0.00 0.00 3.74
2368 7230 5.824904 AATATGCGAAACTTGATTGAGCT 57.175 34.783 0.00 0.00 0.00 4.09
2369 7231 7.134815 ACATAATATGCGAAACTTGATTGAGC 58.865 34.615 0.00 0.00 0.00 4.26
2370 7232 9.507280 AAACATAATATGCGAAACTTGATTGAG 57.493 29.630 0.00 0.00 0.00 3.02
2371 7233 9.502145 GAAACATAATATGCGAAACTTGATTGA 57.498 29.630 0.00 0.00 0.00 2.57
2372 7234 9.288124 TGAAACATAATATGCGAAACTTGATTG 57.712 29.630 0.00 0.00 0.00 2.67
2373 7235 9.507280 CTGAAACATAATATGCGAAACTTGATT 57.493 29.630 0.00 0.00 0.00 2.57
2374 7236 8.892723 TCTGAAACATAATATGCGAAACTTGAT 58.107 29.630 0.00 0.00 0.00 2.57
2375 7237 8.262715 TCTGAAACATAATATGCGAAACTTGA 57.737 30.769 0.00 0.00 0.00 3.02
2376 7238 8.894409 TTCTGAAACATAATATGCGAAACTTG 57.106 30.769 0.00 0.00 0.00 3.16
2377 7239 9.906660 TTTTCTGAAACATAATATGCGAAACTT 57.093 25.926 1.58 0.00 0.00 2.66
2378 7240 9.906660 TTTTTCTGAAACATAATATGCGAAACT 57.093 25.926 1.58 0.00 0.00 2.66
2426 7288 9.647797 TCTTTCATGTACGACTATTTGTATTGT 57.352 29.630 0.00 0.00 0.00 2.71
2431 7293 9.084164 GTGTATCTTTCATGTACGACTATTTGT 57.916 33.333 0.00 0.00 0.00 2.83
2432 7294 9.083080 TGTGTATCTTTCATGTACGACTATTTG 57.917 33.333 0.00 0.00 0.00 2.32
2433 7295 9.647797 TTGTGTATCTTTCATGTACGACTATTT 57.352 29.630 0.00 0.00 0.00 1.40
2434 7296 9.302345 CTTGTGTATCTTTCATGTACGACTATT 57.698 33.333 0.00 0.00 0.00 1.73
2435 7297 8.683615 TCTTGTGTATCTTTCATGTACGACTAT 58.316 33.333 0.00 0.00 0.00 2.12
2436 7298 8.047413 TCTTGTGTATCTTTCATGTACGACTA 57.953 34.615 0.00 0.00 0.00 2.59
2437 7299 6.920817 TCTTGTGTATCTTTCATGTACGACT 58.079 36.000 0.00 0.00 0.00 4.18
2438 7300 7.576750 TTCTTGTGTATCTTTCATGTACGAC 57.423 36.000 0.00 0.00 0.00 4.34
2439 7301 9.863845 TTATTCTTGTGTATCTTTCATGTACGA 57.136 29.630 0.00 0.00 0.00 3.43
2440 7302 9.901724 GTTATTCTTGTGTATCTTTCATGTACG 57.098 33.333 0.00 0.00 0.00 3.67
2444 7306 9.694520 CGAAGTTATTCTTGTGTATCTTTCATG 57.305 33.333 0.00 0.00 36.40 3.07
2445 7307 8.883731 CCGAAGTTATTCTTGTGTATCTTTCAT 58.116 33.333 0.00 0.00 36.40 2.57
2446 7308 7.876068 ACCGAAGTTATTCTTGTGTATCTTTCA 59.124 33.333 0.00 0.00 36.40 2.69
2447 7309 8.252964 ACCGAAGTTATTCTTGTGTATCTTTC 57.747 34.615 0.00 0.00 36.40 2.62
2448 7310 8.617290 AACCGAAGTTATTCTTGTGTATCTTT 57.383 30.769 0.00 0.00 36.40 2.52
2449 7311 8.504005 CAAACCGAAGTTATTCTTGTGTATCTT 58.496 33.333 0.00 0.00 36.40 2.40
2450 7312 7.360946 GCAAACCGAAGTTATTCTTGTGTATCT 60.361 37.037 0.00 0.00 36.40 1.98
2451 7313 6.741358 GCAAACCGAAGTTATTCTTGTGTATC 59.259 38.462 0.00 0.00 36.40 2.24
2452 7314 6.349033 GGCAAACCGAAGTTATTCTTGTGTAT 60.349 38.462 0.00 0.00 36.40 2.29
2453 7315 5.049267 GGCAAACCGAAGTTATTCTTGTGTA 60.049 40.000 0.00 0.00 36.40 2.90
2454 7316 4.261447 GGCAAACCGAAGTTATTCTTGTGT 60.261 41.667 0.00 0.00 36.40 3.72
2455 7317 4.226761 GGCAAACCGAAGTTATTCTTGTG 58.773 43.478 0.00 0.00 36.40 3.33
2456 7318 3.254903 GGGCAAACCGAAGTTATTCTTGT 59.745 43.478 0.00 0.00 36.40 3.16
2457 7319 3.506067 AGGGCAAACCGAAGTTATTCTTG 59.494 43.478 0.00 0.00 46.96 3.02
2458 7320 3.763057 AGGGCAAACCGAAGTTATTCTT 58.237 40.909 0.00 0.00 46.96 2.52
2459 7321 3.434940 AGGGCAAACCGAAGTTATTCT 57.565 42.857 0.00 0.00 46.96 2.40
2460 7322 3.504520 TGAAGGGCAAACCGAAGTTATTC 59.495 43.478 0.00 0.00 46.96 1.75
2461 7323 3.492337 TGAAGGGCAAACCGAAGTTATT 58.508 40.909 0.00 0.00 46.96 1.40
2462 7324 3.081804 CTGAAGGGCAAACCGAAGTTAT 58.918 45.455 0.00 0.00 46.96 1.89
2463 7325 2.500229 CTGAAGGGCAAACCGAAGTTA 58.500 47.619 0.00 0.00 46.96 2.24
2464 7326 1.318576 CTGAAGGGCAAACCGAAGTT 58.681 50.000 0.00 0.00 46.96 2.66
2465 7327 1.172812 GCTGAAGGGCAAACCGAAGT 61.173 55.000 0.00 0.00 46.96 3.01
2466 7328 0.890996 AGCTGAAGGGCAAACCGAAG 60.891 55.000 0.00 0.00 46.96 3.79
2467 7329 1.150536 AGCTGAAGGGCAAACCGAA 59.849 52.632 0.00 0.00 46.96 4.30
2468 7330 1.600636 CAGCTGAAGGGCAAACCGA 60.601 57.895 8.42 0.00 46.96 4.69
2469 7331 2.956987 CAGCTGAAGGGCAAACCG 59.043 61.111 8.42 0.00 46.96 4.44
2470 7332 2.151049 CTGCAGCTGAAGGGCAAACC 62.151 60.000 20.43 0.00 37.06 3.27
2471 7333 1.288127 CTGCAGCTGAAGGGCAAAC 59.712 57.895 20.43 0.00 37.06 2.93
2472 7334 2.567497 GCTGCAGCTGAAGGGCAAA 61.567 57.895 31.33 0.00 37.06 3.68
2473 7335 2.987547 GCTGCAGCTGAAGGGCAA 60.988 61.111 31.33 0.00 37.06 4.52
2475 7337 4.737177 AGGCTGCAGCTGAAGGGC 62.737 66.667 35.82 18.70 41.70 5.19
2476 7338 1.183676 AAAAGGCTGCAGCTGAAGGG 61.184 55.000 35.82 7.48 41.70 3.95
2477 7339 0.243095 GAAAAGGCTGCAGCTGAAGG 59.757 55.000 35.82 9.95 41.70 3.46
2478 7340 1.245732 AGAAAAGGCTGCAGCTGAAG 58.754 50.000 35.82 19.30 41.70 3.02
2479 7341 2.566833 TAGAAAAGGCTGCAGCTGAA 57.433 45.000 35.82 5.87 41.70 3.02
2480 7342 2.795231 ATAGAAAAGGCTGCAGCTGA 57.205 45.000 35.82 14.91 41.70 4.26
2481 7343 3.863142 AAATAGAAAAGGCTGCAGCTG 57.137 42.857 35.82 10.11 41.70 4.24
2482 7344 3.828451 TCAAAATAGAAAAGGCTGCAGCT 59.172 39.130 35.82 18.48 41.70 4.24
2483 7345 3.922850 GTCAAAATAGAAAAGGCTGCAGC 59.077 43.478 30.88 30.88 41.14 5.25
2484 7346 4.219288 AGGTCAAAATAGAAAAGGCTGCAG 59.781 41.667 10.11 10.11 0.00 4.41
2485 7347 4.151883 AGGTCAAAATAGAAAAGGCTGCA 58.848 39.130 0.50 0.00 0.00 4.41
2486 7348 4.218417 TGAGGTCAAAATAGAAAAGGCTGC 59.782 41.667 0.00 0.00 0.00 5.25
2487 7349 5.964958 TGAGGTCAAAATAGAAAAGGCTG 57.035 39.130 0.00 0.00 0.00 4.85
2488 7350 6.012745 ACATGAGGTCAAAATAGAAAAGGCT 58.987 36.000 0.00 0.00 0.00 4.58
2489 7351 6.272822 ACATGAGGTCAAAATAGAAAAGGC 57.727 37.500 0.00 0.00 0.00 4.35
2490 7352 9.196552 GAAAACATGAGGTCAAAATAGAAAAGG 57.803 33.333 0.00 0.00 0.00 3.11
2491 7353 9.748708 TGAAAACATGAGGTCAAAATAGAAAAG 57.251 29.630 0.00 0.00 0.00 2.27
2537 7399 7.984617 GCAGAACTCAAGATAAAGAGGATTAGT 59.015 37.037 0.00 0.00 36.20 2.24
2538 7400 7.984050 TGCAGAACTCAAGATAAAGAGGATTAG 59.016 37.037 0.00 0.00 36.20 1.73
2539 7401 7.851228 TGCAGAACTCAAGATAAAGAGGATTA 58.149 34.615 0.00 0.00 36.20 1.75
2540 7402 6.715280 TGCAGAACTCAAGATAAAGAGGATT 58.285 36.000 0.00 0.00 36.20 3.01
2541 7403 6.305272 TGCAGAACTCAAGATAAAGAGGAT 57.695 37.500 0.00 0.00 36.20 3.24
2542 7404 5.745312 TGCAGAACTCAAGATAAAGAGGA 57.255 39.130 0.00 0.00 36.20 3.71
2543 7405 5.936956 ACTTGCAGAACTCAAGATAAAGAGG 59.063 40.000 9.40 0.00 42.52 3.69
2544 7406 7.600375 TGTACTTGCAGAACTCAAGATAAAGAG 59.400 37.037 9.40 0.00 42.52 2.85
2545 7407 7.441836 TGTACTTGCAGAACTCAAGATAAAGA 58.558 34.615 9.40 0.00 42.52 2.52
2546 7408 7.658179 TGTACTTGCAGAACTCAAGATAAAG 57.342 36.000 9.40 0.00 42.52 1.85
2547 7409 7.497579 TGTTGTACTTGCAGAACTCAAGATAAA 59.502 33.333 9.40 0.00 42.52 1.40
2548 7410 6.989759 TGTTGTACTTGCAGAACTCAAGATAA 59.010 34.615 9.40 0.27 42.52 1.75
2549 7411 6.521162 TGTTGTACTTGCAGAACTCAAGATA 58.479 36.000 9.40 0.00 42.52 1.98
2550 7412 5.368145 TGTTGTACTTGCAGAACTCAAGAT 58.632 37.500 9.40 0.00 42.52 2.40
2551 7413 4.765273 TGTTGTACTTGCAGAACTCAAGA 58.235 39.130 9.40 0.00 42.52 3.02
2552 7414 5.484173 TTGTTGTACTTGCAGAACTCAAG 57.516 39.130 0.00 1.63 44.71 3.02
2553 7415 5.888691 TTTGTTGTACTTGCAGAACTCAA 57.111 34.783 0.00 0.00 0.00 3.02
2554 7416 5.182190 TGTTTTGTTGTACTTGCAGAACTCA 59.818 36.000 14.21 0.00 31.29 3.41
2555 7417 5.636837 TGTTTTGTTGTACTTGCAGAACTC 58.363 37.500 14.21 0.00 31.29 3.01
2556 7418 5.637006 TGTTTTGTTGTACTTGCAGAACT 57.363 34.783 14.21 0.00 31.29 3.01
2557 7419 6.090129 TCTTGTTTTGTTGTACTTGCAGAAC 58.910 36.000 0.00 3.41 0.00 3.01
2558 7420 6.260870 TCTTGTTTTGTTGTACTTGCAGAA 57.739 33.333 0.00 0.00 0.00 3.02
2559 7421 5.888691 TCTTGTTTTGTTGTACTTGCAGA 57.111 34.783 0.00 0.00 0.00 4.26
2560 7422 6.092748 ACTTCTTGTTTTGTTGTACTTGCAG 58.907 36.000 0.00 0.00 0.00 4.41
2561 7423 6.019779 ACTTCTTGTTTTGTTGTACTTGCA 57.980 33.333 0.00 0.00 0.00 4.08
2562 7424 7.966204 TCTTACTTCTTGTTTTGTTGTACTTGC 59.034 33.333 0.00 0.00 0.00 4.01
2563 7425 9.490663 CTCTTACTTCTTGTTTTGTTGTACTTG 57.509 33.333 0.00 0.00 0.00 3.16
2564 7426 9.227777 ACTCTTACTTCTTGTTTTGTTGTACTT 57.772 29.630 0.00 0.00 0.00 2.24
2565 7427 8.788325 ACTCTTACTTCTTGTTTTGTTGTACT 57.212 30.769 0.00 0.00 0.00 2.73
2566 7428 8.121086 GGACTCTTACTTCTTGTTTTGTTGTAC 58.879 37.037 0.00 0.00 0.00 2.90
2567 7429 8.044908 AGGACTCTTACTTCTTGTTTTGTTGTA 58.955 33.333 0.00 0.00 0.00 2.41
2568 7430 6.884836 AGGACTCTTACTTCTTGTTTTGTTGT 59.115 34.615 0.00 0.00 0.00 3.32
2569 7431 7.321745 AGGACTCTTACTTCTTGTTTTGTTG 57.678 36.000 0.00 0.00 0.00 3.33
2570 7432 8.044908 TGTAGGACTCTTACTTCTTGTTTTGTT 58.955 33.333 0.51 0.00 0.00 2.83
2571 7433 7.562135 TGTAGGACTCTTACTTCTTGTTTTGT 58.438 34.615 0.51 0.00 0.00 2.83
2572 7434 8.433421 TTGTAGGACTCTTACTTCTTGTTTTG 57.567 34.615 0.51 0.00 0.00 2.44
2573 7435 9.628500 AATTGTAGGACTCTTACTTCTTGTTTT 57.372 29.630 0.51 0.00 0.00 2.43
2575 7437 9.708092 GTAATTGTAGGACTCTTACTTCTTGTT 57.292 33.333 0.51 0.00 0.00 2.83
2576 7438 8.867097 TGTAATTGTAGGACTCTTACTTCTTGT 58.133 33.333 0.51 0.00 0.00 3.16
2577 7439 9.706691 TTGTAATTGTAGGACTCTTACTTCTTG 57.293 33.333 0.51 0.00 0.00 3.02
2578 7440 9.708092 GTTGTAATTGTAGGACTCTTACTTCTT 57.292 33.333 0.51 0.00 0.00 2.52
2579 7441 8.867097 TGTTGTAATTGTAGGACTCTTACTTCT 58.133 33.333 0.51 0.00 0.00 2.85
2580 7442 9.485206 TTGTTGTAATTGTAGGACTCTTACTTC 57.515 33.333 0.51 0.00 0.00 3.01
2581 7443 9.841295 TTTGTTGTAATTGTAGGACTCTTACTT 57.159 29.630 0.51 0.00 0.00 2.24
2582 7444 9.841295 TTTTGTTGTAATTGTAGGACTCTTACT 57.159 29.630 0.51 0.00 0.00 2.24
2583 7445 9.874215 GTTTTGTTGTAATTGTAGGACTCTTAC 57.126 33.333 0.00 0.00 0.00 2.34
2584 7446 8.767085 CGTTTTGTTGTAATTGTAGGACTCTTA 58.233 33.333 0.00 0.00 0.00 2.10
2585 7447 7.496591 TCGTTTTGTTGTAATTGTAGGACTCTT 59.503 33.333 0.00 0.00 0.00 2.85
2586 7448 6.987992 TCGTTTTGTTGTAATTGTAGGACTCT 59.012 34.615 0.00 0.00 0.00 3.24
2587 7449 7.181143 TCGTTTTGTTGTAATTGTAGGACTC 57.819 36.000 0.00 0.00 0.00 3.36
2588 7450 7.442969 TCATCGTTTTGTTGTAATTGTAGGACT 59.557 33.333 0.00 0.00 0.00 3.85
2589 7451 7.532884 GTCATCGTTTTGTTGTAATTGTAGGAC 59.467 37.037 0.00 0.00 0.00 3.85
2590 7452 7.569774 CGTCATCGTTTTGTTGTAATTGTAGGA 60.570 37.037 0.00 0.00 0.00 2.94
2591 7453 6.518395 CGTCATCGTTTTGTTGTAATTGTAGG 59.482 38.462 0.00 0.00 0.00 3.18
2592 7454 7.285069 TCGTCATCGTTTTGTTGTAATTGTAG 58.715 34.615 0.00 0.00 38.33 2.74
2593 7455 7.175073 TCGTCATCGTTTTGTTGTAATTGTA 57.825 32.000 0.00 0.00 38.33 2.41
2594 7456 6.050454 TCGTCATCGTTTTGTTGTAATTGT 57.950 33.333 0.00 0.00 38.33 2.71
2595 7457 7.112844 ACAATCGTCATCGTTTTGTTGTAATTG 59.887 33.333 0.00 0.00 39.38 2.32
2596 7458 7.136119 ACAATCGTCATCGTTTTGTTGTAATT 58.864 30.769 0.00 0.00 39.38 1.40
2597 7459 6.664515 ACAATCGTCATCGTTTTGTTGTAAT 58.335 32.000 0.00 0.00 39.38 1.89
2598 7460 6.050454 ACAATCGTCATCGTTTTGTTGTAA 57.950 33.333 0.00 0.00 39.38 2.41
2599 7461 5.660629 ACAATCGTCATCGTTTTGTTGTA 57.339 34.783 0.00 0.00 39.38 2.41
2600 7462 4.545823 ACAATCGTCATCGTTTTGTTGT 57.454 36.364 0.00 0.00 39.38 3.32
2601 7463 5.864830 AAACAATCGTCATCGTTTTGTTG 57.135 34.783 17.12 0.00 44.42 3.33
2602 7464 6.254600 CAAAACAATCGTCATCGTTTTGTT 57.745 33.333 15.07 13.59 46.62 2.83
2603 7465 5.864830 CAAAACAATCGTCATCGTTTTGT 57.135 34.783 15.07 7.13 46.62 2.83
2605 7467 4.606961 AGCAAAACAATCGTCATCGTTTT 58.393 34.783 0.00 0.00 41.05 2.43
2606 7468 4.219033 GAGCAAAACAATCGTCATCGTTT 58.781 39.130 0.00 0.00 38.33 3.60
2607 7469 3.249799 TGAGCAAAACAATCGTCATCGTT 59.750 39.130 0.00 0.00 38.33 3.85
2608 7470 2.805671 TGAGCAAAACAATCGTCATCGT 59.194 40.909 0.00 0.00 38.33 3.73
2609 7471 3.454042 TGAGCAAAACAATCGTCATCG 57.546 42.857 0.00 0.00 38.55 3.84
2610 7472 4.618489 CCTTTGAGCAAAACAATCGTCATC 59.382 41.667 0.00 0.00 0.00 2.92
2611 7473 4.278170 TCCTTTGAGCAAAACAATCGTCAT 59.722 37.500 0.00 0.00 0.00 3.06
2612 7474 3.629855 TCCTTTGAGCAAAACAATCGTCA 59.370 39.130 0.00 0.00 0.00 4.35
2613 7475 4.223320 TCCTTTGAGCAAAACAATCGTC 57.777 40.909 0.00 0.00 0.00 4.20
2614 7476 4.853924 ATCCTTTGAGCAAAACAATCGT 57.146 36.364 0.00 0.00 0.00 3.73
2615 7477 7.816945 ATTTATCCTTTGAGCAAAACAATCG 57.183 32.000 0.00 0.00 0.00 3.34
2616 7478 9.860898 ACTATTTATCCTTTGAGCAAAACAATC 57.139 29.630 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.