Multiple sequence alignment - TraesCS5A01G131200

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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 TraesCS5A01G131200 chr5A 100.000 4760 0 0 1 4760 295585795 295590554 0.000000e+00 8791.0
1 TraesCS5A01G131200 chr5A 97.379 1030 27 0 3731 4760 295595011 295596040 0.000000e+00 1753.0
2 TraesCS5A01G131200 chr5A 92.115 279 20 2 2278 2555 632587422 632587699 4.470000e-105 392.0
3 TraesCS5A01G131200 chr5A 77.522 347 52 11 221 544 647608284 647607941 8.130000e-43 185.0
4 TraesCS5A01G131200 chr5A 76.636 214 40 7 4 215 455299770 455299565 5.040000e-20 110.0
5 TraesCS5A01G131200 chr5A 90.909 55 5 0 49 103 148232206 148232260 1.840000e-09 75.0
6 TraesCS5A01G131200 chr5D 92.973 1423 60 21 866 2277 223229352 223230745 0.000000e+00 2037.0
7 TraesCS5A01G131200 chr5D 96.495 1027 30 3 3731 4757 457555866 457556886 0.000000e+00 1692.0
8 TraesCS5A01G131200 chr5D 91.904 877 64 6 1 874 223228339 223229211 0.000000e+00 1219.0
9 TraesCS5A01G131200 chr5D 95.087 631 29 1 2550 3180 223230742 223231370 0.000000e+00 992.0
10 TraesCS5A01G131200 chr5D 97.842 556 11 1 3176 3730 223231450 223232005 0.000000e+00 959.0
11 TraesCS5A01G131200 chr5D 76.596 235 48 7 317 546 306796322 306796090 6.470000e-24 122.0
12 TraesCS5A01G131200 chr5D 92.727 55 4 0 49 103 130669562 130669616 3.950000e-11 80.5
13 TraesCS5A01G131200 chr5D 80.952 105 16 3 4 106 432938036 432938138 3.950000e-11 80.5
14 TraesCS5A01G131200 chrUn 97.681 1035 19 2 3731 4760 353417386 353416352 0.000000e+00 1773.0
15 TraesCS5A01G131200 chrUn 96.505 1030 30 3 3731 4760 98210065 98209042 0.000000e+00 1698.0
16 TraesCS5A01G131200 chr5B 96.714 1065 32 1 2666 3730 249713308 249712247 0.000000e+00 1770.0
17 TraesCS5A01G131200 chr5B 94.772 899 40 4 451 1346 249715089 249714195 0.000000e+00 1393.0
18 TraesCS5A01G131200 chr5B 91.029 836 52 15 1362 2190 249714126 249713307 0.000000e+00 1107.0
19 TraesCS5A01G131200 chr5B 86.141 469 45 7 4 452 249715875 249715407 5.540000e-134 488.0
20 TraesCS5A01G131200 chr3D 96.522 1035 30 3 3731 4760 437767504 437768537 0.000000e+00 1707.0
21 TraesCS5A01G131200 chr3D 96.602 1030 29 2 3731 4760 437762071 437763094 0.000000e+00 1703.0
22 TraesCS5A01G131200 chr3D 84.615 65 10 0 232 296 164305717 164305781 1.110000e-06 65.8
23 TraesCS5A01G131200 chr7D 96.054 1039 35 3 3727 4760 458156366 458155329 0.000000e+00 1687.0
24 TraesCS5A01G131200 chr4D 96.139 1036 33 4 3731 4760 85622290 85621256 0.000000e+00 1685.0
25 TraesCS5A01G131200 chr4B 96.117 1030 39 1 3731 4760 24407689 24408717 0.000000e+00 1679.0
26 TraesCS5A01G131200 chr4B 92.446 278 19 2 2278 2554 467910454 467910178 3.450000e-106 396.0
27 TraesCS5A01G131200 chr4B 76.324 321 52 9 221 519 478572982 478573300 2.970000e-32 150.0
28 TraesCS5A01G131200 chr3A 96.350 274 10 0 2278 2551 681997608 681997881 7.260000e-123 451.0
29 TraesCS5A01G131200 chr3A 76.081 347 60 11 220 546 456717002 456717345 4.930000e-35 159.0
30 TraesCS5A01G131200 chr3A 84.466 103 16 0 4 106 456716745 456716847 8.430000e-18 102.0
31 TraesCS5A01G131200 chr6A 94.182 275 15 1 2279 2552 563538025 563537751 7.370000e-113 418.0
32 TraesCS5A01G131200 chr2A 92.553 282 20 1 2272 2553 62093319 62093599 2.060000e-108 403.0
33 TraesCS5A01G131200 chr2A 92.446 278 20 1 2275 2552 39930257 39930533 3.450000e-106 396.0
34 TraesCS5A01G131200 chr7B 92.806 278 18 2 2278 2554 643118094 643117818 7.420000e-108 401.0
35 TraesCS5A01G131200 chr6B 92.115 279 21 1 2274 2552 664713678 664713401 4.470000e-105 392.0
36 TraesCS5A01G131200 chr1B 91.756 279 22 1 2274 2552 397661867 397661590 2.080000e-103 387.0
37 TraesCS5A01G131200 chr1D 76.923 351 56 12 220 547 208513460 208513808 4.900000e-40 176.0
38 TraesCS5A01G131200 chr1D 75.216 347 64 7 220 546 18988359 18988703 1.380000e-30 145.0
39 TraesCS5A01G131200 chr2D 76.190 336 56 10 232 545 2508184 2507851 6.380000e-34 156.0
40 TraesCS5A01G131200 chr2D 86.957 69 9 0 221 289 617068742 617068810 1.420000e-10 78.7
41 TraesCS5A01G131200 chr2B 73.529 340 68 14 219 538 151101953 151102290 5.040000e-20 110.0
42 TraesCS5A01G131200 chr2B 86.047 86 12 0 4 89 151101708 151101793 5.070000e-15 93.5
43 TraesCS5A01G131200 chr2B 82.828 99 16 1 217 315 673053020 673053117 2.360000e-13 87.9
44 TraesCS5A01G131200 chr7A 86.667 75 10 0 4 78 681815535 681815609 3.050000e-12 84.2
45 TraesCS5A01G131200 chr1A 90.698 43 4 0 220 262 17320852 17320894 1.850000e-04 58.4


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 TraesCS5A01G131200 chr5A 295585795 295590554 4759 False 8791.00 8791 100.0000 1 4760 1 chr5A.!!$F2 4759
1 TraesCS5A01G131200 chr5A 295595011 295596040 1029 False 1753.00 1753 97.3790 3731 4760 1 chr5A.!!$F3 1029
2 TraesCS5A01G131200 chr5D 457555866 457556886 1020 False 1692.00 1692 96.4950 3731 4757 1 chr5D.!!$F3 1026
3 TraesCS5A01G131200 chr5D 223228339 223232005 3666 False 1301.75 2037 94.4515 1 3730 4 chr5D.!!$F4 3729
4 TraesCS5A01G131200 chrUn 353416352 353417386 1034 True 1773.00 1773 97.6810 3731 4760 1 chrUn.!!$R2 1029
5 TraesCS5A01G131200 chrUn 98209042 98210065 1023 True 1698.00 1698 96.5050 3731 4760 1 chrUn.!!$R1 1029
6 TraesCS5A01G131200 chr5B 249712247 249715875 3628 True 1189.50 1770 92.1640 4 3730 4 chr5B.!!$R1 3726
7 TraesCS5A01G131200 chr3D 437767504 437768537 1033 False 1707.00 1707 96.5220 3731 4760 1 chr3D.!!$F3 1029
8 TraesCS5A01G131200 chr3D 437762071 437763094 1023 False 1703.00 1703 96.6020 3731 4760 1 chr3D.!!$F2 1029
9 TraesCS5A01G131200 chr7D 458155329 458156366 1037 True 1687.00 1687 96.0540 3727 4760 1 chr7D.!!$R1 1033
10 TraesCS5A01G131200 chr4D 85621256 85622290 1034 True 1685.00 1685 96.1390 3731 4760 1 chr4D.!!$R1 1029
11 TraesCS5A01G131200 chr4B 24407689 24408717 1028 False 1679.00 1679 96.1170 3731 4760 1 chr4B.!!$F1 1029

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
180 181 0.033504 GTCACTTTCGTCCTGGCTGA 59.966 55.0 0.0 0.0 0.00 4.26 F
792 1136 0.163360 AAAGACGACGAGACGAGACG 59.837 55.0 0.0 0.0 37.03 4.18 F
1784 2335 0.397114 ATCCAGATTTTTCCCGGGGC 60.397 55.0 23.5 3.4 0.00 5.80 F
2280 2846 0.108281 GTCAGAAAGGGACTACGGGC 60.108 60.0 0.0 0.0 38.49 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1094 1590 1.379443 TCGCGTATCTCCACCACCT 60.379 57.895 5.77 0.0 0.00 4.00 R
2267 2833 0.828677 GTACATGCCCGTAGTCCCTT 59.171 55.000 0.00 0.0 0.00 3.95 R
3427 4081 0.244450 CCCGGTAGTTGCACGAGTTA 59.756 55.000 0.00 0.0 0.00 2.24 R
4257 4911 0.101759 GCGACACAATACCGCCTCTA 59.898 55.000 0.00 0.0 42.77 2.43 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
95 96 4.681978 GGCGAGAGGTGTTGCGGT 62.682 66.667 0.00 0.00 0.00 5.68
178 179 1.371558 GGTCACTTTCGTCCTGGCT 59.628 57.895 0.00 0.00 0.00 4.75
180 181 0.033504 GTCACTTTCGTCCTGGCTGA 59.966 55.000 0.00 0.00 0.00 4.26
277 278 1.919240 TCTCTTCGTGTCAGGGCTAA 58.081 50.000 0.00 0.00 0.00 3.09
327 348 1.159905 TAGTGGTCTCTTGGGGGCA 59.840 57.895 0.00 0.00 0.00 5.36
359 380 3.708451 TCTTAGGTGTGCTAGGTCATCA 58.292 45.455 0.00 0.00 0.00 3.07
381 402 1.808945 GTGGGCTGTGTTCAGATCTTG 59.191 52.381 0.00 0.00 43.76 3.02
387 408 2.221169 TGTGTTCAGATCTTGGTGTGC 58.779 47.619 0.00 0.00 0.00 4.57
395 416 1.200948 GATCTTGGTGTGCTCTTTGCC 59.799 52.381 0.00 0.00 42.00 4.52
431 452 2.912900 GCGTTCTGCGTTATCTGATC 57.087 50.000 0.00 0.00 43.66 2.92
449 470 3.327464 TGATCATCATGGGATCGGCTTTA 59.673 43.478 17.68 3.22 43.21 1.85
457 797 2.637872 TGGGATCGGCTTTATAAGAGGG 59.362 50.000 0.00 0.00 0.00 4.30
462 802 3.302161 TCGGCTTTATAAGAGGGCTACA 58.698 45.455 0.00 0.00 0.00 2.74
477 817 3.825014 GGGCTACATCATCATCTTGCATT 59.175 43.478 0.00 0.00 0.00 3.56
478 818 5.005740 GGGCTACATCATCATCTTGCATTA 58.994 41.667 0.00 0.00 0.00 1.90
479 819 5.123502 GGGCTACATCATCATCTTGCATTAG 59.876 44.000 0.00 0.00 0.00 1.73
495 835 4.517453 TGCATTAGTCGCCTTTGTACTTTT 59.483 37.500 0.00 0.00 0.00 2.27
511 852 8.779354 TTGTACTTTTATGGTTGTTGCTTTTT 57.221 26.923 0.00 0.00 0.00 1.94
568 911 6.494893 TTTGAAGGTGAGGATTCATTTACG 57.505 37.500 0.00 0.00 35.47 3.18
719 1063 1.829849 TCTCGTCGTCTCCTCTAGGAA 59.170 52.381 0.00 0.00 44.91 3.36
792 1136 0.163360 AAAGACGACGAGACGAGACG 59.837 55.000 0.00 0.00 37.03 4.18
796 1140 1.341133 CGACGAGACGAGACGAGAC 59.659 63.158 0.00 0.00 35.09 3.36
889 1385 0.947180 TCCGTTCAAACTAGCGTGGC 60.947 55.000 0.00 0.00 0.00 5.01
916 1412 1.203758 CGTGTCAGGCGGCCATATATA 59.796 52.381 23.09 0.00 0.00 0.86
950 1446 1.134788 CGGCGTCATCTATATTCCCCC 60.135 57.143 0.00 0.00 0.00 5.40
1006 1502 2.516589 CGCGACCACATGATGACCG 61.517 63.158 0.00 2.88 0.00 4.79
1079 1575 2.432456 GTCGTCATCGCCACTGCA 60.432 61.111 0.00 0.00 37.32 4.41
1400 1951 2.099062 GTGCTTTGCGCGATCCAG 59.901 61.111 12.10 0.00 43.27 3.86
1439 1990 3.906846 AGAGGTGTCAGTTCATTCCTTCT 59.093 43.478 0.00 0.00 0.00 2.85
1522 2073 2.912900 CGTACTACTACGGCGACTAC 57.087 55.000 16.62 2.37 41.84 2.73
1539 2090 4.380974 CGACTACGATTAATTAGAACCGCC 59.619 45.833 0.00 0.00 42.66 6.13
1541 2092 3.441496 ACGATTAATTAGAACCGCCGA 57.559 42.857 0.00 0.00 0.00 5.54
1593 2144 1.525923 CAGTATGGCTGCTCCTGCT 59.474 57.895 0.00 0.00 38.52 4.24
1784 2335 0.397114 ATCCAGATTTTTCCCGGGGC 60.397 55.000 23.50 3.40 0.00 5.80
1812 2367 5.825151 TGACTACTGACAGGACAGATAGATG 59.175 44.000 7.51 0.00 40.63 2.90
1834 2389 4.700692 TGCTCCTACTATATCGTGGATCAC 59.299 45.833 0.00 0.00 0.00 3.06
1904 2459 3.769739 ACACAGAGAATTGTACCTGCA 57.230 42.857 0.00 0.00 0.00 4.41
1906 2461 3.324846 ACACAGAGAATTGTACCTGCAGA 59.675 43.478 17.39 0.00 0.00 4.26
1919 2474 3.771216 ACCTGCAGAGAATCCAAAATGT 58.229 40.909 17.39 0.00 33.66 2.71
1927 2482 6.530534 GCAGAGAATCCAAAATGTCATTTCTG 59.469 38.462 11.19 11.87 33.66 3.02
1945 2500 6.949578 TTTCTGACAAGAAAGCAAAAACAG 57.050 33.333 0.00 0.00 45.44 3.16
1965 2524 4.194640 CAGACGATCACATCCCTTGAAAT 58.805 43.478 0.00 0.00 0.00 2.17
1999 2558 9.759473 TTCTCCTGAATTTGGAAATATCTTCTT 57.241 29.630 3.31 0.00 32.61 2.52
2118 2678 6.046593 TGACTGGTAGAACAACAAAGTACTG 58.953 40.000 0.00 0.00 0.00 2.74
2122 2682 3.944422 AGAACAACAAAGTACTGCGTG 57.056 42.857 0.00 0.00 0.00 5.34
2127 2693 4.124238 ACAACAAAGTACTGCGTGTGTAT 58.876 39.130 0.00 0.00 0.00 2.29
2154 2720 7.011202 CACGTGTGTAGTACTGTAGTCTGATAT 59.989 40.741 7.58 0.00 0.00 1.63
2157 2723 8.675504 GTGTGTAGTACTGTAGTCTGATATGTT 58.324 37.037 5.39 0.00 0.00 2.71
2158 2724 9.239551 TGTGTAGTACTGTAGTCTGATATGTTT 57.760 33.333 5.39 0.00 0.00 2.83
2192 2758 3.192001 AGAATGTAGGCGACGAGTAACAA 59.808 43.478 0.00 0.00 0.00 2.83
2194 2760 1.608109 TGTAGGCGACGAGTAACAACA 59.392 47.619 0.00 0.00 0.00 3.33
2200 2766 2.110990 CGACGAGTAACAACACGACAA 58.889 47.619 2.50 0.00 0.00 3.18
2208 2774 6.455380 CGAGTAACAACACGACAACCTTTAAA 60.455 38.462 0.00 0.00 0.00 1.52
2211 2777 8.245491 AGTAACAACACGACAACCTTTAAATTT 58.755 29.630 0.00 0.00 0.00 1.82
2244 2810 1.040646 ACTTGCAACCGTCAGAGAGA 58.959 50.000 0.00 0.00 0.00 3.10
2248 2814 1.412710 TGCAACCGTCAGAGAGAAACT 59.587 47.619 0.00 0.00 0.00 2.66
2249 2815 2.062519 GCAACCGTCAGAGAGAAACTC 58.937 52.381 0.00 0.00 45.22 3.01
2267 2833 9.498307 GAGAAACTCGTTTTTATTTTGTCAGAA 57.502 29.630 0.00 0.00 32.11 3.02
2273 2839 7.197703 TCGTTTTTATTTTGTCAGAAAGGGAC 58.802 34.615 0.00 0.00 35.83 4.46
2275 2841 8.347035 CGTTTTTATTTTGTCAGAAAGGGACTA 58.653 33.333 0.00 0.00 38.49 2.59
2276 2842 9.459640 GTTTTTATTTTGTCAGAAAGGGACTAC 57.540 33.333 0.00 0.00 38.49 2.73
2277 2843 7.429636 TTTATTTTGTCAGAAAGGGACTACG 57.570 36.000 0.00 0.00 38.49 3.51
2278 2844 3.396260 TTTGTCAGAAAGGGACTACGG 57.604 47.619 0.00 0.00 38.49 4.02
2279 2845 1.263356 TGTCAGAAAGGGACTACGGG 58.737 55.000 0.00 0.00 38.49 5.28
2280 2846 0.108281 GTCAGAAAGGGACTACGGGC 60.108 60.000 0.00 0.00 38.49 6.13
2281 2847 0.543410 TCAGAAAGGGACTACGGGCA 60.543 55.000 0.00 0.00 38.49 5.36
2282 2848 0.541863 CAGAAAGGGACTACGGGCAT 59.458 55.000 0.00 0.00 38.49 4.40
2283 2849 0.541863 AGAAAGGGACTACGGGCATG 59.458 55.000 0.00 0.00 38.49 4.06
2284 2850 0.252197 GAAAGGGACTACGGGCATGT 59.748 55.000 0.00 0.00 38.49 3.21
2285 2851 1.483415 GAAAGGGACTACGGGCATGTA 59.517 52.381 0.00 0.00 38.49 2.29
2286 2852 0.828677 AAGGGACTACGGGCATGTAC 59.171 55.000 0.00 0.00 38.49 2.90
2287 2853 0.324923 AGGGACTACGGGCATGTACA 60.325 55.000 0.00 0.00 36.02 2.90
2288 2854 0.538118 GGGACTACGGGCATGTACAA 59.462 55.000 0.00 0.00 0.00 2.41
2289 2855 1.140252 GGGACTACGGGCATGTACAAT 59.860 52.381 0.00 0.00 0.00 2.71
2290 2856 2.366266 GGGACTACGGGCATGTACAATA 59.634 50.000 0.00 0.00 0.00 1.90
2291 2857 3.554337 GGGACTACGGGCATGTACAATAG 60.554 52.174 0.00 0.00 0.00 1.73
2292 2858 3.069158 GGACTACGGGCATGTACAATAGT 59.931 47.826 0.00 1.65 0.00 2.12
2293 2859 4.442472 GGACTACGGGCATGTACAATAGTT 60.442 45.833 0.00 0.00 0.00 2.24
2294 2860 4.690122 ACTACGGGCATGTACAATAGTTC 58.310 43.478 0.00 0.00 0.00 3.01
2295 2861 3.906720 ACGGGCATGTACAATAGTTCT 57.093 42.857 0.00 0.00 0.00 3.01
2296 2862 5.595542 ACTACGGGCATGTACAATAGTTCTA 59.404 40.000 0.00 0.00 0.00 2.10
2297 2863 5.546621 ACGGGCATGTACAATAGTTCTAT 57.453 39.130 0.00 0.00 0.00 1.98
2298 2864 5.539048 ACGGGCATGTACAATAGTTCTATC 58.461 41.667 0.00 0.00 0.00 2.08
2299 2865 5.304614 ACGGGCATGTACAATAGTTCTATCT 59.695 40.000 0.00 0.00 0.00 1.98
2300 2866 6.183360 ACGGGCATGTACAATAGTTCTATCTT 60.183 38.462 0.00 0.00 0.00 2.40
2301 2867 7.014905 ACGGGCATGTACAATAGTTCTATCTTA 59.985 37.037 0.00 0.00 0.00 2.10
2302 2868 7.542477 CGGGCATGTACAATAGTTCTATCTTAG 59.458 40.741 0.00 0.00 0.00 2.18
2303 2869 7.332182 GGGCATGTACAATAGTTCTATCTTAGC 59.668 40.741 0.00 0.00 0.00 3.09
2304 2870 7.872993 GGCATGTACAATAGTTCTATCTTAGCA 59.127 37.037 0.00 0.00 0.00 3.49
2305 2871 9.261180 GCATGTACAATAGTTCTATCTTAGCAA 57.739 33.333 0.00 0.00 0.00 3.91
2308 2874 9.261180 TGTACAATAGTTCTATCTTAGCAATGC 57.739 33.333 0.00 0.00 0.00 3.56
2309 2875 7.736447 ACAATAGTTCTATCTTAGCAATGCC 57.264 36.000 0.00 0.00 0.00 4.40
2310 2876 7.282585 ACAATAGTTCTATCTTAGCAATGCCA 58.717 34.615 0.00 0.00 0.00 4.92
2311 2877 7.941238 ACAATAGTTCTATCTTAGCAATGCCAT 59.059 33.333 0.00 0.00 0.00 4.40
2312 2878 7.918536 ATAGTTCTATCTTAGCAATGCCATG 57.081 36.000 0.00 0.00 0.00 3.66
2313 2879 5.688807 AGTTCTATCTTAGCAATGCCATGT 58.311 37.500 0.00 0.00 0.00 3.21
2314 2880 6.830912 AGTTCTATCTTAGCAATGCCATGTA 58.169 36.000 0.00 0.00 0.00 2.29
2315 2881 7.456725 AGTTCTATCTTAGCAATGCCATGTAT 58.543 34.615 0.00 0.00 0.00 2.29
2316 2882 7.389884 AGTTCTATCTTAGCAATGCCATGTATG 59.610 37.037 0.00 0.00 0.00 2.39
2317 2883 7.008021 TCTATCTTAGCAATGCCATGTATGA 57.992 36.000 0.00 0.00 0.00 2.15
2318 2884 7.627311 TCTATCTTAGCAATGCCATGTATGAT 58.373 34.615 0.00 4.03 0.00 2.45
2319 2885 8.761689 TCTATCTTAGCAATGCCATGTATGATA 58.238 33.333 0.00 4.93 0.00 2.15
2320 2886 9.387257 CTATCTTAGCAATGCCATGTATGATAA 57.613 33.333 0.00 0.00 0.00 1.75
2321 2887 8.640063 ATCTTAGCAATGCCATGTATGATAAA 57.360 30.769 0.00 0.00 0.00 1.40
2322 2888 8.640063 TCTTAGCAATGCCATGTATGATAAAT 57.360 30.769 0.00 0.00 0.00 1.40
2323 2889 8.517056 TCTTAGCAATGCCATGTATGATAAATG 58.483 33.333 0.00 0.00 0.00 2.32
2324 2890 6.904463 AGCAATGCCATGTATGATAAATGA 57.096 33.333 0.00 0.00 0.00 2.57
2325 2891 7.476540 AGCAATGCCATGTATGATAAATGAT 57.523 32.000 0.00 0.00 0.00 2.45
2326 2892 7.320399 AGCAATGCCATGTATGATAAATGATG 58.680 34.615 0.00 0.28 0.00 3.07
2327 2893 7.177744 AGCAATGCCATGTATGATAAATGATGA 59.822 33.333 0.00 0.00 0.00 2.92
2328 2894 7.488150 GCAATGCCATGTATGATAAATGATGAG 59.512 37.037 4.17 0.00 0.00 2.90
2329 2895 7.640597 ATGCCATGTATGATAAATGATGAGG 57.359 36.000 4.17 0.00 0.00 3.86
2330 2896 6.545567 TGCCATGTATGATAAATGATGAGGT 58.454 36.000 4.17 0.00 0.00 3.85
2331 2897 6.431852 TGCCATGTATGATAAATGATGAGGTG 59.568 38.462 4.17 0.00 0.00 4.00
2332 2898 6.127814 GCCATGTATGATAAATGATGAGGTGG 60.128 42.308 4.17 0.00 0.00 4.61
2333 2899 7.170277 CCATGTATGATAAATGATGAGGTGGA 58.830 38.462 4.17 0.00 0.00 4.02
2334 2900 7.336176 CCATGTATGATAAATGATGAGGTGGAG 59.664 40.741 4.17 0.00 0.00 3.86
2335 2901 6.772605 TGTATGATAAATGATGAGGTGGAGG 58.227 40.000 0.00 0.00 0.00 4.30
2336 2902 6.558394 TGTATGATAAATGATGAGGTGGAGGA 59.442 38.462 0.00 0.00 0.00 3.71
2337 2903 5.557576 TGATAAATGATGAGGTGGAGGAG 57.442 43.478 0.00 0.00 0.00 3.69
2338 2904 5.218959 TGATAAATGATGAGGTGGAGGAGA 58.781 41.667 0.00 0.00 0.00 3.71
2339 2905 5.306419 TGATAAATGATGAGGTGGAGGAGAG 59.694 44.000 0.00 0.00 0.00 3.20
2340 2906 3.411454 AATGATGAGGTGGAGGAGAGA 57.589 47.619 0.00 0.00 0.00 3.10
2341 2907 2.450867 TGATGAGGTGGAGGAGAGAG 57.549 55.000 0.00 0.00 0.00 3.20
2342 2908 1.925959 TGATGAGGTGGAGGAGAGAGA 59.074 52.381 0.00 0.00 0.00 3.10
2343 2909 2.313041 TGATGAGGTGGAGGAGAGAGAA 59.687 50.000 0.00 0.00 0.00 2.87
2344 2910 3.245766 TGATGAGGTGGAGGAGAGAGAAA 60.246 47.826 0.00 0.00 0.00 2.52
2345 2911 3.481559 TGAGGTGGAGGAGAGAGAAAT 57.518 47.619 0.00 0.00 0.00 2.17
2346 2912 3.796111 TGAGGTGGAGGAGAGAGAAATT 58.204 45.455 0.00 0.00 0.00 1.82
2347 2913 4.947883 TGAGGTGGAGGAGAGAGAAATTA 58.052 43.478 0.00 0.00 0.00 1.40
2348 2914 5.533112 TGAGGTGGAGGAGAGAGAAATTAT 58.467 41.667 0.00 0.00 0.00 1.28
2349 2915 6.683537 TGAGGTGGAGGAGAGAGAAATTATA 58.316 40.000 0.00 0.00 0.00 0.98
2350 2916 7.132805 TGAGGTGGAGGAGAGAGAAATTATAA 58.867 38.462 0.00 0.00 0.00 0.98
2351 2917 7.623677 TGAGGTGGAGGAGAGAGAAATTATAAA 59.376 37.037 0.00 0.00 0.00 1.40
2352 2918 8.393959 AGGTGGAGGAGAGAGAAATTATAAAA 57.606 34.615 0.00 0.00 0.00 1.52
2353 2919 8.836735 AGGTGGAGGAGAGAGAAATTATAAAAA 58.163 33.333 0.00 0.00 0.00 1.94
2391 2957 7.259088 TCTTATTTAAGAGAAGGCAAGAGGT 57.741 36.000 0.00 0.00 37.40 3.85
2392 2958 7.106239 TCTTATTTAAGAGAAGGCAAGAGGTG 58.894 38.462 0.00 0.00 37.40 4.00
2393 2959 4.974645 TTTAAGAGAAGGCAAGAGGTGA 57.025 40.909 0.00 0.00 0.00 4.02
2394 2960 5.505181 TTTAAGAGAAGGCAAGAGGTGAT 57.495 39.130 0.00 0.00 0.00 3.06
2395 2961 3.625649 AAGAGAAGGCAAGAGGTGATC 57.374 47.619 0.00 0.00 0.00 2.92
2396 2962 2.831565 AGAGAAGGCAAGAGGTGATCT 58.168 47.619 0.00 0.00 41.27 2.75
2397 2963 2.765699 AGAGAAGGCAAGAGGTGATCTC 59.234 50.000 0.00 0.00 37.23 2.75
2412 2978 8.359060 GAGGTGATCTCTTAACACAATATGTC 57.641 38.462 0.00 0.00 38.97 3.06
2413 2979 8.083828 AGGTGATCTCTTAACACAATATGTCT 57.916 34.615 0.00 0.00 42.31 3.41
2414 2980 8.200792 AGGTGATCTCTTAACACAATATGTCTC 58.799 37.037 0.00 0.00 42.31 3.36
2415 2981 7.981789 GGTGATCTCTTAACACAATATGTCTCA 59.018 37.037 0.00 0.00 42.31 3.27
2416 2982 8.812329 GTGATCTCTTAACACAATATGTCTCAC 58.188 37.037 0.00 0.00 42.31 3.51
2417 2983 7.981789 TGATCTCTTAACACAATATGTCTCACC 59.018 37.037 0.00 0.00 42.31 4.02
2418 2984 7.239763 TCTCTTAACACAATATGTCTCACCA 57.760 36.000 0.00 0.00 42.31 4.17
2419 2985 7.851228 TCTCTTAACACAATATGTCTCACCAT 58.149 34.615 0.00 0.00 42.31 3.55
2420 2986 8.977412 TCTCTTAACACAATATGTCTCACCATA 58.023 33.333 0.00 0.00 42.31 2.74
2421 2987 9.770097 CTCTTAACACAATATGTCTCACCATAT 57.230 33.333 0.00 0.00 42.31 1.78
2453 3019 9.825109 GGAATATCTAGTTATTGGAGATAAGGC 57.175 37.037 10.19 0.00 36.15 4.35
2458 3024 9.830186 ATCTAGTTATTGGAGATAAGGCTAAGA 57.170 33.333 0.00 0.00 0.00 2.10
2459 3025 9.303116 TCTAGTTATTGGAGATAAGGCTAAGAG 57.697 37.037 0.00 0.00 0.00 2.85
2460 3026 9.303116 CTAGTTATTGGAGATAAGGCTAAGAGA 57.697 37.037 0.00 0.00 0.00 3.10
2461 3027 8.734593 AGTTATTGGAGATAAGGCTAAGAGAT 57.265 34.615 0.00 0.00 0.00 2.75
2462 3028 8.592809 AGTTATTGGAGATAAGGCTAAGAGATG 58.407 37.037 0.00 0.00 0.00 2.90
2463 3029 8.589338 GTTATTGGAGATAAGGCTAAGAGATGA 58.411 37.037 0.00 0.00 0.00 2.92
2464 3030 6.412362 TTGGAGATAAGGCTAAGAGATGAC 57.588 41.667 0.00 0.00 0.00 3.06
2465 3031 4.835615 TGGAGATAAGGCTAAGAGATGACC 59.164 45.833 0.00 0.00 0.00 4.02
2466 3032 4.221924 GGAGATAAGGCTAAGAGATGACCC 59.778 50.000 0.00 0.00 0.00 4.46
2467 3033 4.820775 AGATAAGGCTAAGAGATGACCCA 58.179 43.478 0.00 0.00 0.00 4.51
2468 3034 5.410602 AGATAAGGCTAAGAGATGACCCAT 58.589 41.667 0.00 0.00 0.00 4.00
2469 3035 5.848921 AGATAAGGCTAAGAGATGACCCATT 59.151 40.000 0.00 0.00 0.00 3.16
2470 3036 3.853355 AGGCTAAGAGATGACCCATTG 57.147 47.619 0.00 0.00 0.00 2.82
2471 3037 3.118531 AGGCTAAGAGATGACCCATTGT 58.881 45.455 0.00 0.00 0.00 2.71
2472 3038 4.298626 AGGCTAAGAGATGACCCATTGTA 58.701 43.478 0.00 0.00 0.00 2.41
2473 3039 4.346418 AGGCTAAGAGATGACCCATTGTAG 59.654 45.833 0.00 0.00 0.00 2.74
2474 3040 4.345257 GGCTAAGAGATGACCCATTGTAGA 59.655 45.833 0.00 0.00 0.00 2.59
2475 3041 5.163301 GGCTAAGAGATGACCCATTGTAGAA 60.163 44.000 0.00 0.00 0.00 2.10
2476 3042 5.755861 GCTAAGAGATGACCCATTGTAGAAC 59.244 44.000 0.00 0.00 0.00 3.01
2477 3043 5.762179 AAGAGATGACCCATTGTAGAACA 57.238 39.130 0.00 0.00 0.00 3.18
2478 3044 5.965033 AGAGATGACCCATTGTAGAACAT 57.035 39.130 0.00 0.00 0.00 2.71
2479 3045 5.678583 AGAGATGACCCATTGTAGAACATG 58.321 41.667 0.00 0.00 0.00 3.21
2480 3046 5.190528 AGAGATGACCCATTGTAGAACATGT 59.809 40.000 0.00 0.00 0.00 3.21
2481 3047 5.819991 AGATGACCCATTGTAGAACATGTT 58.180 37.500 11.78 11.78 0.00 2.71
2482 3048 6.248433 AGATGACCCATTGTAGAACATGTTT 58.752 36.000 13.36 5.60 0.00 2.83
2483 3049 6.721208 AGATGACCCATTGTAGAACATGTTTT 59.279 34.615 13.36 9.88 0.00 2.43
2484 3050 6.723298 TGACCCATTGTAGAACATGTTTTT 57.277 33.333 13.36 7.13 0.00 1.94
2544 3110 8.862325 AAGATTGTCTTATCAACCATTGTACA 57.138 30.769 0.00 0.00 34.42 2.90
2545 3111 9.466497 AAGATTGTCTTATCAACCATTGTACAT 57.534 29.630 0.00 0.00 34.42 2.29
2546 3112 8.896744 AGATTGTCTTATCAACCATTGTACATG 58.103 33.333 0.00 0.00 0.00 3.21
2547 3113 6.435430 TGTCTTATCAACCATTGTACATGC 57.565 37.500 0.00 0.00 0.00 4.06
2548 3114 5.356751 TGTCTTATCAACCATTGTACATGCC 59.643 40.000 0.00 0.00 0.00 4.40
2559 3125 2.725637 TGTACATGCCCTACTACACGA 58.274 47.619 0.00 0.00 0.00 4.35
2562 3128 3.179443 ACATGCCCTACTACACGAATG 57.821 47.619 0.00 0.00 0.00 2.67
2584 3150 6.462073 TGAACTTTGACATCTTAACTACGC 57.538 37.500 0.00 0.00 0.00 4.42
2585 3151 5.407387 TGAACTTTGACATCTTAACTACGCC 59.593 40.000 0.00 0.00 0.00 5.68
2672 3238 4.434520 GCCTAGAGAAAGCGAAATAGTGT 58.565 43.478 0.00 0.00 0.00 3.55
2721 3287 2.810439 ACATCAAGGCGAGATAGCTC 57.190 50.000 0.00 0.00 37.81 4.09
2738 3304 2.874701 AGCTCACGCTAAGCATATTTGG 59.125 45.455 6.99 0.00 46.79 3.28
2765 3331 5.181811 TGACTAAAGCTGATCAATTGTGTGG 59.818 40.000 5.13 0.00 0.00 4.17
2881 3447 2.415625 GGAGTTGTACGTCGCAGATTCT 60.416 50.000 0.00 0.00 40.67 2.40
2983 3549 2.813908 GCCAACGGCGTCGAGATT 60.814 61.111 20.03 0.00 39.62 2.40
3092 3658 7.308951 GCTTACTTTGGTGAAGTTTTAGGCATA 60.309 37.037 0.00 0.00 46.34 3.14
3167 3733 5.927030 ACACACAAGCATCGTTATTTGTAG 58.073 37.500 0.00 0.00 32.86 2.74
3168 3734 5.468746 ACACACAAGCATCGTTATTTGTAGT 59.531 36.000 0.00 0.00 32.86 2.73
3169 3735 6.647481 ACACACAAGCATCGTTATTTGTAGTA 59.353 34.615 0.00 0.00 32.86 1.82
3282 3936 5.066505 GCTCAAATATGACCCTAACACCAAG 59.933 44.000 0.00 0.00 0.00 3.61
3423 4077 2.091283 ACCCAAGGCCTCAACCCTT 61.091 57.895 5.23 0.00 43.29 3.95
3438 4092 1.414919 ACCCTTGAGTAACTCGTGCAA 59.585 47.619 0.00 0.00 32.35 4.08
3579 4233 1.607178 CATGAAGCTGCCACCCCAA 60.607 57.895 0.00 0.00 0.00 4.12
3631 4285 3.558321 CCGGTTTGGAAGTCAGGTGATTA 60.558 47.826 0.00 0.00 42.00 1.75
3681 4335 3.270877 GTTGGAAGAGGTAATCGTGCAT 58.729 45.455 0.00 0.00 37.56 3.96
4257 4911 9.233649 GCCGATAGCTGTATATATATTAGGACT 57.766 37.037 0.00 0.00 38.99 3.85
4288 4942 1.374252 GTGTCGCGACCACAATCCT 60.374 57.895 34.34 0.00 0.00 3.24
4294 4948 1.816074 GCGACCACAATCCTAAACCA 58.184 50.000 0.00 0.00 0.00 3.67
4296 4950 2.752903 GCGACCACAATCCTAAACCAAT 59.247 45.455 0.00 0.00 0.00 3.16
4325 4979 9.301153 GGTTTCTAATTCGTATACTTACCGAAA 57.699 33.333 0.56 1.18 30.45 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 2.422803 CCCACACAAACCAGAAGGAGAA 60.423 50.000 0.00 0.00 38.69 2.87
109 110 2.752238 CCCGAGGACAGAGAGCGT 60.752 66.667 0.00 0.00 0.00 5.07
110 111 2.752238 ACCCGAGGACAGAGAGCG 60.752 66.667 0.00 0.00 0.00 5.03
277 278 1.143073 GTGGACAAAGGTCTTCACCCT 59.857 52.381 0.00 0.00 45.12 4.34
309 310 0.253160 ATGCCCCCAAGAGACCACTA 60.253 55.000 0.00 0.00 0.00 2.74
327 348 3.861840 CACACCTAAGATCCACGACAAT 58.138 45.455 0.00 0.00 0.00 2.71
359 380 0.320771 GATCTGAACACAGCCCACGT 60.321 55.000 0.00 0.00 0.00 4.49
387 408 0.172803 ACTACGCTACCGGCAAAGAG 59.827 55.000 0.00 0.63 41.91 2.85
423 444 3.133542 GCCGATCCCATGATGATCAGATA 59.866 47.826 19.06 0.00 38.83 1.98
431 452 5.491070 TCTTATAAAGCCGATCCCATGATG 58.509 41.667 0.00 0.00 0.00 3.07
449 470 6.709281 CAAGATGATGATGTAGCCCTCTTAT 58.291 40.000 0.00 0.00 0.00 1.73
457 797 6.400834 CGACTAATGCAAGATGATGATGTAGC 60.401 42.308 0.00 0.00 0.00 3.58
462 802 3.750130 GGCGACTAATGCAAGATGATGAT 59.250 43.478 0.00 0.00 0.00 2.45
477 817 5.797051 ACCATAAAAGTACAAAGGCGACTA 58.203 37.500 0.00 0.00 42.68 2.59
479 819 5.151389 CAACCATAAAAGTACAAAGGCGAC 58.849 41.667 0.00 0.00 0.00 5.19
519 860 7.076446 TCTCTCTAAATAGGCTTTAGTCCCAT 58.924 38.462 0.00 0.00 34.51 4.00
520 861 6.441222 TCTCTCTAAATAGGCTTTAGTCCCA 58.559 40.000 0.00 0.00 34.51 4.37
526 867 9.838339 CCTTCAAATCTCTCTAAATAGGCTTTA 57.162 33.333 0.00 0.00 0.00 1.85
538 879 5.486775 TGAATCCTCACCTTCAAATCTCTCT 59.513 40.000 0.00 0.00 0.00 3.10
568 911 4.083862 AGGTCGGAAAGCTCGCCC 62.084 66.667 0.00 0.00 0.00 6.13
581 924 8.261522 AGTAAAGTCTGATTTAATCCTGAGGTC 58.738 37.037 0.00 0.00 0.00 3.85
719 1063 2.927856 TGGTCACGGTGCCCAGAT 60.928 61.111 6.83 0.00 0.00 2.90
792 1136 5.278561 GCAGTATAGTATGTCTGGTGGTCTC 60.279 48.000 14.59 0.00 0.00 3.36
796 1140 4.937201 TGCAGTATAGTATGTCTGGTGG 57.063 45.455 14.59 0.00 0.00 4.61
828 1175 0.462581 TGGAGTCCTACGCGTCGTAT 60.463 55.000 18.63 0.00 41.53 3.06
950 1446 2.576893 CCACGATCGATGGAACGCG 61.577 63.158 24.34 3.53 41.58 6.01
996 1492 0.741927 TGCAGCTGACGGTCATCATG 60.742 55.000 20.43 11.36 0.00 3.07
997 1493 0.461516 CTGCAGCTGACGGTCATCAT 60.462 55.000 20.43 0.00 0.00 2.45
1094 1590 1.379443 TCGCGTATCTCCACCACCT 60.379 57.895 5.77 0.00 0.00 4.00
1522 2073 4.985044 AATCGGCGGTTCTAATTAATCG 57.015 40.909 7.21 0.00 36.06 3.34
1541 2092 7.338449 ACACCATTACCAAACGATTTAGCTAAT 59.662 33.333 7.08 0.00 0.00 1.73
1784 2335 2.152016 TGTCCTGTCAGTAGTCAGTCG 58.848 52.381 0.00 0.00 0.00 4.18
1812 2367 4.700692 TGTGATCCACGATATAGTAGGAGC 59.299 45.833 12.39 12.39 37.14 4.70
1834 2389 8.068977 TCCATTTTTGAAAAGAAAATTCGCATG 58.931 29.630 0.00 0.00 35.21 4.06
1870 2425 8.682895 CAATTCTCTGTGTATCTACGTTAATCG 58.317 37.037 0.00 0.00 46.00 3.34
1904 2459 7.449395 TGTCAGAAATGACATTTTGGATTCTCT 59.551 33.333 14.46 2.32 43.09 3.10
1906 2461 7.528996 TGTCAGAAATGACATTTTGGATTCT 57.471 32.000 14.46 3.70 43.09 2.40
1919 2474 7.095910 TGTTTTTGCTTTCTTGTCAGAAATGA 58.904 30.769 0.00 0.00 46.01 2.57
1927 2482 4.658071 TCGTCTGTTTTTGCTTTCTTGTC 58.342 39.130 0.00 0.00 0.00 3.18
1945 2500 6.867662 ATAATTTCAAGGGATGTGATCGTC 57.132 37.500 0.00 0.00 0.00 4.20
1965 2524 9.753674 ATTTCCAAATTCAGGAGAAGTGTATAA 57.246 29.630 0.52 0.00 37.14 0.98
2039 2599 5.131594 TCTGACATGATCGGATCAAGATC 57.868 43.478 25.08 20.32 43.50 2.75
2122 2682 5.039480 ACAGTACTACACACGTGATACAC 57.961 43.478 25.01 11.54 0.00 2.90
2127 2693 4.450080 CAGACTACAGTACTACACACGTGA 59.550 45.833 25.01 0.00 0.00 4.35
2180 2746 1.745566 TGTCGTGTTGTTACTCGTCG 58.254 50.000 0.00 0.00 40.90 5.12
2192 2758 5.358725 ACCTGAAATTTAAAGGTTGTCGTGT 59.641 36.000 16.03 0.00 41.65 4.49
2200 2766 7.354751 TGCAACTAACCTGAAATTTAAAGGT 57.645 32.000 16.03 16.03 46.40 3.50
2208 2774 4.620982 GCAAGTTGCAACTAACCTGAAAT 58.379 39.130 31.31 10.58 44.26 2.17
2244 2810 9.083080 CCTTTCTGACAAAATAAAAACGAGTTT 57.917 29.630 0.00 0.00 0.00 2.66
2248 2814 7.067737 AGTCCCTTTCTGACAAAATAAAAACGA 59.932 33.333 0.00 0.00 35.15 3.85
2249 2815 7.200455 AGTCCCTTTCTGACAAAATAAAAACG 58.800 34.615 0.00 0.00 35.15 3.60
2250 2816 9.459640 GTAGTCCCTTTCTGACAAAATAAAAAC 57.540 33.333 0.00 0.00 35.15 2.43
2256 2822 4.324267 CCGTAGTCCCTTTCTGACAAAAT 58.676 43.478 0.00 0.00 35.15 1.82
2260 2826 1.263356 CCCGTAGTCCCTTTCTGACA 58.737 55.000 0.00 0.00 35.15 3.58
2267 2833 0.828677 GTACATGCCCGTAGTCCCTT 59.171 55.000 0.00 0.00 0.00 3.95
2273 2839 4.945246 AGAACTATTGTACATGCCCGTAG 58.055 43.478 0.00 0.00 0.00 3.51
2274 2840 6.492429 AGATAGAACTATTGTACATGCCCGTA 59.508 38.462 0.00 0.00 0.00 4.02
2275 2841 3.906720 AGAACTATTGTACATGCCCGT 57.093 42.857 0.00 0.00 0.00 5.28
2276 2842 5.784177 AGATAGAACTATTGTACATGCCCG 58.216 41.667 0.00 0.00 0.00 6.13
2277 2843 7.332182 GCTAAGATAGAACTATTGTACATGCCC 59.668 40.741 0.00 0.00 0.00 5.36
2278 2844 7.872993 TGCTAAGATAGAACTATTGTACATGCC 59.127 37.037 0.00 0.00 0.00 4.40
2279 2845 8.818141 TGCTAAGATAGAACTATTGTACATGC 57.182 34.615 0.00 0.00 0.00 4.06
2282 2848 9.261180 GCATTGCTAAGATAGAACTATTGTACA 57.739 33.333 0.16 0.00 0.00 2.90
2283 2849 8.713271 GGCATTGCTAAGATAGAACTATTGTAC 58.287 37.037 8.82 0.00 0.00 2.90
2284 2850 8.428852 TGGCATTGCTAAGATAGAACTATTGTA 58.571 33.333 8.82 0.00 0.00 2.41
2285 2851 7.282585 TGGCATTGCTAAGATAGAACTATTGT 58.717 34.615 8.82 0.00 0.00 2.71
2286 2852 7.734924 TGGCATTGCTAAGATAGAACTATTG 57.265 36.000 8.82 0.00 0.00 1.90
2287 2853 7.941238 ACATGGCATTGCTAAGATAGAACTATT 59.059 33.333 8.82 0.00 0.00 1.73
2288 2854 7.456725 ACATGGCATTGCTAAGATAGAACTAT 58.543 34.615 8.82 0.00 0.00 2.12
2289 2855 6.830912 ACATGGCATTGCTAAGATAGAACTA 58.169 36.000 8.82 0.00 0.00 2.24
2290 2856 5.688807 ACATGGCATTGCTAAGATAGAACT 58.311 37.500 8.82 0.00 0.00 3.01
2291 2857 7.388776 TCATACATGGCATTGCTAAGATAGAAC 59.611 37.037 8.82 0.00 0.00 3.01
2292 2858 7.452562 TCATACATGGCATTGCTAAGATAGAA 58.547 34.615 8.82 0.00 0.00 2.10
2293 2859 7.008021 TCATACATGGCATTGCTAAGATAGA 57.992 36.000 8.82 0.00 0.00 1.98
2294 2860 7.860918 ATCATACATGGCATTGCTAAGATAG 57.139 36.000 8.82 0.00 0.00 2.08
2295 2861 9.737844 TTTATCATACATGGCATTGCTAAGATA 57.262 29.630 8.82 3.12 0.00 1.98
2296 2862 8.640063 TTTATCATACATGGCATTGCTAAGAT 57.360 30.769 8.82 4.01 0.00 2.40
2297 2863 8.517056 CATTTATCATACATGGCATTGCTAAGA 58.483 33.333 8.82 0.00 0.00 2.10
2298 2864 8.517056 TCATTTATCATACATGGCATTGCTAAG 58.483 33.333 8.82 1.77 0.00 2.18
2299 2865 8.406730 TCATTTATCATACATGGCATTGCTAA 57.593 30.769 8.82 0.00 0.00 3.09
2300 2866 7.999450 TCATTTATCATACATGGCATTGCTA 57.001 32.000 8.82 2.16 0.00 3.49
2301 2867 6.904463 TCATTTATCATACATGGCATTGCT 57.096 33.333 8.82 0.00 0.00 3.91
2302 2868 7.317390 TCATCATTTATCATACATGGCATTGC 58.683 34.615 0.00 0.00 0.00 3.56
2303 2869 7.973944 CCTCATCATTTATCATACATGGCATTG 59.026 37.037 0.00 0.00 0.00 2.82
2304 2870 7.672660 ACCTCATCATTTATCATACATGGCATT 59.327 33.333 0.00 0.00 0.00 3.56
2305 2871 7.122204 CACCTCATCATTTATCATACATGGCAT 59.878 37.037 0.00 0.00 0.00 4.40
2306 2872 6.431852 CACCTCATCATTTATCATACATGGCA 59.568 38.462 0.00 0.00 0.00 4.92
2307 2873 6.127814 CCACCTCATCATTTATCATACATGGC 60.128 42.308 0.00 0.00 0.00 4.40
2308 2874 7.170277 TCCACCTCATCATTTATCATACATGG 58.830 38.462 0.00 0.00 0.00 3.66
2309 2875 7.336176 CCTCCACCTCATCATTTATCATACATG 59.664 40.741 0.00 0.00 0.00 3.21
2310 2876 7.238305 TCCTCCACCTCATCATTTATCATACAT 59.762 37.037 0.00 0.00 0.00 2.29
2311 2877 6.558394 TCCTCCACCTCATCATTTATCATACA 59.442 38.462 0.00 0.00 0.00 2.29
2312 2878 7.009179 TCCTCCACCTCATCATTTATCATAC 57.991 40.000 0.00 0.00 0.00 2.39
2313 2879 7.018769 TCTCCTCCACCTCATCATTTATCATA 58.981 38.462 0.00 0.00 0.00 2.15
2314 2880 5.848369 TCTCCTCCACCTCATCATTTATCAT 59.152 40.000 0.00 0.00 0.00 2.45
2315 2881 5.218959 TCTCCTCCACCTCATCATTTATCA 58.781 41.667 0.00 0.00 0.00 2.15
2316 2882 5.541868 TCTCTCCTCCACCTCATCATTTATC 59.458 44.000 0.00 0.00 0.00 1.75
2317 2883 5.471424 TCTCTCCTCCACCTCATCATTTAT 58.529 41.667 0.00 0.00 0.00 1.40
2318 2884 4.883759 TCTCTCCTCCACCTCATCATTTA 58.116 43.478 0.00 0.00 0.00 1.40
2319 2885 3.710677 CTCTCTCCTCCACCTCATCATTT 59.289 47.826 0.00 0.00 0.00 2.32
2320 2886 3.052262 TCTCTCTCCTCCACCTCATCATT 60.052 47.826 0.00 0.00 0.00 2.57
2321 2887 2.517553 TCTCTCTCCTCCACCTCATCAT 59.482 50.000 0.00 0.00 0.00 2.45
2322 2888 1.925959 TCTCTCTCCTCCACCTCATCA 59.074 52.381 0.00 0.00 0.00 3.07
2323 2889 2.746279 TCTCTCTCCTCCACCTCATC 57.254 55.000 0.00 0.00 0.00 2.92
2324 2890 3.481559 TTTCTCTCTCCTCCACCTCAT 57.518 47.619 0.00 0.00 0.00 2.90
2325 2891 3.481559 ATTTCTCTCTCCTCCACCTCA 57.518 47.619 0.00 0.00 0.00 3.86
2326 2892 7.604657 TTATAATTTCTCTCTCCTCCACCTC 57.395 40.000 0.00 0.00 0.00 3.85
2327 2893 7.996758 TTTATAATTTCTCTCTCCTCCACCT 57.003 36.000 0.00 0.00 0.00 4.00
2367 2933 7.038302 TCACCTCTTGCCTTCTCTTAAATAAGA 60.038 37.037 3.08 3.08 39.82 2.10
2368 2934 7.106239 TCACCTCTTGCCTTCTCTTAAATAAG 58.894 38.462 0.00 0.00 34.65 1.73
2369 2935 7.016153 TCACCTCTTGCCTTCTCTTAAATAA 57.984 36.000 0.00 0.00 0.00 1.40
2370 2936 6.620877 TCACCTCTTGCCTTCTCTTAAATA 57.379 37.500 0.00 0.00 0.00 1.40
2371 2937 5.505181 TCACCTCTTGCCTTCTCTTAAAT 57.495 39.130 0.00 0.00 0.00 1.40
2372 2938 4.974645 TCACCTCTTGCCTTCTCTTAAA 57.025 40.909 0.00 0.00 0.00 1.52
2373 2939 4.780021 AGATCACCTCTTGCCTTCTCTTAA 59.220 41.667 0.00 0.00 0.00 1.85
2374 2940 4.357325 AGATCACCTCTTGCCTTCTCTTA 58.643 43.478 0.00 0.00 0.00 2.10
2375 2941 3.180507 AGATCACCTCTTGCCTTCTCTT 58.819 45.455 0.00 0.00 0.00 2.85
2376 2942 2.765699 GAGATCACCTCTTGCCTTCTCT 59.234 50.000 0.00 0.00 38.86 3.10
2377 2943 3.177997 GAGATCACCTCTTGCCTTCTC 57.822 52.381 0.00 0.00 38.86 2.87
2385 2951 8.543774 ACATATTGTGTTAAGAGATCACCTCTT 58.456 33.333 11.44 11.44 46.54 2.85
2386 2952 8.083828 ACATATTGTGTTAAGAGATCACCTCT 57.916 34.615 0.00 0.00 46.13 3.69
2387 2953 8.200792 AGACATATTGTGTTAAGAGATCACCTC 58.799 37.037 0.00 0.00 42.36 3.85
2388 2954 8.083828 AGACATATTGTGTTAAGAGATCACCT 57.916 34.615 0.00 0.00 42.36 4.00
2389 2955 7.981789 TGAGACATATTGTGTTAAGAGATCACC 59.018 37.037 0.00 0.00 42.36 4.02
2390 2956 8.812329 GTGAGACATATTGTGTTAAGAGATCAC 58.188 37.037 0.00 0.00 42.36 3.06
2391 2957 7.981789 GGTGAGACATATTGTGTTAAGAGATCA 59.018 37.037 0.00 0.00 42.36 2.92
2392 2958 7.981789 TGGTGAGACATATTGTGTTAAGAGATC 59.018 37.037 0.00 0.00 42.36 2.75
2393 2959 7.851228 TGGTGAGACATATTGTGTTAAGAGAT 58.149 34.615 0.00 0.00 42.36 2.75
2394 2960 7.239763 TGGTGAGACATATTGTGTTAAGAGA 57.760 36.000 0.00 0.00 42.36 3.10
2395 2961 9.770097 ATATGGTGAGACATATTGTGTTAAGAG 57.230 33.333 0.00 0.00 42.36 2.85
2427 2993 9.825109 GCCTTATCTCCAATAACTAGATATTCC 57.175 37.037 2.45 0.00 33.44 3.01
2432 2998 9.830186 TCTTAGCCTTATCTCCAATAACTAGAT 57.170 33.333 0.00 0.00 34.44 1.98
2433 2999 9.303116 CTCTTAGCCTTATCTCCAATAACTAGA 57.697 37.037 0.00 0.00 0.00 2.43
2434 3000 9.303116 TCTCTTAGCCTTATCTCCAATAACTAG 57.697 37.037 0.00 0.00 0.00 2.57
2435 3001 9.830186 ATCTCTTAGCCTTATCTCCAATAACTA 57.170 33.333 0.00 0.00 0.00 2.24
2436 3002 8.592809 CATCTCTTAGCCTTATCTCCAATAACT 58.407 37.037 0.00 0.00 0.00 2.24
2437 3003 8.589338 TCATCTCTTAGCCTTATCTCCAATAAC 58.411 37.037 0.00 0.00 0.00 1.89
2438 3004 8.589338 GTCATCTCTTAGCCTTATCTCCAATAA 58.411 37.037 0.00 0.00 0.00 1.40
2439 3005 7.179338 GGTCATCTCTTAGCCTTATCTCCAATA 59.821 40.741 0.00 0.00 0.00 1.90
2440 3006 6.013812 GGTCATCTCTTAGCCTTATCTCCAAT 60.014 42.308 0.00 0.00 0.00 3.16
2441 3007 5.305644 GGTCATCTCTTAGCCTTATCTCCAA 59.694 44.000 0.00 0.00 0.00 3.53
2442 3008 4.835615 GGTCATCTCTTAGCCTTATCTCCA 59.164 45.833 0.00 0.00 0.00 3.86
2443 3009 4.221924 GGGTCATCTCTTAGCCTTATCTCC 59.778 50.000 0.00 0.00 0.00 3.71
2444 3010 4.835615 TGGGTCATCTCTTAGCCTTATCTC 59.164 45.833 0.00 0.00 34.30 2.75
2445 3011 4.820775 TGGGTCATCTCTTAGCCTTATCT 58.179 43.478 0.00 0.00 34.30 1.98
2446 3012 5.753721 ATGGGTCATCTCTTAGCCTTATC 57.246 43.478 0.00 0.00 34.30 1.75
2447 3013 5.370880 ACAATGGGTCATCTCTTAGCCTTAT 59.629 40.000 0.00 0.00 34.30 1.73
2448 3014 4.721776 ACAATGGGTCATCTCTTAGCCTTA 59.278 41.667 0.00 0.00 34.30 2.69
2449 3015 3.525199 ACAATGGGTCATCTCTTAGCCTT 59.475 43.478 0.00 0.00 34.30 4.35
2450 3016 3.118531 ACAATGGGTCATCTCTTAGCCT 58.881 45.455 0.00 0.00 34.30 4.58
2451 3017 3.567478 ACAATGGGTCATCTCTTAGCC 57.433 47.619 0.00 0.00 0.00 3.93
2452 3018 5.537300 TCTACAATGGGTCATCTCTTAGC 57.463 43.478 0.00 0.00 0.00 3.09
2453 3019 6.878317 TGTTCTACAATGGGTCATCTCTTAG 58.122 40.000 0.00 0.00 0.00 2.18
2454 3020 6.867519 TGTTCTACAATGGGTCATCTCTTA 57.132 37.500 0.00 0.00 0.00 2.10
2455 3021 5.762179 TGTTCTACAATGGGTCATCTCTT 57.238 39.130 0.00 0.00 0.00 2.85
2456 3022 5.190528 ACATGTTCTACAATGGGTCATCTCT 59.809 40.000 0.00 0.00 0.00 3.10
2457 3023 5.431765 ACATGTTCTACAATGGGTCATCTC 58.568 41.667 0.00 0.00 0.00 2.75
2458 3024 5.441718 ACATGTTCTACAATGGGTCATCT 57.558 39.130 0.00 0.00 0.00 2.90
2459 3025 6.515272 AAACATGTTCTACAATGGGTCATC 57.485 37.500 12.39 0.00 0.00 2.92
2460 3026 6.916360 AAAACATGTTCTACAATGGGTCAT 57.084 33.333 12.39 0.00 0.00 3.06
2461 3027 6.723298 AAAAACATGTTCTACAATGGGTCA 57.277 33.333 12.39 0.00 0.00 4.02
2518 3084 9.952030 TGTACAATGGTTGATAAGACAATCTTA 57.048 29.630 0.00 0.95 42.49 2.10
2519 3085 8.862325 TGTACAATGGTTGATAAGACAATCTT 57.138 30.769 0.00 0.00 40.35 2.40
2520 3086 8.896744 CATGTACAATGGTTGATAAGACAATCT 58.103 33.333 0.00 0.00 32.76 2.40
2521 3087 7.645340 GCATGTACAATGGTTGATAAGACAATC 59.355 37.037 0.00 0.00 32.36 2.67
2522 3088 7.416664 GGCATGTACAATGGTTGATAAGACAAT 60.417 37.037 0.00 0.00 32.36 2.71
2523 3089 6.127758 GGCATGTACAATGGTTGATAAGACAA 60.128 38.462 0.00 0.00 0.00 3.18
2524 3090 5.356751 GGCATGTACAATGGTTGATAAGACA 59.643 40.000 0.00 0.00 0.00 3.41
2525 3091 5.221048 GGGCATGTACAATGGTTGATAAGAC 60.221 44.000 0.00 0.00 0.00 3.01
2526 3092 4.887071 GGGCATGTACAATGGTTGATAAGA 59.113 41.667 0.00 0.00 0.00 2.10
2527 3093 4.889409 AGGGCATGTACAATGGTTGATAAG 59.111 41.667 0.00 0.00 0.00 1.73
2528 3094 4.865905 AGGGCATGTACAATGGTTGATAA 58.134 39.130 0.00 0.00 0.00 1.75
2529 3095 4.518278 AGGGCATGTACAATGGTTGATA 57.482 40.909 0.00 0.00 0.00 2.15
2530 3096 3.386932 AGGGCATGTACAATGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
2531 3097 2.897271 AGGGCATGTACAATGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
2532 3098 3.620488 AGTAGGGCATGTACAATGGTTG 58.380 45.455 0.00 0.00 0.00 3.77
2533 3099 4.226394 TGTAGTAGGGCATGTACAATGGTT 59.774 41.667 0.00 0.00 0.00 3.67
2534 3100 3.778075 TGTAGTAGGGCATGTACAATGGT 59.222 43.478 0.00 0.00 0.00 3.55
2535 3101 4.127171 GTGTAGTAGGGCATGTACAATGG 58.873 47.826 0.00 0.00 0.00 3.16
2536 3102 3.802139 CGTGTAGTAGGGCATGTACAATG 59.198 47.826 0.00 0.12 0.00 2.82
2537 3103 3.702548 TCGTGTAGTAGGGCATGTACAAT 59.297 43.478 0.00 0.00 0.00 2.71
2538 3104 3.090790 TCGTGTAGTAGGGCATGTACAA 58.909 45.455 0.00 0.00 0.00 2.41
2539 3105 2.725637 TCGTGTAGTAGGGCATGTACA 58.274 47.619 0.00 0.00 0.00 2.90
2540 3106 3.788333 TTCGTGTAGTAGGGCATGTAC 57.212 47.619 0.00 0.00 0.00 2.90
2541 3107 3.955551 TCATTCGTGTAGTAGGGCATGTA 59.044 43.478 0.00 0.00 0.00 2.29
2542 3108 2.764010 TCATTCGTGTAGTAGGGCATGT 59.236 45.455 0.00 0.00 0.00 3.21
2543 3109 3.452755 TCATTCGTGTAGTAGGGCATG 57.547 47.619 0.00 0.00 0.00 4.06
2544 3110 3.451178 AGTTCATTCGTGTAGTAGGGCAT 59.549 43.478 0.00 0.00 0.00 4.40
2545 3111 2.829720 AGTTCATTCGTGTAGTAGGGCA 59.170 45.455 0.00 0.00 0.00 5.36
2546 3112 3.521947 AGTTCATTCGTGTAGTAGGGC 57.478 47.619 0.00 0.00 0.00 5.19
2547 3113 5.347907 GTCAAAGTTCATTCGTGTAGTAGGG 59.652 44.000 0.00 0.00 0.00 3.53
2548 3114 5.924254 TGTCAAAGTTCATTCGTGTAGTAGG 59.076 40.000 0.00 0.00 0.00 3.18
2559 3125 7.360946 GGCGTAGTTAAGATGTCAAAGTTCATT 60.361 37.037 0.00 0.00 0.00 2.57
2562 3128 5.444218 CGGCGTAGTTAAGATGTCAAAGTTC 60.444 44.000 0.00 0.00 0.00 3.01
2585 3151 3.865011 ATGATCATCCCGAGAAGATCG 57.135 47.619 1.18 0.00 45.89 3.69
2672 3238 4.135747 TGCGGATGATGTTGATACTCAA 57.864 40.909 0.00 0.00 33.32 3.02
2691 3257 5.064707 TCTCGCCTTGATGTTAAGTAAATGC 59.935 40.000 0.00 0.00 0.00 3.56
2721 3287 4.793216 GTCAAACCAAATATGCTTAGCGTG 59.207 41.667 9.46 0.00 0.00 5.34
2733 3299 6.899393 TGATCAGCTTTAGTCAAACCAAAT 57.101 33.333 0.00 0.00 0.00 2.32
2738 3304 7.113965 CACACAATTGATCAGCTTTAGTCAAAC 59.886 37.037 13.59 0.00 34.62 2.93
2765 3331 3.273434 TGCAACTATCCAATCTGCAGAC 58.727 45.455 20.97 1.78 38.06 3.51
2881 3447 3.073798 TGACCACTCTCAGCCCAAAATAA 59.926 43.478 0.00 0.00 0.00 1.40
3092 3658 6.389830 TGCGGATATTCATGCACTTAAAAT 57.610 33.333 0.00 0.00 31.31 1.82
3167 3733 8.480643 TCACTCGTTAGGTTAACTAGTAGTAC 57.519 38.462 2.50 0.00 41.12 2.73
3168 3734 7.766278 CCTCACTCGTTAGGTTAACTAGTAGTA 59.234 40.741 2.50 0.00 41.12 1.82
3169 3735 6.597280 CCTCACTCGTTAGGTTAACTAGTAGT 59.403 42.308 5.42 0.00 41.12 2.73
3282 3936 1.343465 TCGACCAAGACTTGAACCTCC 59.657 52.381 16.99 0.00 0.00 4.30
3423 4077 2.351060 CGGTAGTTGCACGAGTTACTCA 60.351 50.000 13.14 0.00 0.00 3.41
3427 4081 0.244450 CCCGGTAGTTGCACGAGTTA 59.756 55.000 0.00 0.00 0.00 2.24
3631 4285 2.651361 CTCGCTGACCCTCAACGT 59.349 61.111 0.00 0.00 37.27 3.99
3681 4335 3.449227 ATCTTCCTCGCCGCGTCA 61.449 61.111 13.39 0.00 0.00 4.35
3844 4498 3.985279 CAGCTACTGTTACGTGTTTGCTA 59.015 43.478 0.00 0.00 0.00 3.49
4008 4662 1.616865 TCTTCATCACGGGTCGTCTTT 59.383 47.619 0.00 0.00 38.32 2.52
4257 4911 0.101759 GCGACACAATACCGCCTCTA 59.898 55.000 0.00 0.00 42.77 2.43
4296 4950 7.643764 CGGTAAGTATACGAATTAGAAACCGAA 59.356 37.037 14.10 0.00 45.79 4.30
4347 5001 6.750148 TGCCGTTTTATTTTTATGTCTTGGT 58.250 32.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.