Multiple sequence alignment - TraesCS6D01G129300

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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 TraesCS6D01G129300 chr6D 100.000 2662 0 0 1 2662 94052427 94055088 0.000000e+00 4916.0
1 TraesCS6D01G129300 chr6D 88.583 1524 65 40 840 2304 93971107 93972580 0.000000e+00 1749.0
2 TraesCS6D01G129300 chr6B 90.521 844 43 12 930 1754 179274203 179273378 0.000000e+00 1081.0
3 TraesCS6D01G129300 chr6B 88.676 680 43 15 179 829 179274905 179274231 0.000000e+00 798.0
4 TraesCS6D01G129300 chr6B 90.378 582 21 5 1756 2304 179273318 179272739 0.000000e+00 732.0
5 TraesCS6D01G129300 chr6B 95.745 94 4 0 2569 2662 179272736 179272643 4.590000e-33 152.0
6 TraesCS6D01G129300 chr6B 90.385 104 6 1 84 183 179276263 179276160 1.660000e-27 134.0
7 TraesCS6D01G129300 chr6B 93.023 86 5 1 1 85 179276701 179276616 1.000000e-24 124.0
8 TraesCS6D01G129300 chr6A 88.713 505 40 9 114 613 114847929 114848421 3.790000e-168 601.0
9 TraesCS6D01G129300 chr6A 100.000 29 0 0 2193 2221 114846619 114846647 1.000000e-03 54.7
10 TraesCS6D01G129300 chr7A 95.367 259 11 1 2307 2564 688269547 688269289 6.860000e-111 411.0
11 TraesCS6D01G129300 chr5A 94.656 262 13 1 2304 2564 338384167 338383906 3.190000e-109 405.0
12 TraesCS6D01G129300 chr5A 93.385 257 15 2 2306 2561 510471067 510471322 1.930000e-101 379.0
13 TraesCS6D01G129300 chr4D 94.297 263 12 3 2302 2562 47329444 47329183 1.480000e-107 399.0
14 TraesCS6D01G129300 chr3B 93.462 260 15 2 2304 2562 797022957 797022699 4.160000e-103 385.0
15 TraesCS6D01G129300 chr3D 92.748 262 17 2 2304 2564 593842186 593841926 6.960000e-101 377.0
16 TraesCS6D01G129300 chr7D 90.272 257 24 1 2307 2562 573619872 573619616 4.250000e-88 335.0
17 TraesCS6D01G129300 chr7D 86.842 266 31 4 2305 2568 404059700 404059437 7.210000e-76 294.0
18 TraesCS6D01G129300 chr1D 89.189 259 23 2 2311 2564 445382540 445382798 4.280000e-83 318.0


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 TraesCS6D01G129300 chr6D 94052427 94055088 2661 False 4916.00 4916 100.000000 1 2662 1 chr6D.!!$F2 2661
1 TraesCS6D01G129300 chr6D 93971107 93972580 1473 False 1749.00 1749 88.583000 840 2304 1 chr6D.!!$F1 1464
2 TraesCS6D01G129300 chr6B 179272643 179276701 4058 True 503.50 1081 91.454667 1 2662 6 chr6B.!!$R1 2661
3 TraesCS6D01G129300 chr6A 114846619 114848421 1802 False 327.85 601 94.356500 114 2221 2 chr6A.!!$F1 2107

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
235 2697 0.033503 TGGAGATACCGAGGCAGTGA 60.034 55.0 0.0 0.0 42.61 3.41 F
1054 3555 0.035056 AATTGTTGCTCCTCCTCCCG 60.035 55.0 0.0 0.0 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1168 3700 1.133761 TCCTGCGGTGTAGCTAGAGAT 60.134 52.381 0.0 0.0 38.13 2.75 R
2462 5115 0.035152 ATTGCTTGCCTCCATCACGA 60.035 50.000 0.0 0.0 0.00 4.35 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
69 71 0.967380 GCAAGGGGTGGATGAGGTTG 60.967 60.000 0.00 0.00 0.00 3.77
73 75 1.380302 GGGTGGATGAGGTTGCTGT 59.620 57.895 0.00 0.00 0.00 4.40
127 1325 4.717280 ACATCTTAACCTCCTTGGACTAGG 59.283 45.833 0.00 0.00 39.71 3.02
160 1358 2.167693 AGTCACAAAGAACACGGTGAGA 59.832 45.455 16.29 0.00 40.59 3.27
190 2652 6.095440 GGAATAGGCTCTCTCTATTAGCTGAG 59.905 46.154 0.00 0.00 37.50 3.35
229 2691 7.217200 TCTTTCAAATAATGGAGATACCGAGG 58.783 38.462 0.00 0.00 42.61 4.63
235 2697 0.033503 TGGAGATACCGAGGCAGTGA 60.034 55.000 0.00 0.00 42.61 3.41
262 2724 0.616395 TGTTCCCACCGGCTATCAGA 60.616 55.000 0.00 0.00 0.00 3.27
276 2738 5.920193 GCTATCAGAATAGGCTCTCATCT 57.080 43.478 0.00 0.00 36.20 2.90
321 2783 4.576216 TTTGCAACGTGGAATTATGTGT 57.424 36.364 0.00 0.00 0.00 3.72
325 2787 4.036852 TGCAACGTGGAATTATGTGTTTCA 59.963 37.500 0.00 0.00 0.00 2.69
331 2793 6.431543 ACGTGGAATTATGTGTTTCATGGTTA 59.568 34.615 0.00 0.00 37.91 2.85
439 2906 3.915437 ACAACAATGAAAACGCCCTAG 57.085 42.857 0.00 0.00 0.00 3.02
489 2981 6.803320 CCAACTAACACATGTAGAATTGCAAG 59.197 38.462 4.94 0.00 0.00 4.01
595 3087 0.724549 CTCTCTCACGAGTCACGAGG 59.275 60.000 0.00 0.00 45.77 4.63
627 3119 0.604243 TACGTGCTCCATGCCGTTTT 60.604 50.000 0.00 0.00 42.66 2.43
629 3121 0.179200 CGTGCTCCATGCCGTTTTAC 60.179 55.000 0.00 0.00 42.00 2.01
644 3138 6.654161 TGCCGTTTTACCATAGCTTAAAAGTA 59.346 34.615 0.00 0.00 29.84 2.24
659 3153 6.313164 GCTTAAAAGTACTACAACTGCTAGGG 59.687 42.308 0.00 0.00 0.00 3.53
666 3160 1.222936 CAACTGCTAGGGCCCTCAG 59.777 63.158 32.80 31.18 37.74 3.35
683 3177 3.695606 GTCCCTCGCACAGAGCCA 61.696 66.667 0.00 0.00 45.54 4.75
686 3180 3.200593 CCTCGCACAGAGCCATGC 61.201 66.667 0.00 0.00 45.54 4.06
708 3202 4.025647 GCTCGTTATCAAATCCTTCCTTCG 60.026 45.833 0.00 0.00 0.00 3.79
731 3225 3.253188 TGAGGAAACGAGAAAATTGCAGG 59.747 43.478 0.00 0.00 0.00 4.85
732 3226 2.029918 AGGAAACGAGAAAATTGCAGGC 60.030 45.455 0.00 0.00 0.00 4.85
733 3227 2.288152 GGAAACGAGAAAATTGCAGGCA 60.288 45.455 0.00 0.00 0.00 4.75
734 3228 2.712057 AACGAGAAAATTGCAGGCAG 57.288 45.000 0.00 0.00 0.00 4.85
829 3323 1.077716 CGTCCATCCCCACCTTTCC 60.078 63.158 0.00 0.00 0.00 3.13
830 3324 1.847798 CGTCCATCCCCACCTTTCCA 61.848 60.000 0.00 0.00 0.00 3.53
831 3325 0.323451 GTCCATCCCCACCTTTCCAC 60.323 60.000 0.00 0.00 0.00 4.02
832 3326 0.477597 TCCATCCCCACCTTTCCACT 60.478 55.000 0.00 0.00 0.00 4.00
833 3327 0.409484 CCATCCCCACCTTTCCACTT 59.591 55.000 0.00 0.00 0.00 3.16
834 3328 1.616994 CCATCCCCACCTTTCCACTTC 60.617 57.143 0.00 0.00 0.00 3.01
835 3329 1.355720 CATCCCCACCTTTCCACTTCT 59.644 52.381 0.00 0.00 0.00 2.85
836 3330 0.771127 TCCCCACCTTTCCACTTCTG 59.229 55.000 0.00 0.00 0.00 3.02
837 3331 0.895559 CCCCACCTTTCCACTTCTGC 60.896 60.000 0.00 0.00 0.00 4.26
838 3332 0.178992 CCCACCTTTCCACTTCTGCA 60.179 55.000 0.00 0.00 0.00 4.41
861 3355 4.773117 GCGTCGTCGTCTCCCACC 62.773 72.222 3.66 0.00 39.49 4.61
877 3371 4.845541 TCCCACCACCCATCCTAAATATA 58.154 43.478 0.00 0.00 0.00 0.86
879 3373 6.585909 TCCCACCACCCATCCTAAATATATA 58.414 40.000 0.00 0.00 0.00 0.86
883 3377 7.365652 CCACCACCCATCCTAAATATATACCTC 60.366 44.444 0.00 0.00 0.00 3.85
885 3379 6.101296 CCACCCATCCTAAATATATACCTCCC 59.899 46.154 0.00 0.00 0.00 4.30
886 3380 5.903589 ACCCATCCTAAATATATACCTCCCG 59.096 44.000 0.00 0.00 0.00 5.14
887 3381 5.221661 CCCATCCTAAATATATACCTCCCGC 60.222 48.000 0.00 0.00 0.00 6.13
888 3382 5.602978 CCATCCTAAATATATACCTCCCGCT 59.397 44.000 0.00 0.00 0.00 5.52
889 3383 6.239345 CCATCCTAAATATATACCTCCCGCTC 60.239 46.154 0.00 0.00 0.00 5.03
890 3384 5.206587 TCCTAAATATATACCTCCCGCTCC 58.793 45.833 0.00 0.00 0.00 4.70
891 3385 4.344390 CCTAAATATATACCTCCCGCTCCC 59.656 50.000 0.00 0.00 0.00 4.30
892 3386 2.068834 ATATATACCTCCCGCTCCCG 57.931 55.000 0.00 0.00 0.00 5.14
905 3399 2.525629 TCCCGGTGTGCCTTGAGA 60.526 61.111 0.00 0.00 0.00 3.27
953 3451 1.673665 CTTCCACTCCACTGCCAGC 60.674 63.158 0.00 0.00 0.00 4.85
958 3456 2.210013 ACTCCACTGCCAGCGAGAA 61.210 57.895 14.47 0.00 0.00 2.87
963 3461 2.125350 CTGCCAGCGAGAACTCCC 60.125 66.667 0.00 0.00 0.00 4.30
1053 3554 1.683319 GGAATTGTTGCTCCTCCTCCC 60.683 57.143 0.00 0.00 0.00 4.30
1054 3555 0.035056 AATTGTTGCTCCTCCTCCCG 60.035 55.000 0.00 0.00 0.00 5.14
1055 3556 1.915078 ATTGTTGCTCCTCCTCCCGG 61.915 60.000 0.00 0.00 0.00 5.73
1165 3693 3.117171 CGCAGCTGCAGGTCAGTC 61.117 66.667 36.03 5.81 44.66 3.51
1168 3700 1.670015 CAGCTGCAGGTCAGTCAGA 59.330 57.895 17.16 0.00 44.66 3.27
1202 3734 1.003355 CAGGAGCGGGACACAATGT 60.003 57.895 0.00 0.00 0.00 2.71
1620 4156 0.174617 CCTCGGTCTCTTCTTCCTGC 59.825 60.000 0.00 0.00 0.00 4.85
1629 4165 2.492449 CTTCTTCCTGCTCGGCGTCA 62.492 60.000 6.85 5.58 0.00 4.35
1700 4236 0.388649 CACGCGTTGCTTCTCTACCT 60.389 55.000 10.22 0.00 0.00 3.08
1736 4279 4.225984 GCTATATCTGTTCTGAGCACTCG 58.774 47.826 0.00 0.00 0.00 4.18
1898 4521 4.657814 ACCTTAGCCAAATTTCTCTCCA 57.342 40.909 0.00 0.00 0.00 3.86
1927 4550 7.158099 ACTACCTTGGTCAAATAAAAGCATC 57.842 36.000 0.00 0.00 0.00 3.91
2011 4634 2.102070 TTGTGTGGTTATAGGTGCCG 57.898 50.000 0.00 0.00 0.00 5.69
2021 4669 1.038280 ATAGGTGCCGGTAGTGCTAC 58.962 55.000 1.90 0.95 35.40 3.58
2127 4776 1.676678 GCGTCAGGATAGTCTGGGCA 61.677 60.000 0.00 0.00 35.89 5.36
2139 4788 3.431415 AGTCTGGGCAAAAATAACCCTC 58.569 45.455 0.00 0.00 44.56 4.30
2140 4789 2.163613 GTCTGGGCAAAAATAACCCTCG 59.836 50.000 0.00 0.00 44.56 4.63
2245 4898 3.485877 GCAGACAAGGAATGAATACACGC 60.486 47.826 0.00 0.00 0.00 5.34
2262 4915 2.156446 GCGCATGCAACAGTGATGC 61.156 57.895 19.57 17.76 44.08 3.91
2265 4918 0.387622 GCATGCAACAGTGATGCGTT 60.388 50.000 16.65 6.13 46.76 4.84
2270 4923 0.943673 CAACAGTGATGCGTTGACCA 59.056 50.000 0.00 0.00 44.20 4.02
2295 4948 3.620719 CGATGGGAATGGTGCATATAGCT 60.621 47.826 0.00 0.00 45.94 3.32
2304 4957 7.310113 GGAATGGTGCATATAGCTACTAGACTT 60.310 40.741 0.00 0.00 45.94 3.01
2305 4958 6.978674 TGGTGCATATAGCTACTAGACTTT 57.021 37.500 0.00 0.00 45.94 2.66
2306 4959 7.361457 TGGTGCATATAGCTACTAGACTTTT 57.639 36.000 0.00 0.00 45.94 2.27
2307 4960 7.792032 TGGTGCATATAGCTACTAGACTTTTT 58.208 34.615 0.00 0.00 45.94 1.94
2329 4982 4.470334 TTTTGAAACAGAGGCAAAAGCT 57.530 36.364 0.00 0.00 36.80 3.74
2330 4983 4.470334 TTTGAAACAGAGGCAAAAGCTT 57.530 36.364 0.00 0.00 0.00 3.74
2331 4984 4.470334 TTGAAACAGAGGCAAAAGCTTT 57.530 36.364 5.69 5.69 0.00 3.51
2332 4985 3.784338 TGAAACAGAGGCAAAAGCTTTG 58.216 40.909 13.54 8.26 0.00 2.77
2333 4986 2.229675 AACAGAGGCAAAAGCTTTGC 57.770 45.000 13.54 17.13 44.22 3.68
2340 4993 1.718396 GCAAAAGCTTTGCCTCATCC 58.282 50.000 13.54 0.00 39.38 3.51
2341 4994 1.001181 GCAAAAGCTTTGCCTCATCCA 59.999 47.619 13.54 0.00 39.38 3.41
2342 4995 2.354403 GCAAAAGCTTTGCCTCATCCAT 60.354 45.455 13.54 0.00 39.38 3.41
2343 4996 3.867216 GCAAAAGCTTTGCCTCATCCATT 60.867 43.478 13.54 0.00 39.38 3.16
2344 4997 4.621274 GCAAAAGCTTTGCCTCATCCATTA 60.621 41.667 13.54 0.00 39.38 1.90
2345 4998 5.481105 CAAAAGCTTTGCCTCATCCATTAA 58.519 37.500 13.54 0.00 0.00 1.40
2346 4999 5.743636 AAAGCTTTGCCTCATCCATTAAA 57.256 34.783 11.80 0.00 0.00 1.52
2347 5000 5.945144 AAGCTTTGCCTCATCCATTAAAT 57.055 34.783 0.00 0.00 0.00 1.40
2348 5001 7.422465 AAAGCTTTGCCTCATCCATTAAATA 57.578 32.000 11.80 0.00 0.00 1.40
2349 5002 7.422465 AAGCTTTGCCTCATCCATTAAATAA 57.578 32.000 0.00 0.00 0.00 1.40
2350 5003 7.047460 AGCTTTGCCTCATCCATTAAATAAG 57.953 36.000 0.00 0.00 0.00 1.73
2351 5004 6.835488 AGCTTTGCCTCATCCATTAAATAAGA 59.165 34.615 0.00 0.00 0.00 2.10
2352 5005 7.014038 AGCTTTGCCTCATCCATTAAATAAGAG 59.986 37.037 0.00 0.00 0.00 2.85
2353 5006 7.013655 GCTTTGCCTCATCCATTAAATAAGAGA 59.986 37.037 0.00 0.00 0.00 3.10
2354 5007 8.455903 TTTGCCTCATCCATTAAATAAGAGAG 57.544 34.615 0.00 0.00 0.00 3.20
2355 5008 7.379059 TGCCTCATCCATTAAATAAGAGAGA 57.621 36.000 0.00 0.00 0.00 3.10
2356 5009 7.805163 TGCCTCATCCATTAAATAAGAGAGAA 58.195 34.615 0.00 0.00 0.00 2.87
2357 5010 8.443176 TGCCTCATCCATTAAATAAGAGAGAAT 58.557 33.333 0.00 0.00 0.00 2.40
2358 5011 9.950496 GCCTCATCCATTAAATAAGAGAGAATA 57.050 33.333 0.00 0.00 0.00 1.75
2374 5027 9.944376 AAGAGAGAATATAGTTTGTTACAAGCA 57.056 29.630 13.93 1.41 0.00 3.91
2375 5028 9.944376 AGAGAGAATATAGTTTGTTACAAGCAA 57.056 29.630 13.93 0.24 0.00 3.91
2376 5029 9.974750 GAGAGAATATAGTTTGTTACAAGCAAC 57.025 33.333 13.93 2.77 0.00 4.17
2377 5030 8.947115 AGAGAATATAGTTTGTTACAAGCAACC 58.053 33.333 13.93 0.00 0.00 3.77
2378 5031 8.051901 AGAATATAGTTTGTTACAAGCAACCC 57.948 34.615 13.93 0.00 0.00 4.11
2379 5032 4.759516 ATAGTTTGTTACAAGCAACCCG 57.240 40.909 13.93 0.00 0.00 5.28
2380 5033 2.645802 AGTTTGTTACAAGCAACCCGA 58.354 42.857 13.93 0.00 0.00 5.14
2381 5034 3.219281 AGTTTGTTACAAGCAACCCGAT 58.781 40.909 13.93 0.00 0.00 4.18
2382 5035 3.634910 AGTTTGTTACAAGCAACCCGATT 59.365 39.130 13.93 0.00 0.00 3.34
2383 5036 4.822896 AGTTTGTTACAAGCAACCCGATTA 59.177 37.500 13.93 0.00 0.00 1.75
2384 5037 4.752661 TTGTTACAAGCAACCCGATTAC 57.247 40.909 0.00 0.00 0.00 1.89
2385 5038 3.741249 TGTTACAAGCAACCCGATTACA 58.259 40.909 0.00 0.00 0.00 2.41
2386 5039 3.499157 TGTTACAAGCAACCCGATTACAC 59.501 43.478 0.00 0.00 0.00 2.90
2387 5040 1.153353 ACAAGCAACCCGATTACACG 58.847 50.000 0.00 0.00 0.00 4.49
2394 5047 3.731136 CCGATTACACGGCATGGG 58.269 61.111 0.00 0.00 46.20 4.00
2395 5048 1.145156 CCGATTACACGGCATGGGA 59.855 57.895 0.00 0.00 46.20 4.37
2396 5049 0.462937 CCGATTACACGGCATGGGAA 60.463 55.000 0.00 0.00 46.20 3.97
2397 5050 1.593196 CGATTACACGGCATGGGAAT 58.407 50.000 0.00 0.00 0.00 3.01
2398 5051 1.946768 CGATTACACGGCATGGGAATT 59.053 47.619 0.00 0.00 0.00 2.17
2399 5052 3.135225 CGATTACACGGCATGGGAATTA 58.865 45.455 0.00 0.00 0.00 1.40
2400 5053 3.059188 CGATTACACGGCATGGGAATTAC 60.059 47.826 0.00 0.00 0.00 1.89
2401 5054 3.637911 TTACACGGCATGGGAATTACT 57.362 42.857 0.00 0.00 0.00 2.24
2402 5055 2.038387 ACACGGCATGGGAATTACTC 57.962 50.000 0.00 0.00 0.00 2.59
2403 5056 1.559682 ACACGGCATGGGAATTACTCT 59.440 47.619 0.00 0.00 0.00 3.24
2404 5057 2.213499 CACGGCATGGGAATTACTCTC 58.787 52.381 0.00 0.00 0.00 3.20
2405 5058 1.202533 ACGGCATGGGAATTACTCTCG 60.203 52.381 0.00 0.00 0.00 4.04
2406 5059 1.202533 CGGCATGGGAATTACTCTCGT 60.203 52.381 0.00 0.00 0.00 4.18
2407 5060 2.035449 CGGCATGGGAATTACTCTCGTA 59.965 50.000 0.00 0.00 0.00 3.43
2408 5061 3.491964 CGGCATGGGAATTACTCTCGTAA 60.492 47.826 0.00 0.00 39.73 3.18
2409 5062 3.808174 GGCATGGGAATTACTCTCGTAAC 59.192 47.826 0.00 0.00 38.35 2.50
2410 5063 4.439057 GCATGGGAATTACTCTCGTAACA 58.561 43.478 0.00 0.00 38.35 2.41
2411 5064 5.057149 GCATGGGAATTACTCTCGTAACAT 58.943 41.667 0.00 0.00 38.35 2.71
2412 5065 5.527582 GCATGGGAATTACTCTCGTAACATT 59.472 40.000 0.00 0.00 38.35 2.71
2413 5066 6.704493 GCATGGGAATTACTCTCGTAACATTA 59.296 38.462 0.00 0.00 38.35 1.90
2414 5067 7.387948 GCATGGGAATTACTCTCGTAACATTAT 59.612 37.037 0.00 0.00 38.35 1.28
2415 5068 8.712363 CATGGGAATTACTCTCGTAACATTATG 58.288 37.037 0.00 0.00 38.35 1.90
2416 5069 7.214381 TGGGAATTACTCTCGTAACATTATGG 58.786 38.462 0.00 0.00 38.35 2.74
2417 5070 7.070198 TGGGAATTACTCTCGTAACATTATGGA 59.930 37.037 0.00 0.00 38.35 3.41
2418 5071 7.384387 GGGAATTACTCTCGTAACATTATGGAC 59.616 40.741 0.00 0.00 38.35 4.02
2419 5072 7.384387 GGAATTACTCTCGTAACATTATGGACC 59.616 40.741 0.00 0.00 38.35 4.46
2420 5073 4.667519 ACTCTCGTAACATTATGGACCC 57.332 45.455 0.00 0.00 0.00 4.46
2421 5074 4.287552 ACTCTCGTAACATTATGGACCCT 58.712 43.478 0.00 0.00 0.00 4.34
2422 5075 5.452255 ACTCTCGTAACATTATGGACCCTA 58.548 41.667 0.00 0.00 0.00 3.53
2423 5076 5.535406 ACTCTCGTAACATTATGGACCCTAG 59.465 44.000 0.00 0.00 0.00 3.02
2424 5077 5.452255 TCTCGTAACATTATGGACCCTAGT 58.548 41.667 0.00 0.00 0.00 2.57
2425 5078 5.895534 TCTCGTAACATTATGGACCCTAGTT 59.104 40.000 0.00 0.00 0.00 2.24
2426 5079 6.381994 TCTCGTAACATTATGGACCCTAGTTT 59.618 38.462 0.00 0.00 0.00 2.66
2427 5080 6.949715 TCGTAACATTATGGACCCTAGTTTT 58.050 36.000 0.00 0.00 0.00 2.43
2428 5081 7.396418 TCGTAACATTATGGACCCTAGTTTTT 58.604 34.615 0.00 0.00 0.00 1.94
2446 5099 1.173043 TTTTGCACCGGTGATGATCC 58.827 50.000 38.30 19.13 0.00 3.36
2447 5100 0.037447 TTTGCACCGGTGATGATCCA 59.963 50.000 38.30 21.61 0.00 3.41
2448 5101 0.392863 TTGCACCGGTGATGATCCAG 60.393 55.000 38.30 8.74 0.00 3.86
2449 5102 1.264045 TGCACCGGTGATGATCCAGA 61.264 55.000 38.30 6.22 0.00 3.86
2450 5103 0.531532 GCACCGGTGATGATCCAGAG 60.532 60.000 38.30 7.32 0.00 3.35
2451 5104 0.105593 CACCGGTGATGATCCAGAGG 59.894 60.000 31.31 0.00 0.00 3.69
2452 5105 1.070445 CCGGTGATGATCCAGAGGC 59.930 63.158 0.00 0.00 0.00 4.70
2453 5106 1.406065 CCGGTGATGATCCAGAGGCT 61.406 60.000 0.00 0.00 0.00 4.58
2454 5107 1.332195 CGGTGATGATCCAGAGGCTA 58.668 55.000 0.00 0.00 0.00 3.93
2455 5108 1.271934 CGGTGATGATCCAGAGGCTAG 59.728 57.143 0.00 0.00 0.00 3.42
2456 5109 1.001860 GGTGATGATCCAGAGGCTAGC 59.998 57.143 6.04 6.04 0.00 3.42
2457 5110 1.001860 GTGATGATCCAGAGGCTAGCC 59.998 57.143 27.19 27.19 0.00 3.93
2466 5119 3.141488 AGGCTAGCCTCGGTCGTG 61.141 66.667 31.30 0.00 44.43 4.35
2467 5120 3.138798 GGCTAGCCTCGGTCGTGA 61.139 66.667 27.17 0.00 0.00 4.35
2468 5121 2.491022 GGCTAGCCTCGGTCGTGAT 61.491 63.158 27.17 0.00 0.00 3.06
2469 5122 1.299468 GCTAGCCTCGGTCGTGATG 60.299 63.158 2.29 0.00 0.00 3.07
2470 5123 1.360551 CTAGCCTCGGTCGTGATGG 59.639 63.158 0.00 0.00 0.00 3.51
2471 5124 1.077285 TAGCCTCGGTCGTGATGGA 60.077 57.895 0.00 0.00 0.00 3.41
2472 5125 1.101635 TAGCCTCGGTCGTGATGGAG 61.102 60.000 0.00 0.00 0.00 3.86
2473 5126 2.808315 CCTCGGTCGTGATGGAGG 59.192 66.667 5.21 5.21 40.05 4.30
2474 5127 2.105128 CTCGGTCGTGATGGAGGC 59.895 66.667 0.00 0.00 0.00 4.70
2475 5128 2.678580 TCGGTCGTGATGGAGGCA 60.679 61.111 0.00 0.00 0.00 4.75
2476 5129 2.225791 CTCGGTCGTGATGGAGGCAA 62.226 60.000 0.00 0.00 0.00 4.52
2477 5130 1.811266 CGGTCGTGATGGAGGCAAG 60.811 63.158 0.00 0.00 0.00 4.01
2478 5131 2.109126 GGTCGTGATGGAGGCAAGC 61.109 63.158 0.00 0.00 0.00 4.01
2479 5132 1.375908 GTCGTGATGGAGGCAAGCA 60.376 57.895 0.00 0.00 0.00 3.91
2480 5133 0.955428 GTCGTGATGGAGGCAAGCAA 60.955 55.000 0.00 0.00 0.00 3.91
2481 5134 0.035152 TCGTGATGGAGGCAAGCAAT 60.035 50.000 0.00 0.00 0.00 3.56
2482 5135 0.099968 CGTGATGGAGGCAAGCAATG 59.900 55.000 0.00 0.00 0.00 2.82
2483 5136 1.180029 GTGATGGAGGCAAGCAATGT 58.820 50.000 0.00 0.00 0.00 2.71
2484 5137 2.368439 GTGATGGAGGCAAGCAATGTA 58.632 47.619 0.00 0.00 0.00 2.29
2485 5138 2.357009 GTGATGGAGGCAAGCAATGTAG 59.643 50.000 0.00 0.00 0.00 2.74
2486 5139 2.025981 TGATGGAGGCAAGCAATGTAGT 60.026 45.455 0.00 0.00 0.00 2.73
2487 5140 2.113860 TGGAGGCAAGCAATGTAGTC 57.886 50.000 0.00 0.00 0.00 2.59
2488 5141 1.009829 GGAGGCAAGCAATGTAGTCG 58.990 55.000 0.00 0.00 0.00 4.18
2489 5142 1.009829 GAGGCAAGCAATGTAGTCGG 58.990 55.000 0.00 0.00 0.00 4.79
2490 5143 0.324943 AGGCAAGCAATGTAGTCGGT 59.675 50.000 0.00 0.00 0.00 4.69
2491 5144 0.447801 GGCAAGCAATGTAGTCGGTG 59.552 55.000 0.00 0.00 0.00 4.94
2492 5145 1.438651 GCAAGCAATGTAGTCGGTGA 58.561 50.000 0.00 0.00 0.00 4.02
2493 5146 1.128692 GCAAGCAATGTAGTCGGTGAC 59.871 52.381 0.00 0.00 0.00 3.67
2505 5158 3.482783 GGTGACGCGCTCTTCTGC 61.483 66.667 5.73 0.00 0.00 4.26
2506 5159 2.431601 GTGACGCGCTCTTCTGCT 60.432 61.111 5.73 0.00 0.00 4.24
2507 5160 2.024319 GTGACGCGCTCTTCTGCTT 61.024 57.895 5.73 0.00 0.00 3.91
2508 5161 2.023771 TGACGCGCTCTTCTGCTTG 61.024 57.895 5.73 0.00 0.00 4.01
2509 5162 1.734477 GACGCGCTCTTCTGCTTGA 60.734 57.895 5.73 0.00 0.00 3.02
2510 5163 1.284982 GACGCGCTCTTCTGCTTGAA 61.285 55.000 5.73 0.00 0.00 2.69
2511 5164 1.131420 CGCGCTCTTCTGCTTGAAC 59.869 57.895 5.56 0.00 0.00 3.18
2512 5165 1.560004 CGCGCTCTTCTGCTTGAACA 61.560 55.000 5.56 0.00 0.00 3.18
2513 5166 0.110464 GCGCTCTTCTGCTTGAACAC 60.110 55.000 0.00 0.00 0.00 3.32
2514 5167 1.506493 CGCTCTTCTGCTTGAACACT 58.494 50.000 0.00 0.00 0.00 3.55
2515 5168 1.458827 CGCTCTTCTGCTTGAACACTC 59.541 52.381 0.00 0.00 0.00 3.51
2516 5169 2.765122 GCTCTTCTGCTTGAACACTCT 58.235 47.619 0.00 0.00 0.00 3.24
2517 5170 2.736192 GCTCTTCTGCTTGAACACTCTC 59.264 50.000 0.00 0.00 0.00 3.20
2518 5171 2.985809 CTCTTCTGCTTGAACACTCTCG 59.014 50.000 0.00 0.00 0.00 4.04
2519 5172 1.458827 CTTCTGCTTGAACACTCTCGC 59.541 52.381 0.00 0.00 0.00 5.03
2520 5173 0.664466 TCTGCTTGAACACTCTCGCG 60.664 55.000 0.00 0.00 0.00 5.87
2521 5174 0.941463 CTGCTTGAACACTCTCGCGT 60.941 55.000 5.77 0.00 0.00 6.01
2522 5175 0.529773 TGCTTGAACACTCTCGCGTT 60.530 50.000 5.77 0.00 0.00 4.84
2523 5176 0.582005 GCTTGAACACTCTCGCGTTT 59.418 50.000 5.77 0.00 0.00 3.60
2524 5177 1.397315 GCTTGAACACTCTCGCGTTTC 60.397 52.381 5.77 1.48 0.00 2.78
2525 5178 0.850217 TTGAACACTCTCGCGTTTCG 59.150 50.000 5.77 0.00 40.15 3.46
2539 5192 3.021355 CGTTTCGCTCGTTCCAAATAG 57.979 47.619 0.00 0.00 0.00 1.73
2540 5193 2.410730 CGTTTCGCTCGTTCCAAATAGT 59.589 45.455 0.00 0.00 0.00 2.12
2541 5194 3.481467 CGTTTCGCTCGTTCCAAATAGTC 60.481 47.826 0.00 0.00 0.00 2.59
2542 5195 2.288961 TCGCTCGTTCCAAATAGTCC 57.711 50.000 0.00 0.00 0.00 3.85
2543 5196 1.546923 TCGCTCGTTCCAAATAGTCCA 59.453 47.619 0.00 0.00 0.00 4.02
2544 5197 2.167693 TCGCTCGTTCCAAATAGTCCAT 59.832 45.455 0.00 0.00 0.00 3.41
2545 5198 2.285220 CGCTCGTTCCAAATAGTCCATG 59.715 50.000 0.00 0.00 0.00 3.66
2546 5199 3.531538 GCTCGTTCCAAATAGTCCATGA 58.468 45.455 0.00 0.00 0.00 3.07
2547 5200 3.557595 GCTCGTTCCAAATAGTCCATGAG 59.442 47.826 0.00 0.00 0.00 2.90
2548 5201 4.680708 GCTCGTTCCAAATAGTCCATGAGA 60.681 45.833 0.00 0.00 0.00 3.27
2549 5202 5.414789 TCGTTCCAAATAGTCCATGAGAA 57.585 39.130 0.00 0.00 0.00 2.87
2550 5203 5.800296 TCGTTCCAAATAGTCCATGAGAAA 58.200 37.500 0.00 0.00 0.00 2.52
2551 5204 5.874810 TCGTTCCAAATAGTCCATGAGAAAG 59.125 40.000 0.00 0.00 0.00 2.62
2552 5205 5.643777 CGTTCCAAATAGTCCATGAGAAAGT 59.356 40.000 0.00 0.00 0.00 2.66
2553 5206 6.816640 CGTTCCAAATAGTCCATGAGAAAGTA 59.183 38.462 0.00 0.00 0.00 2.24
2554 5207 7.495934 CGTTCCAAATAGTCCATGAGAAAGTAT 59.504 37.037 0.00 0.00 0.00 2.12
2555 5208 8.616076 GTTCCAAATAGTCCATGAGAAAGTATG 58.384 37.037 0.00 0.00 0.00 2.39
2556 5209 7.282585 TCCAAATAGTCCATGAGAAAGTATGG 58.717 38.462 0.00 0.00 44.15 2.74
2557 5210 7.056635 CCAAATAGTCCATGAGAAAGTATGGT 58.943 38.462 0.00 0.00 43.43 3.55
2558 5211 7.012704 CCAAATAGTCCATGAGAAAGTATGGTG 59.987 40.741 0.00 0.00 43.43 4.17
2559 5212 7.437713 AATAGTCCATGAGAAAGTATGGTGA 57.562 36.000 0.00 0.00 43.43 4.02
2560 5213 5.350504 AGTCCATGAGAAAGTATGGTGAG 57.649 43.478 0.00 0.00 43.43 3.51
2561 5214 4.163078 AGTCCATGAGAAAGTATGGTGAGG 59.837 45.833 0.00 0.00 43.43 3.86
2562 5215 3.455910 TCCATGAGAAAGTATGGTGAGGG 59.544 47.826 0.00 0.00 43.43 4.30
2563 5216 3.455910 CCATGAGAAAGTATGGTGAGGGA 59.544 47.826 0.00 0.00 39.18 4.20
2564 5217 4.446371 CATGAGAAAGTATGGTGAGGGAC 58.554 47.826 0.00 0.00 0.00 4.46
2565 5218 2.838202 TGAGAAAGTATGGTGAGGGACC 59.162 50.000 0.00 0.00 46.37 4.46
2566 5219 2.170817 GAGAAAGTATGGTGAGGGACCC 59.829 54.545 0.59 0.59 45.45 4.46
2567 5220 2.197465 GAAAGTATGGTGAGGGACCCT 58.803 52.381 14.79 14.79 45.45 4.34
2577 5230 3.105283 GTGAGGGACCCTAGTGTACAAT 58.895 50.000 14.87 0.00 31.76 2.71
2585 5238 8.657712 AGGGACCCTAGTGTACAATATAATTTC 58.342 37.037 12.85 0.00 28.47 2.17
2586 5239 8.657712 GGGACCCTAGTGTACAATATAATTTCT 58.342 37.037 2.09 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 1.754226 TGTCACCCCTTTTCTTGTTGC 59.246 47.619 0.00 0.00 0.00 4.17
127 1325 6.316890 TGTTCTTTGTGACTGGTTAGGTTAAC 59.683 38.462 0.00 0.00 37.94 2.01
131 1329 4.196971 GTGTTCTTTGTGACTGGTTAGGT 58.803 43.478 0.00 0.00 0.00 3.08
145 1343 1.808891 CGGGTTCTCACCGTGTTCTTT 60.809 52.381 0.00 0.00 45.39 2.52
160 1358 1.062810 AGAGAGAGCCTATTCCGGGTT 60.063 52.381 0.00 0.00 34.32 4.11
222 2684 1.228769 AGTGGTCACTGCCTCGGTA 60.229 57.895 2.46 0.00 40.75 4.02
262 2724 5.826737 CACCATTTGAAGATGAGAGCCTATT 59.173 40.000 0.00 0.00 0.00 1.73
276 2738 9.454859 AAAACTAAATTTCCAACACCATTTGAA 57.545 25.926 0.00 0.00 0.00 2.69
381 2847 9.803315 CACATAGATGCGTATACCACTTTATAT 57.197 33.333 0.00 0.00 0.00 0.86
396 2863 6.198029 TGTTTTCAAAACAACACATAGATGCG 59.802 34.615 13.46 0.00 0.00 4.73
465 2957 6.306356 GCTTGCAATTCTACATGTGTTAGTTG 59.694 38.462 9.11 7.99 0.00 3.16
472 2964 3.057386 TGTGGCTTGCAATTCTACATGTG 60.057 43.478 9.11 0.00 0.00 3.21
473 2965 3.156293 TGTGGCTTGCAATTCTACATGT 58.844 40.909 2.69 2.69 0.00 3.21
489 2981 3.834231 AGGGCCATATTATTGATTGTGGC 59.166 43.478 6.18 5.66 42.79 5.01
556 3048 3.309296 AGCGATGGATTAGAGGAGGAAA 58.691 45.455 0.00 0.00 0.00 3.13
613 3105 1.102978 ATGGTAAAACGGCATGGAGC 58.897 50.000 0.00 0.00 44.65 4.70
627 3119 9.865321 CAGTTGTAGTACTTTTAAGCTATGGTA 57.135 33.333 0.00 0.00 0.00 3.25
629 3121 7.549488 AGCAGTTGTAGTACTTTTAAGCTATGG 59.451 37.037 0.00 0.00 0.00 2.74
644 3138 0.252742 AGGGCCCTAGCAGTTGTAGT 60.253 55.000 27.42 0.00 42.56 2.73
659 3153 4.459089 GTGCGAGGGACTGAGGGC 62.459 72.222 0.00 0.00 41.55 5.19
666 3160 3.023949 ATGGCTCTGTGCGAGGGAC 62.024 63.158 0.00 0.00 44.05 4.46
683 3177 5.041191 AGGAAGGATTTGATAACGAGCAT 57.959 39.130 0.00 0.00 0.00 3.79
686 3180 5.005779 CACGAAGGAAGGATTTGATAACGAG 59.994 44.000 0.00 0.00 0.00 4.18
688 3182 4.868171 TCACGAAGGAAGGATTTGATAACG 59.132 41.667 0.00 0.00 0.00 3.18
708 3202 4.222114 CTGCAATTTTCTCGTTTCCTCAC 58.778 43.478 0.00 0.00 0.00 3.51
731 3225 1.362717 GCATGTGATGGGATGCTGC 59.637 57.895 0.00 0.00 41.52 5.25
732 3226 1.652563 CGCATGTGATGGGATGCTG 59.347 57.895 0.00 0.00 45.09 4.41
733 3227 1.527611 CCGCATGTGATGGGATGCT 60.528 57.895 8.11 0.00 45.09 3.79
734 3228 1.512996 CTCCGCATGTGATGGGATGC 61.513 60.000 8.11 0.00 45.09 3.91
738 3232 1.070601 TGATACTCCGCATGTGATGGG 59.929 52.381 8.11 0.00 42.27 4.00
740 3234 1.788886 CGTGATACTCCGCATGTGATG 59.211 52.381 8.11 2.37 0.00 3.07
750 3244 3.925090 CCCCGCCCGTGATACTCC 61.925 72.222 0.00 0.00 0.00 3.85
794 3288 1.523711 CGTCTTGGCCAGTGTGTGT 60.524 57.895 5.11 0.00 0.00 3.72
858 3352 7.365652 GGAGGTATATATTTAGGATGGGTGGTG 60.366 44.444 0.00 0.00 0.00 4.17
859 3353 6.677076 GGAGGTATATATTTAGGATGGGTGGT 59.323 42.308 0.00 0.00 0.00 4.16
860 3354 6.101296 GGGAGGTATATATTTAGGATGGGTGG 59.899 46.154 0.00 0.00 0.00 4.61
861 3355 6.183360 CGGGAGGTATATATTTAGGATGGGTG 60.183 46.154 0.00 0.00 0.00 4.61
877 3371 4.153330 ACCGGGAGCGGGAGGTAT 62.153 66.667 6.32 0.00 43.00 2.73
886 3380 4.329545 TCAAGGCACACCGGGAGC 62.330 66.667 6.32 6.43 42.76 4.70
887 3381 2.046892 CTCAAGGCACACCGGGAG 60.047 66.667 6.32 0.00 42.76 4.30
888 3382 2.525629 TCTCAAGGCACACCGGGA 60.526 61.111 6.32 0.00 42.76 5.14
889 3383 2.046892 CTCTCAAGGCACACCGGG 60.047 66.667 6.32 0.00 42.76 5.73
890 3384 2.743928 GCTCTCAAGGCACACCGG 60.744 66.667 0.00 0.00 42.76 5.28
891 3385 1.739562 GAGCTCTCAAGGCACACCG 60.740 63.158 6.43 0.00 42.76 4.94
892 3386 0.035630 ATGAGCTCTCAAGGCACACC 60.036 55.000 16.19 0.00 43.58 4.16
893 3387 1.338484 TGATGAGCTCTCAAGGCACAC 60.338 52.381 16.19 0.00 43.58 3.82
894 3388 0.978907 TGATGAGCTCTCAAGGCACA 59.021 50.000 16.19 1.08 43.58 4.57
895 3389 1.066286 AGTGATGAGCTCTCAAGGCAC 60.066 52.381 16.19 12.79 43.58 5.01
953 3451 2.182030 GACGCAGGGGAGTTCTCG 59.818 66.667 0.00 0.00 0.00 4.04
1036 3537 1.604378 CGGGAGGAGGAGCAACAAT 59.396 57.895 0.00 0.00 0.00 2.71
1037 3538 3.068881 CGGGAGGAGGAGCAACAA 58.931 61.111 0.00 0.00 0.00 2.83
1053 3554 4.552365 ATGCGCATCACCCCTCCG 62.552 66.667 19.28 0.00 0.00 4.63
1054 3555 2.592861 GATGCGCATCACCCCTCC 60.593 66.667 38.55 14.95 37.74 4.30
1055 3556 2.592861 GGATGCGCATCACCCCTC 60.593 66.667 41.80 25.01 39.54 4.30
1084 3612 4.451150 GAGGACGATGTGCGCCCA 62.451 66.667 4.18 0.00 45.95 5.36
1125 3653 2.915659 AGGTTGACGGCGAGGACA 60.916 61.111 16.62 5.28 0.00 4.02
1135 3663 2.743928 CTGCGGCTGGAGGTTGAC 60.744 66.667 6.08 0.00 0.00 3.18
1165 3693 1.950216 TGCGGTGTAGCTAGAGATCTG 59.050 52.381 0.00 0.00 38.13 2.90
1168 3700 1.133761 TCCTGCGGTGTAGCTAGAGAT 60.134 52.381 0.00 0.00 38.13 2.75
1190 3722 3.403038 AGAAGAAGAACATTGTGTCCCG 58.597 45.455 0.00 0.00 0.00 5.14
1202 3734 6.926272 CGAGGAAGAAAGAAGAAGAAGAAGAA 59.074 38.462 0.00 0.00 0.00 2.52
1482 4018 3.103911 GACGTTGTCGAGGCGGTG 61.104 66.667 7.85 0.00 40.62 4.94
1629 4165 2.125512 GGCGGAGATCAACGTGCT 60.126 61.111 10.16 0.00 0.00 4.40
1700 4236 8.637196 AACAGATATAGCACTAGTACTGCATA 57.363 34.615 5.39 0.00 37.08 3.14
1758 4361 6.039382 ACACACATACATAATCAGTCGCTAGA 59.961 38.462 0.00 0.00 0.00 2.43
1806 4409 1.134995 GGCATCATCGTCTCTCACACA 60.135 52.381 0.00 0.00 0.00 3.72
1898 4521 8.141909 GCTTTTATTTGACCAAGGTAGTTCTTT 58.858 33.333 0.00 0.00 0.00 2.52
1927 4550 8.446273 CAAGATATGCATAAAAATCTACTCCGG 58.554 37.037 11.13 0.00 0.00 5.14
2021 4669 4.695928 GCCAAAAAGTAGTGAAGGGAGTAG 59.304 45.833 0.00 0.00 0.00 2.57
2127 4776 1.629861 TCGGGTCCGAGGGTTATTTTT 59.370 47.619 8.14 0.00 44.01 1.94
2139 4788 2.210116 CACTTTCCATTATCGGGTCCG 58.790 52.381 2.52 2.52 41.35 4.79
2140 4789 1.947456 GCACTTTCCATTATCGGGTCC 59.053 52.381 0.00 0.00 0.00 4.46
2221 4874 4.393062 CGTGTATTCATTCCTTGTCTGCTT 59.607 41.667 0.00 0.00 0.00 3.91
2245 4898 4.066769 GCATCACTGTTGCATGCG 57.933 55.556 14.09 0.35 39.90 4.73
2262 4915 0.953471 TTCCCATCGCTTGGTCAACG 60.953 55.000 3.90 0.00 44.83 4.10
2265 4918 0.394216 CCATTCCCATCGCTTGGTCA 60.394 55.000 3.90 0.00 44.83 4.02
2270 4923 0.396139 ATGCACCATTCCCATCGCTT 60.396 50.000 0.00 0.00 0.00 4.68
2322 4975 3.604875 ATGGATGAGGCAAAGCTTTTG 57.395 42.857 9.53 6.62 0.00 2.44
2323 4976 5.743636 TTAATGGATGAGGCAAAGCTTTT 57.256 34.783 9.53 0.00 0.00 2.27
2324 4977 5.743636 TTTAATGGATGAGGCAAAGCTTT 57.256 34.783 5.69 5.69 0.00 3.51
2325 4978 5.945144 ATTTAATGGATGAGGCAAAGCTT 57.055 34.783 0.00 0.00 0.00 3.74
2326 4979 6.835488 TCTTATTTAATGGATGAGGCAAAGCT 59.165 34.615 0.00 0.00 0.00 3.74
2327 4980 7.013655 TCTCTTATTTAATGGATGAGGCAAAGC 59.986 37.037 0.00 0.00 0.00 3.51
2328 4981 8.455903 TCTCTTATTTAATGGATGAGGCAAAG 57.544 34.615 0.00 0.00 0.00 2.77
2329 4982 8.274322 TCTCTCTTATTTAATGGATGAGGCAAA 58.726 33.333 0.00 0.00 0.00 3.68
2330 4983 7.805163 TCTCTCTTATTTAATGGATGAGGCAA 58.195 34.615 0.00 0.00 0.00 4.52
2331 4984 7.379059 TCTCTCTTATTTAATGGATGAGGCA 57.621 36.000 0.00 0.00 0.00 4.75
2332 4985 8.860780 ATTCTCTCTTATTTAATGGATGAGGC 57.139 34.615 0.00 0.00 0.00 4.70
2348 5001 9.944376 TGCTTGTAACAAACTATATTCTCTCTT 57.056 29.630 0.00 0.00 0.00 2.85
2349 5002 9.944376 TTGCTTGTAACAAACTATATTCTCTCT 57.056 29.630 0.00 0.00 0.00 3.10
2350 5003 9.974750 GTTGCTTGTAACAAACTATATTCTCTC 57.025 33.333 0.00 0.00 0.00 3.20
2351 5004 8.947115 GGTTGCTTGTAACAAACTATATTCTCT 58.053 33.333 4.20 0.00 31.86 3.10
2352 5005 8.182227 GGGTTGCTTGTAACAAACTATATTCTC 58.818 37.037 4.20 0.00 35.04 2.87
2353 5006 7.148306 CGGGTTGCTTGTAACAAACTATATTCT 60.148 37.037 4.20 0.00 35.04 2.40
2354 5007 6.964934 CGGGTTGCTTGTAACAAACTATATTC 59.035 38.462 4.20 0.00 35.04 1.75
2355 5008 6.655848 TCGGGTTGCTTGTAACAAACTATATT 59.344 34.615 4.20 0.00 35.04 1.28
2356 5009 6.174760 TCGGGTTGCTTGTAACAAACTATAT 58.825 36.000 4.20 0.00 35.04 0.86
2357 5010 5.549347 TCGGGTTGCTTGTAACAAACTATA 58.451 37.500 4.20 0.00 35.04 1.31
2358 5011 4.391155 TCGGGTTGCTTGTAACAAACTAT 58.609 39.130 4.20 0.00 35.04 2.12
2359 5012 3.806380 TCGGGTTGCTTGTAACAAACTA 58.194 40.909 4.20 0.00 35.04 2.24
2360 5013 2.645802 TCGGGTTGCTTGTAACAAACT 58.354 42.857 4.20 0.00 35.04 2.66
2361 5014 3.636282 ATCGGGTTGCTTGTAACAAAC 57.364 42.857 4.20 0.00 33.86 2.93
2362 5015 4.579340 TGTAATCGGGTTGCTTGTAACAAA 59.421 37.500 4.20 0.00 32.22 2.83
2363 5016 4.023878 GTGTAATCGGGTTGCTTGTAACAA 60.024 41.667 4.20 0.00 32.22 2.83
2364 5017 3.499157 GTGTAATCGGGTTGCTTGTAACA 59.501 43.478 4.20 0.00 32.22 2.41
2365 5018 3.423907 CGTGTAATCGGGTTGCTTGTAAC 60.424 47.826 0.00 0.00 0.00 2.50
2366 5019 2.737783 CGTGTAATCGGGTTGCTTGTAA 59.262 45.455 0.00 0.00 0.00 2.41
2367 5020 2.339418 CGTGTAATCGGGTTGCTTGTA 58.661 47.619 0.00 0.00 0.00 2.41
2368 5021 1.153353 CGTGTAATCGGGTTGCTTGT 58.847 50.000 0.00 0.00 0.00 3.16
2369 5022 0.446222 CCGTGTAATCGGGTTGCTTG 59.554 55.000 0.00 0.00 45.88 4.01
2370 5023 2.849081 CCGTGTAATCGGGTTGCTT 58.151 52.632 0.00 0.00 45.88 3.91
2371 5024 4.609995 CCGTGTAATCGGGTTGCT 57.390 55.556 0.00 0.00 45.88 3.91
2378 5031 1.593196 ATTCCCATGCCGTGTAATCG 58.407 50.000 0.00 0.00 0.00 3.34
2379 5032 4.134563 AGTAATTCCCATGCCGTGTAATC 58.865 43.478 0.00 0.00 0.00 1.75
2380 5033 4.134563 GAGTAATTCCCATGCCGTGTAAT 58.865 43.478 0.00 0.00 0.00 1.89
2381 5034 3.199071 AGAGTAATTCCCATGCCGTGTAA 59.801 43.478 0.00 0.00 0.00 2.41
2382 5035 2.769663 AGAGTAATTCCCATGCCGTGTA 59.230 45.455 0.00 0.00 0.00 2.90
2383 5036 1.559682 AGAGTAATTCCCATGCCGTGT 59.440 47.619 0.00 0.00 0.00 4.49
2384 5037 2.213499 GAGAGTAATTCCCATGCCGTG 58.787 52.381 0.00 0.00 0.00 4.94
2385 5038 1.202533 CGAGAGTAATTCCCATGCCGT 60.203 52.381 0.00 0.00 0.00 5.68
2386 5039 1.202533 ACGAGAGTAATTCCCATGCCG 60.203 52.381 0.00 0.00 46.88 5.69
2387 5040 2.622064 ACGAGAGTAATTCCCATGCC 57.378 50.000 0.00 0.00 46.88 4.40
2398 5051 5.452255 AGGGTCCATAATGTTACGAGAGTA 58.548 41.667 0.00 0.00 46.88 2.59
2400 5053 4.939052 AGGGTCCATAATGTTACGAGAG 57.061 45.455 0.00 0.00 0.00 3.20
2401 5054 5.452255 ACTAGGGTCCATAATGTTACGAGA 58.548 41.667 0.00 0.00 0.00 4.04
2402 5055 5.786264 ACTAGGGTCCATAATGTTACGAG 57.214 43.478 0.00 0.00 0.00 4.18
2403 5056 6.549433 AAACTAGGGTCCATAATGTTACGA 57.451 37.500 0.00 0.00 0.00 3.43
2404 5057 7.619964 AAAAACTAGGGTCCATAATGTTACG 57.380 36.000 0.00 0.00 0.00 3.18
2426 5079 1.543802 GGATCATCACCGGTGCAAAAA 59.456 47.619 30.25 12.91 0.00 1.94
2427 5080 1.173043 GGATCATCACCGGTGCAAAA 58.827 50.000 30.25 13.34 0.00 2.44
2428 5081 0.037447 TGGATCATCACCGGTGCAAA 59.963 50.000 30.25 16.66 0.00 3.68
2429 5082 0.392863 CTGGATCATCACCGGTGCAA 60.393 55.000 30.25 14.58 0.00 4.08
2430 5083 1.221566 CTGGATCATCACCGGTGCA 59.778 57.895 30.25 18.77 0.00 4.57
2431 5084 0.531532 CTCTGGATCATCACCGGTGC 60.532 60.000 30.25 15.04 35.49 5.01
2432 5085 0.105593 CCTCTGGATCATCACCGGTG 59.894 60.000 29.26 29.26 35.49 4.94
2433 5086 1.690219 GCCTCTGGATCATCACCGGT 61.690 60.000 0.00 0.00 35.49 5.28
2434 5087 1.070445 GCCTCTGGATCATCACCGG 59.930 63.158 0.00 0.00 35.32 5.28
2435 5088 1.271934 CTAGCCTCTGGATCATCACCG 59.728 57.143 0.00 0.00 0.00 4.94
2436 5089 1.001860 GCTAGCCTCTGGATCATCACC 59.998 57.143 2.29 0.00 0.00 4.02
2437 5090 1.001860 GGCTAGCCTCTGGATCATCAC 59.998 57.143 27.17 0.00 0.00 3.06
2438 5091 1.132913 AGGCTAGCCTCTGGATCATCA 60.133 52.381 31.30 0.00 44.43 3.07
2439 5092 1.643310 AGGCTAGCCTCTGGATCATC 58.357 55.000 31.30 0.28 44.43 2.92
2440 5093 3.888772 AGGCTAGCCTCTGGATCAT 57.111 52.632 31.30 5.38 44.43 2.45
2450 5103 2.491022 ATCACGACCGAGGCTAGCC 61.491 63.158 27.19 27.19 0.00 3.93
2451 5104 1.299468 CATCACGACCGAGGCTAGC 60.299 63.158 6.04 6.04 0.00 3.42
2452 5105 1.101635 TCCATCACGACCGAGGCTAG 61.102 60.000 0.00 0.00 0.00 3.42
2453 5106 1.077285 TCCATCACGACCGAGGCTA 60.077 57.895 0.00 0.00 0.00 3.93
2454 5107 2.362503 TCCATCACGACCGAGGCT 60.363 61.111 0.00 0.00 0.00 4.58
2455 5108 2.105128 CTCCATCACGACCGAGGC 59.895 66.667 0.00 0.00 0.00 4.70
2456 5109 2.808315 CCTCCATCACGACCGAGG 59.192 66.667 0.00 0.00 36.23 4.63
2457 5110 2.105128 GCCTCCATCACGACCGAG 59.895 66.667 0.00 0.00 0.00 4.63
2458 5111 2.225791 CTTGCCTCCATCACGACCGA 62.226 60.000 0.00 0.00 0.00 4.69
2459 5112 1.811266 CTTGCCTCCATCACGACCG 60.811 63.158 0.00 0.00 0.00 4.79
2460 5113 2.109126 GCTTGCCTCCATCACGACC 61.109 63.158 0.00 0.00 0.00 4.79
2461 5114 0.955428 TTGCTTGCCTCCATCACGAC 60.955 55.000 0.00 0.00 0.00 4.34
2462 5115 0.035152 ATTGCTTGCCTCCATCACGA 60.035 50.000 0.00 0.00 0.00 4.35
2463 5116 0.099968 CATTGCTTGCCTCCATCACG 59.900 55.000 0.00 0.00 0.00 4.35
2464 5117 1.180029 ACATTGCTTGCCTCCATCAC 58.820 50.000 0.00 0.00 0.00 3.06
2465 5118 2.025981 ACTACATTGCTTGCCTCCATCA 60.026 45.455 0.00 0.00 0.00 3.07
2466 5119 2.615912 GACTACATTGCTTGCCTCCATC 59.384 50.000 0.00 0.00 0.00 3.51
2467 5120 2.648059 GACTACATTGCTTGCCTCCAT 58.352 47.619 0.00 0.00 0.00 3.41
2468 5121 1.675714 CGACTACATTGCTTGCCTCCA 60.676 52.381 0.00 0.00 0.00 3.86
2469 5122 1.009829 CGACTACATTGCTTGCCTCC 58.990 55.000 0.00 0.00 0.00 4.30
2470 5123 1.009829 CCGACTACATTGCTTGCCTC 58.990 55.000 0.00 0.00 0.00 4.70
2471 5124 0.324943 ACCGACTACATTGCTTGCCT 59.675 50.000 0.00 0.00 0.00 4.75
2472 5125 0.447801 CACCGACTACATTGCTTGCC 59.552 55.000 0.00 0.00 0.00 4.52
2473 5126 1.128692 GTCACCGACTACATTGCTTGC 59.871 52.381 0.00 0.00 0.00 4.01
2474 5127 1.390123 CGTCACCGACTACATTGCTTG 59.610 52.381 0.00 0.00 35.63 4.01
2475 5128 1.710013 CGTCACCGACTACATTGCTT 58.290 50.000 0.00 0.00 35.63 3.91
2476 5129 0.736325 GCGTCACCGACTACATTGCT 60.736 55.000 0.00 0.00 35.63 3.91
2477 5130 1.708027 GCGTCACCGACTACATTGC 59.292 57.895 0.00 0.00 35.63 3.56
2478 5131 1.988409 CGCGTCACCGACTACATTG 59.012 57.895 0.00 0.00 35.63 2.82
2479 5132 1.804326 GCGCGTCACCGACTACATT 60.804 57.895 8.43 0.00 35.63 2.71
2480 5133 2.202570 GCGCGTCACCGACTACAT 60.203 61.111 8.43 0.00 35.63 2.29
2481 5134 3.318539 GAGCGCGTCACCGACTACA 62.319 63.158 8.43 0.00 35.63 2.74
2482 5135 2.524636 AAGAGCGCGTCACCGACTAC 62.525 60.000 8.43 0.00 35.63 2.73
2483 5136 2.249557 GAAGAGCGCGTCACCGACTA 62.250 60.000 8.43 0.00 35.63 2.59
2484 5137 3.612371 GAAGAGCGCGTCACCGACT 62.612 63.158 8.43 0.00 35.63 4.18
2485 5138 3.173240 GAAGAGCGCGTCACCGAC 61.173 66.667 8.43 0.00 35.63 4.79
2486 5139 3.362797 AGAAGAGCGCGTCACCGA 61.363 61.111 8.43 0.00 35.63 4.69
2487 5140 3.175240 CAGAAGAGCGCGTCACCG 61.175 66.667 8.43 0.00 37.07 4.94
2488 5141 3.482783 GCAGAAGAGCGCGTCACC 61.483 66.667 8.43 0.60 0.00 4.02
2489 5142 2.024319 AAGCAGAAGAGCGCGTCAC 61.024 57.895 8.43 0.00 40.15 3.67
2490 5143 2.023771 CAAGCAGAAGAGCGCGTCA 61.024 57.895 8.43 0.00 40.15 4.35
2491 5144 1.284982 TTCAAGCAGAAGAGCGCGTC 61.285 55.000 8.43 4.09 40.15 5.19
2492 5145 1.300931 TTCAAGCAGAAGAGCGCGT 60.301 52.632 8.43 0.00 40.15 6.01
2493 5146 1.131420 GTTCAAGCAGAAGAGCGCG 59.869 57.895 0.00 0.00 36.78 6.86
2494 5147 0.110464 GTGTTCAAGCAGAAGAGCGC 60.110 55.000 0.00 0.00 36.78 5.92
2495 5148 1.458827 GAGTGTTCAAGCAGAAGAGCG 59.541 52.381 0.00 0.00 36.78 5.03
2496 5149 2.736192 GAGAGTGTTCAAGCAGAAGAGC 59.264 50.000 0.00 0.00 36.78 4.09
2497 5150 2.985809 CGAGAGTGTTCAAGCAGAAGAG 59.014 50.000 0.00 0.00 36.78 2.85
2498 5151 2.864097 GCGAGAGTGTTCAAGCAGAAGA 60.864 50.000 0.00 0.00 36.78 2.87
2499 5152 1.458827 GCGAGAGTGTTCAAGCAGAAG 59.541 52.381 0.00 0.00 36.78 2.85
2500 5153 1.502231 GCGAGAGTGTTCAAGCAGAA 58.498 50.000 0.00 0.00 0.00 3.02
2501 5154 0.664466 CGCGAGAGTGTTCAAGCAGA 60.664 55.000 0.00 0.00 36.71 4.26
2502 5155 1.777819 CGCGAGAGTGTTCAAGCAG 59.222 57.895 0.00 0.00 36.71 4.24
2503 5156 3.936653 CGCGAGAGTGTTCAAGCA 58.063 55.556 0.00 0.00 36.71 3.91
2519 5172 2.410730 ACTATTTGGAACGAGCGAAACG 59.589 45.455 0.00 0.00 0.00 3.60
2520 5173 3.181523 GGACTATTTGGAACGAGCGAAAC 60.182 47.826 0.00 0.00 0.00 2.78
2521 5174 2.997986 GGACTATTTGGAACGAGCGAAA 59.002 45.455 0.00 0.00 0.00 3.46
2522 5175 2.028839 TGGACTATTTGGAACGAGCGAA 60.029 45.455 0.00 0.00 0.00 4.70
2523 5176 1.546923 TGGACTATTTGGAACGAGCGA 59.453 47.619 0.00 0.00 0.00 4.93
2524 5177 2.004583 TGGACTATTTGGAACGAGCG 57.995 50.000 0.00 0.00 0.00 5.03
2525 5178 3.531538 TCATGGACTATTTGGAACGAGC 58.468 45.455 0.00 0.00 0.00 5.03
2526 5179 5.011090 TCTCATGGACTATTTGGAACGAG 57.989 43.478 0.00 0.00 0.00 4.18
2527 5180 5.414789 TTCTCATGGACTATTTGGAACGA 57.585 39.130 0.00 0.00 0.00 3.85
2528 5181 5.643777 ACTTTCTCATGGACTATTTGGAACG 59.356 40.000 0.00 0.00 0.00 3.95
2529 5182 8.616076 CATACTTTCTCATGGACTATTTGGAAC 58.384 37.037 0.00 0.00 0.00 3.62
2530 5183 7.775093 CCATACTTTCTCATGGACTATTTGGAA 59.225 37.037 0.00 0.00 43.80 3.53
2531 5184 7.092444 ACCATACTTTCTCATGGACTATTTGGA 60.092 37.037 7.57 0.00 43.80 3.53
2532 5185 7.012704 CACCATACTTTCTCATGGACTATTTGG 59.987 40.741 7.57 0.00 43.80 3.28
2533 5186 7.770433 TCACCATACTTTCTCATGGACTATTTG 59.230 37.037 7.57 0.00 43.80 2.32
2534 5187 7.861629 TCACCATACTTTCTCATGGACTATTT 58.138 34.615 7.57 0.00 43.80 1.40
2535 5188 7.419518 CCTCACCATACTTTCTCATGGACTATT 60.420 40.741 7.57 0.00 43.80 1.73
2536 5189 6.042552 CCTCACCATACTTTCTCATGGACTAT 59.957 42.308 7.57 0.00 43.80 2.12
2537 5190 5.363868 CCTCACCATACTTTCTCATGGACTA 59.636 44.000 7.57 0.00 43.80 2.59
2538 5191 4.163078 CCTCACCATACTTTCTCATGGACT 59.837 45.833 7.57 0.00 43.80 3.85
2539 5192 4.446371 CCTCACCATACTTTCTCATGGAC 58.554 47.826 7.57 0.00 43.80 4.02
2540 5193 3.455910 CCCTCACCATACTTTCTCATGGA 59.544 47.826 7.57 0.00 43.80 3.41
2541 5194 3.455910 TCCCTCACCATACTTTCTCATGG 59.544 47.826 0.00 0.00 46.05 3.66
2542 5195 4.446371 GTCCCTCACCATACTTTCTCATG 58.554 47.826 0.00 0.00 0.00 3.07
2543 5196 3.456277 GGTCCCTCACCATACTTTCTCAT 59.544 47.826 0.00 0.00 45.98 2.90
2544 5197 2.838202 GGTCCCTCACCATACTTTCTCA 59.162 50.000 0.00 0.00 45.98 3.27
2545 5198 3.545366 GGTCCCTCACCATACTTTCTC 57.455 52.381 0.00 0.00 45.98 2.87
2555 5208 1.272872 TGTACACTAGGGTCCCTCACC 60.273 57.143 15.84 0.00 45.97 4.02
2556 5209 2.226962 TGTACACTAGGGTCCCTCAC 57.773 55.000 15.84 6.64 34.61 3.51
2557 5210 3.484953 ATTGTACACTAGGGTCCCTCA 57.515 47.619 15.84 1.49 34.61 3.86
2558 5211 7.793948 ATTATATTGTACACTAGGGTCCCTC 57.206 40.000 15.84 0.00 34.61 4.30
2559 5212 8.577164 AAATTATATTGTACACTAGGGTCCCT 57.423 34.615 16.73 16.73 37.71 4.20
2560 5213 8.657712 AGAAATTATATTGTACACTAGGGTCCC 58.342 37.037 0.00 0.00 0.00 4.46
2561 5214 9.708092 GAGAAATTATATTGTACACTAGGGTCC 57.292 37.037 0.00 0.00 0.00 4.46
2610 5263 6.696411 TGGAACAGAAATTGGCGAATTTAAT 58.304 32.000 17.94 8.47 41.06 1.40


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

AutoCloner maintained by Alex Coulton.