Multiple sequence alignment - TraesCS2D01G024400

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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 TraesCS2D01G024400 chr2D 100.000 5741 0 0 1 5741 10832015 10826275 0.000000e+00 10602.0
1 TraesCS2D01G024400 chr2D 86.792 318 38 3 5046 5363 476912055 476912368 9.150000e-93 351.0
2 TraesCS2D01G024400 chr2D 89.011 91 10 0 4788 4878 8575452 8575362 4.700000e-21 113.0
3 TraesCS2D01G024400 chr2D 90.385 52 5 0 4894 4945 326789047 326788996 1.030000e-07 69.4
4 TraesCS2D01G024400 chr2D 100.000 28 0 0 4908 4935 145898601 145898628 1.000000e-02 52.8
5 TraesCS2D01G024400 chr2A 98.147 3022 39 5 1 3015 11376365 11373354 0.000000e+00 5254.0
6 TraesCS2D01G024400 chr2A 90.955 785 35 8 4894 5659 11372689 11371922 0.000000e+00 1024.0
7 TraesCS2D01G024400 chr2A 92.038 628 14 5 4285 4883 11373367 11372747 0.000000e+00 850.0
8 TraesCS2D01G024400 chr3D 90.290 1277 97 20 3028 4280 609022867 609024140 0.000000e+00 1646.0
9 TraesCS2D01G024400 chr3D 87.037 324 41 1 5043 5366 13812523 13812845 1.180000e-96 364.0
10 TraesCS2D01G024400 chr3D 80.288 208 32 6 5497 5697 65174292 65174087 1.290000e-31 148.0
11 TraesCS2D01G024400 chr3D 86.022 93 13 0 4786 4878 536203505 536203413 3.660000e-17 100.0
12 TraesCS2D01G024400 chr3D 90.769 65 4 1 4769 4831 468193328 468193392 1.020000e-12 86.1
13 TraesCS2D01G024400 chr3D 91.667 60 3 1 4769 4826 468377091 468377150 1.330000e-11 82.4
14 TraesCS2D01G024400 chr3D 95.556 45 2 0 5695 5739 297820039 297819995 7.980000e-09 73.1
15 TraesCS2D01G024400 chr3D 95.556 45 2 0 5695 5739 483694021 483694065 7.980000e-09 73.1
16 TraesCS2D01G024400 chr3D 100.000 33 0 0 2984 3016 466817896 466817864 1.730000e-05 62.1
17 TraesCS2D01G024400 chr4D 90.434 1244 108 10 3045 4280 502704030 502705270 0.000000e+00 1628.0
18 TraesCS2D01G024400 chr4D 82.381 210 27 8 5495 5697 421335277 421335483 2.130000e-39 174.0
19 TraesCS2D01G024400 chr4D 77.220 259 30 13 4788 5023 483589974 483589722 2.170000e-24 124.0
20 TraesCS2D01G024400 chr4D 75.000 268 39 13 4786 5025 483587821 483588088 1.320000e-16 99.0
21 TraesCS2D01G024400 chr4D 88.710 62 7 0 4788 4849 17428306 17428245 6.170000e-10 76.8
22 TraesCS2D01G024400 chr4D 95.745 47 2 0 4786 4832 83271250 83271204 6.170000e-10 76.8
23 TraesCS2D01G024400 chr4D 95.556 45 2 0 5697 5741 109373652 109373608 7.980000e-09 73.1
24 TraesCS2D01G024400 chr4D 95.556 45 2 0 4788 4832 315516301 315516257 7.980000e-09 73.1
25 TraesCS2D01G024400 chr4D 92.000 50 4 0 4783 4832 507878875 507878826 2.870000e-08 71.3
26 TraesCS2D01G024400 chr4D 92.683 41 2 1 4786 4826 476860788 476860827 2.230000e-04 58.4
27 TraesCS2D01G024400 chr2B 89.457 1252 117 13 3049 4287 239613223 239611974 0.000000e+00 1567.0
28 TraesCS2D01G024400 chr2B 88.356 1271 124 19 3027 4288 705883054 705881799 0.000000e+00 1506.0
29 TraesCS2D01G024400 chr2B 82.931 662 106 6 1 660 16247690 16247034 1.780000e-164 590.0
30 TraesCS2D01G024400 chr2B 81.051 533 92 7 1 530 16196252 16196778 3.200000e-112 416.0
31 TraesCS2D01G024400 chr2B 75.420 476 81 20 699 1143 16247023 16246553 1.260000e-46 198.0
32 TraesCS2D01G024400 chr5B 89.630 1244 110 15 3049 4286 222418454 222417224 0.000000e+00 1565.0
33 TraesCS2D01G024400 chr5B 85.938 320 44 1 5046 5365 635192260 635191942 1.980000e-89 340.0
34 TraesCS2D01G024400 chr5B 81.517 211 29 7 5495 5697 303229162 303229370 1.280000e-36 165.0
35 TraesCS2D01G024400 chr5B 87.234 94 12 0 4785 4878 600012067 600012160 2.190000e-19 108.0
36 TraesCS2D01G024400 chr5B 87.234 94 12 0 4785 4878 600033461 600033554 2.190000e-19 108.0
37 TraesCS2D01G024400 chr7D 89.432 1249 113 16 3057 4294 185241192 185242432 0.000000e+00 1557.0
38 TraesCS2D01G024400 chr7D 86.103 331 43 3 5046 5376 412892457 412892130 2.540000e-93 353.0
39 TraesCS2D01G024400 chr7D 87.912 91 10 1 4788 4878 258229493 258229582 7.870000e-19 106.0
40 TraesCS2D01G024400 chr7D 84.946 93 14 0 4786 4878 629538874 629538782 1.700000e-15 95.3
41 TraesCS2D01G024400 chr7D 80.952 105 12 6 4942 5040 596430978 596430876 6.170000e-10 76.8
42 TraesCS2D01G024400 chr7D 95.556 45 2 0 5695 5739 203669507 203669463 7.980000e-09 73.1
43 TraesCS2D01G024400 chr3B 88.898 1252 124 13 3049 4289 610536143 610537390 0.000000e+00 1528.0
44 TraesCS2D01G024400 chr3B 97.222 36 1 0 2942 2977 812340198 812340233 1.730000e-05 62.1
45 TraesCS2D01G024400 chr7B 88.660 1261 128 15 3034 4283 676029154 676027898 0.000000e+00 1522.0
46 TraesCS2D01G024400 chr7B 92.308 52 4 0 5690 5741 165958991 165959042 2.220000e-09 75.0
47 TraesCS2D01G024400 chr6B 88.727 1233 124 15 3066 4288 32123766 32122539 0.000000e+00 1493.0
48 TraesCS2D01G024400 chr6B 100.000 28 0 0 2866 2893 29733958 29733985 1.000000e-02 52.8
49 TraesCS2D01G024400 chr1D 87.926 323 38 1 5046 5368 24063853 24063532 4.200000e-101 379.0
50 TraesCS2D01G024400 chr1D 80.500 200 29 7 5495 5686 7423470 7423667 1.670000e-30 145.0
51 TraesCS2D01G024400 chr1D 84.404 109 15 2 4788 4895 487473243 487473350 7.870000e-19 106.0
52 TraesCS2D01G024400 chr1D 86.170 94 13 0 4785 4878 192915447 192915540 1.020000e-17 102.0
53 TraesCS2D01G024400 chr1D 96.000 50 2 0 4783 4832 360393937 360393986 1.330000e-11 82.4
54 TraesCS2D01G024400 chr1D 97.778 45 1 0 4788 4832 67002766 67002810 1.720000e-10 78.7
55 TraesCS2D01G024400 chr1D 93.878 49 2 1 5691 5739 8517216 8517263 7.980000e-09 73.1
56 TraesCS2D01G024400 chr1D 95.556 45 2 0 5695 5739 59684398 59684442 7.980000e-09 73.1
57 TraesCS2D01G024400 chr1D 95.556 45 2 0 5695 5739 385202896 385202852 7.980000e-09 73.1
58 TraesCS2D01G024400 chr1D 92.000 50 4 0 5690 5739 36449211 36449162 2.870000e-08 71.3
59 TraesCS2D01G024400 chr5A 87.736 318 37 2 5046 5363 513223305 513222990 2.530000e-98 370.0
60 TraesCS2D01G024400 chr5A 82.381 210 27 7 5495 5697 476664968 476664762 2.130000e-39 174.0
61 TraesCS2D01G024400 chr5A 79.524 210 33 7 5495 5697 303188881 303189087 2.160000e-29 141.0
62 TraesCS2D01G024400 chr5D 86.916 321 39 2 5046 5364 9032233 9031914 1.970000e-94 357.0
63 TraesCS2D01G024400 chr5D 83.333 204 27 4 5495 5692 267851586 267851788 1.270000e-41 182.0
64 TraesCS2D01G024400 chr5D 79.717 212 34 5 5495 5699 9058180 9057971 1.670000e-30 145.0
65 TraesCS2D01G024400 chr5D 90.323 93 9 0 4786 4878 364232109 364232017 7.810000e-24 122.0
66 TraesCS2D01G024400 chr5D 97.917 48 1 0 4785 4832 263163017 263162970 3.690000e-12 84.2
67 TraesCS2D01G024400 chr5D 96.000 50 2 0 4783 4832 58518331 58518282 1.330000e-11 82.4
68 TraesCS2D01G024400 chr1A 86.164 318 43 1 5046 5363 559543455 559543139 5.510000e-90 342.0
69 TraesCS2D01G024400 chr1A 82.143 140 24 1 4894 5033 453567900 453567762 1.010000e-22 119.0
70 TraesCS2D01G024400 chr1A 83.333 114 13 6 2867 2978 458568057 458567948 3.660000e-17 100.0
71 TraesCS2D01G024400 chr1B 82.063 223 33 4 314 532 4867903 4867684 3.530000e-42 183.0
72 TraesCS2D01G024400 chr1B 87.879 66 8 0 4784 4849 489526481 489526546 1.720000e-10 78.7
73 TraesCS2D01G024400 chr1B 87.692 65 8 0 4785 4849 566555081 566555145 6.170000e-10 76.8
74 TraesCS2D01G024400 chr1B 81.522 92 14 3 4788 4878 596320938 596320849 7.980000e-09 73.1
75 TraesCS2D01G024400 chr1B 85.000 60 7 2 2919 2977 480898711 480898769 6.210000e-05 60.2
76 TraesCS2D01G024400 chr4B 77.259 343 56 17 5040 5382 57805358 57805678 1.270000e-41 182.0
77 TraesCS2D01G024400 chr7A 82.609 138 19 2 4908 5040 641726279 641726142 3.630000e-22 117.0
78 TraesCS2D01G024400 chr7A 84.127 63 10 0 4956 5018 32061387 32061449 1.730000e-05 62.1
79 TraesCS2D01G024400 chr6A 82.796 93 16 0 4786 4878 596592867 596592775 3.690000e-12 84.2
80 TraesCS2D01G024400 chr6A 81.522 92 16 1 4788 4878 493863616 493863707 2.220000e-09 75.0
81 TraesCS2D01G024400 chr4A 79.592 98 16 4 2883 2977 580297645 580297741 3.710000e-07 67.6
82 TraesCS2D01G024400 chr6D 83.607 61 8 2 2918 2977 27493987 27494046 8.040000e-04 56.5
83 TraesCS2D01G024400 chr3A 94.444 36 2 0 2942 2977 734786098 734786133 8.040000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G024400 chr2D 10826275 10832015 5740 True 10602 10602 100.000000 1 5741 1 chr2D.!!$R2 5740
1 TraesCS2D01G024400 chr2A 11371922 11376365 4443 True 2376 5254 93.713333 1 5659 3 chr2A.!!$R1 5658
2 TraesCS2D01G024400 chr3D 609022867 609024140 1273 False 1646 1646 90.290000 3028 4280 1 chr3D.!!$F5 1252
3 TraesCS2D01G024400 chr4D 502704030 502705270 1240 False 1628 1628 90.434000 3045 4280 1 chr4D.!!$F4 1235
4 TraesCS2D01G024400 chr2B 239611974 239613223 1249 True 1567 1567 89.457000 3049 4287 1 chr2B.!!$R1 1238
5 TraesCS2D01G024400 chr2B 705881799 705883054 1255 True 1506 1506 88.356000 3027 4288 1 chr2B.!!$R2 1261
6 TraesCS2D01G024400 chr2B 16196252 16196778 526 False 416 416 81.051000 1 530 1 chr2B.!!$F1 529
7 TraesCS2D01G024400 chr2B 16246553 16247690 1137 True 394 590 79.175500 1 1143 2 chr2B.!!$R3 1142
8 TraesCS2D01G024400 chr5B 222417224 222418454 1230 True 1565 1565 89.630000 3049 4286 1 chr5B.!!$R1 1237
9 TraesCS2D01G024400 chr7D 185241192 185242432 1240 False 1557 1557 89.432000 3057 4294 1 chr7D.!!$F1 1237
10 TraesCS2D01G024400 chr3B 610536143 610537390 1247 False 1528 1528 88.898000 3049 4289 1 chr3B.!!$F1 1240
11 TraesCS2D01G024400 chr7B 676027898 676029154 1256 True 1522 1522 88.660000 3034 4283 1 chr7B.!!$R1 1249
12 TraesCS2D01G024400 chr6B 32122539 32123766 1227 True 1493 1493 88.727000 3066 4288 1 chr6B.!!$R1 1222

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
712 715 0.893270 AAGTGCATAACAGCCCGCAA 60.893 50.0 0.0 0.0 35.87 4.85 F
1030 1060 1.160137 CAAGCAAGTGTGGAGCTACC 58.840 55.0 0.0 0.0 37.70 3.18 F
1881 1916 0.111446 TCCTGCCAACCATTTTCCGA 59.889 50.0 0.0 0.0 0.00 4.55 F
1882 1917 0.965439 CCTGCCAACCATTTTCCGAA 59.035 50.0 0.0 0.0 0.00 4.30 F
3037 3072 0.252558 TGTAACCCACTCCTCCTCCC 60.253 60.0 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 1891 1.839424 AATGGTTGGCAGGAGTTAGC 58.161 50.0 0.0 0.0 0.00 3.09 R
3018 3053 0.252558 GGGAGGAGGAGTGGGTTACA 60.253 60.0 0.0 0.0 0.00 2.41 R
3019 3054 0.981801 GGGGAGGAGGAGTGGGTTAC 60.982 65.0 0.0 0.0 0.00 2.50 R
3656 3737 1.379642 GCAATAGCAGGAGCACACCC 61.380 60.0 0.0 0.0 45.49 4.61 R
4994 5155 0.177373 GTGGCTAGGGTTTAGTCCGG 59.823 60.0 0.0 0.0 0.00 5.14 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
391 392 6.040166 CAGGAGATTTCTGGAATAATTGGGTG 59.960 42.308 0.00 0.00 0.00 4.61
570 571 3.310774 CCCATCGACATCAAGTGAACATC 59.689 47.826 0.00 0.00 0.00 3.06
712 715 0.893270 AAGTGCATAACAGCCCGCAA 60.893 50.000 0.00 0.00 35.87 4.85
813 817 3.744942 CACATCTCTGCTGTATGGCATAC 59.255 47.826 26.86 26.86 41.63 2.39
819 823 7.539034 TCTCTGCTGTATGGCATACTAATAA 57.461 36.000 31.37 14.85 41.63 1.40
831 835 5.130350 GCATACTAATAACCAGAAAGGGCA 58.870 41.667 0.00 0.00 43.89 5.36
860 864 7.778382 ACTCAACTTCCACCTTTTATTGTTACT 59.222 33.333 0.00 0.00 0.00 2.24
1030 1060 1.160137 CAAGCAAGTGTGGAGCTACC 58.840 55.000 0.00 0.00 37.70 3.18
1285 1319 5.163642 ACGAGAAGTACAACGATGCTATCTT 60.164 40.000 0.00 0.00 0.00 2.40
1498 1532 3.138468 GGGAAGCCCTTGTCCTATACATT 59.862 47.826 0.00 0.00 41.34 2.71
1811 1846 8.872845 CCAATTTCAAATAGTCCAACATAAAGC 58.127 33.333 0.00 0.00 0.00 3.51
1856 1891 6.362016 TGTTTGAGCATTAATTAAGTTGTGCG 59.638 34.615 13.23 0.00 37.64 5.34
1877 1912 2.562738 GCTAACTCCTGCCAACCATTTT 59.437 45.455 0.00 0.00 0.00 1.82
1878 1913 3.367395 GCTAACTCCTGCCAACCATTTTC 60.367 47.826 0.00 0.00 0.00 2.29
1879 1914 1.632589 ACTCCTGCCAACCATTTTCC 58.367 50.000 0.00 0.00 0.00 3.13
1880 1915 0.527565 CTCCTGCCAACCATTTTCCG 59.472 55.000 0.00 0.00 0.00 4.30
1881 1916 0.111446 TCCTGCCAACCATTTTCCGA 59.889 50.000 0.00 0.00 0.00 4.55
1882 1917 0.965439 CCTGCCAACCATTTTCCGAA 59.035 50.000 0.00 0.00 0.00 4.30
1883 1918 1.336795 CCTGCCAACCATTTTCCGAAC 60.337 52.381 0.00 0.00 0.00 3.95
1884 1919 1.339610 CTGCCAACCATTTTCCGAACA 59.660 47.619 0.00 0.00 0.00 3.18
1885 1920 1.967066 TGCCAACCATTTTCCGAACAT 59.033 42.857 0.00 0.00 0.00 2.71
1886 1921 3.157881 TGCCAACCATTTTCCGAACATA 58.842 40.909 0.00 0.00 0.00 2.29
2037 2072 5.642491 GGACTTTGCTCTTAGTTTCGGTTAT 59.358 40.000 0.00 0.00 0.00 1.89
2040 2075 6.592994 ACTTTGCTCTTAGTTTCGGTTATACC 59.407 38.462 0.00 0.00 34.05 2.73
2125 2160 1.282875 GGCAAAAGTGGCGAGTGTC 59.717 57.895 0.00 0.00 40.97 3.67
2393 2428 7.586664 GGCGTTTTTGTTTTGTTTTGTTTAGAA 59.413 29.630 0.00 0.00 0.00 2.10
2505 2540 7.510675 AATGGAAGAACATTAGGACTCCTTA 57.489 36.000 1.94 0.00 39.18 2.69
2599 2634 5.894393 TCCAACATATATCTCCTAGCCTAGC 59.106 44.000 0.00 0.00 0.00 3.42
2716 2751 1.717032 TCTCATCCCTACCCAATCCG 58.283 55.000 0.00 0.00 0.00 4.18
2806 2841 2.350868 GCCTTCAAAGTCCTTTCGAAGC 60.351 50.000 17.32 12.70 36.94 3.86
3014 3049 6.616774 ATTGCCATGAAAAACGTTTGATTT 57.383 29.167 15.46 5.13 0.00 2.17
3015 3050 5.401033 TGCCATGAAAAACGTTTGATTTG 57.599 34.783 15.46 10.27 0.00 2.32
3016 3051 5.111989 TGCCATGAAAAACGTTTGATTTGA 58.888 33.333 15.46 0.00 0.00 2.69
3017 3052 5.006165 TGCCATGAAAAACGTTTGATTTGAC 59.994 36.000 15.46 4.24 0.00 3.18
3018 3053 5.234116 GCCATGAAAAACGTTTGATTTGACT 59.766 36.000 15.46 0.00 0.00 3.41
3019 3054 6.639212 CCATGAAAAACGTTTGATTTGACTG 58.361 36.000 15.46 4.81 0.00 3.51
3020 3055 6.255453 CCATGAAAAACGTTTGATTTGACTGT 59.745 34.615 15.46 0.00 0.00 3.55
3021 3056 7.433719 CCATGAAAAACGTTTGATTTGACTGTA 59.566 33.333 15.46 0.00 0.00 2.74
3022 3057 8.802856 CATGAAAAACGTTTGATTTGACTGTAA 58.197 29.630 15.46 0.00 0.00 2.41
3023 3058 8.164058 TGAAAAACGTTTGATTTGACTGTAAC 57.836 30.769 15.46 0.00 0.00 2.50
3024 3059 7.273815 TGAAAAACGTTTGATTTGACTGTAACC 59.726 33.333 15.46 0.00 0.00 2.85
3025 3060 4.823790 ACGTTTGATTTGACTGTAACCC 57.176 40.909 0.00 0.00 0.00 4.11
3026 3061 4.200874 ACGTTTGATTTGACTGTAACCCA 58.799 39.130 0.00 0.00 0.00 4.51
3037 3072 0.252558 TGTAACCCACTCCTCCTCCC 60.253 60.000 0.00 0.00 0.00 4.30
3038 3073 0.981801 GTAACCCACTCCTCCTCCCC 60.982 65.000 0.00 0.00 0.00 4.81
3143 3214 1.689233 CTTCCCCCGTCCAGATCCA 60.689 63.158 0.00 0.00 0.00 3.41
3198 3270 4.824515 CCCGAGCTCCTCTCCCGT 62.825 72.222 8.47 0.00 38.62 5.28
3205 3277 3.670629 CTCCTCTCCCGTGGGCTCT 62.671 68.421 0.00 0.00 34.68 4.09
3225 3297 3.756783 CCTCCCTCGTCTCCCCCT 61.757 72.222 0.00 0.00 0.00 4.79
3352 3427 2.193536 GTGCACCTCGGTTTGGCTT 61.194 57.895 5.22 0.00 0.00 4.35
3536 3616 3.120385 CTCATTGTCTGCGGCGCA 61.120 61.111 34.06 34.06 36.92 6.09
3761 3842 1.611491 CCTAGTCTCGGCTCTGATTCC 59.389 57.143 0.00 0.00 0.00 3.01
3778 3859 3.114616 CTTGCCGTGCTGTCCTCG 61.115 66.667 0.00 0.00 0.00 4.63
3888 3969 4.041762 GGGTGCGGGTTGGGATCA 62.042 66.667 0.00 0.00 0.00 2.92
4192 4275 5.006746 GCTCTTTCTCTGTCGTTTCTTTTGA 59.993 40.000 0.00 0.00 0.00 2.69
4198 4281 2.004017 TGTCGTTTCTTTTGAGCGTGT 58.996 42.857 0.00 0.00 33.02 4.49
4377 4461 6.044682 GCCATGTGAATTTTATAGCAAGCTT 58.955 36.000 0.00 0.00 0.00 3.74
4378 4462 6.019318 GCCATGTGAATTTTATAGCAAGCTTG 60.019 38.462 22.44 22.44 0.00 4.01
4379 4463 7.259882 CCATGTGAATTTTATAGCAAGCTTGA 58.740 34.615 30.39 10.67 0.00 3.02
4380 4464 7.924412 CCATGTGAATTTTATAGCAAGCTTGAT 59.076 33.333 30.39 26.40 0.00 2.57
4381 4465 9.955208 CATGTGAATTTTATAGCAAGCTTGATA 57.045 29.630 30.39 27.76 33.15 2.15
4383 4467 9.177608 TGTGAATTTTATAGCAAGCTTGATAGT 57.822 29.630 30.39 18.39 32.01 2.12
4533 4617 2.232208 ACTCAATGTGCAGATCGTCAGA 59.768 45.455 0.00 0.00 0.00 3.27
4535 4619 2.995939 TCAATGTGCAGATCGTCAGAAC 59.004 45.455 0.00 0.00 0.00 3.01
4546 4657 0.037697 CGTCAGAACGGGGTTGATGA 60.038 55.000 0.00 0.00 45.21 2.92
4618 4729 3.274288 CAGAAGCCTGAATCTAACCCAC 58.726 50.000 0.00 0.00 43.02 4.61
4642 4753 1.079612 CTGCCGCACAGTCTCATCA 60.080 57.895 0.00 0.00 41.86 3.07
4689 4800 2.433664 CCCTACCGTCAACACCGC 60.434 66.667 0.00 0.00 0.00 5.68
4816 4928 2.046217 GCCGGACCTCTCAAACCC 60.046 66.667 5.05 0.00 0.00 4.11
4825 4937 1.473434 CCTCTCAAACCCGCCTCATAC 60.473 57.143 0.00 0.00 0.00 2.39
4829 4941 1.087771 CAAACCCGCCTCATACGTCC 61.088 60.000 0.00 0.00 0.00 4.79
4836 4948 0.956633 GCCTCATACGTCCGGACATA 59.043 55.000 32.80 24.11 0.00 2.29
4905 5065 0.455410 TTGACAGCAAATATGGCGCC 59.545 50.000 22.73 22.73 36.08 6.53
4994 5155 0.249657 ATTCCTCTTCATCCGCTCGC 60.250 55.000 0.00 0.00 0.00 5.03
5024 5185 1.208293 CCCTAGCCACTTCACTTCCTC 59.792 57.143 0.00 0.00 0.00 3.71
5043 5204 4.379243 CGCCACCCAAGCTCGTCT 62.379 66.667 0.00 0.00 0.00 4.18
5044 5205 2.978824 GCCACCCAAGCTCGTCTA 59.021 61.111 0.00 0.00 0.00 2.59
5058 5219 1.716826 CGTCTAGAGTCCGGTGAGCC 61.717 65.000 0.00 0.00 0.00 4.70
5078 5239 3.402681 CTCGTGTCCCATGCCCCT 61.403 66.667 0.00 0.00 0.00 4.79
5079 5240 2.039787 TCGTGTCCCATGCCCCTA 59.960 61.111 0.00 0.00 0.00 3.53
5090 5251 1.132500 ATGCCCCTACTCTACCTTGC 58.868 55.000 0.00 0.00 0.00 4.01
5153 5314 3.321648 ATGGCCACGGCAGAGACA 61.322 61.111 8.16 0.00 42.43 3.41
5162 5323 4.121669 GCAGAGACAGGCGAGCGA 62.122 66.667 0.00 0.00 0.00 4.93
5184 5345 4.452733 CGGAACCGGGTGAGCTCC 62.453 72.222 12.15 2.59 35.56 4.70
5231 5392 9.365906 TGCATGTAATAATATGGATTTGAGGTT 57.634 29.630 0.00 0.00 0.00 3.50
5243 5404 7.466746 TGGATTTGAGGTTTCTAATTTGAGG 57.533 36.000 0.00 0.00 30.54 3.86
5244 5405 7.010160 TGGATTTGAGGTTTCTAATTTGAGGT 58.990 34.615 0.00 0.00 30.54 3.85
5332 5493 2.920912 AGGCGTTTGAGGGGTCGA 60.921 61.111 0.00 0.00 0.00 4.20
5353 5514 2.851263 TTTGCCAAGTCCGACTGTAT 57.149 45.000 0.65 0.00 0.00 2.29
5393 5554 2.887152 ACCAGAGCACAATTTGGAAGAC 59.113 45.455 0.78 0.00 34.76 3.01
5396 5557 2.555757 AGAGCACAATTTGGAAGACTGC 59.444 45.455 0.78 0.64 0.00 4.40
5417 5578 0.881118 CAACCAACAAGCGGTGCTAT 59.119 50.000 0.00 0.00 38.25 2.97
5420 5581 1.009829 CCAACAAGCGGTGCTATCTC 58.990 55.000 0.00 0.00 38.25 2.75
5554 5733 5.651387 TCTTCTCACTCATCACAGGTAAG 57.349 43.478 0.00 0.00 0.00 2.34
5621 5800 2.576615 GCTTAGCTAATTGGGGTGAGG 58.423 52.381 6.64 0.00 0.00 3.86
5649 5828 1.062275 AGAGGAGAGAGATGGTGGCAT 60.062 52.381 0.00 0.00 0.00 4.40
5659 5838 0.609662 ATGGTGGCATTTTCCAGTGC 59.390 50.000 0.91 0.00 40.55 4.40
5660 5839 0.758310 TGGTGGCATTTTCCAGTGCA 60.758 50.000 0.00 0.00 43.00 4.57
5661 5840 0.609662 GGTGGCATTTTCCAGTGCAT 59.390 50.000 0.00 0.00 43.00 3.96
5662 5841 1.002315 GGTGGCATTTTCCAGTGCATT 59.998 47.619 0.00 0.00 43.00 3.56
5663 5842 2.550639 GGTGGCATTTTCCAGTGCATTT 60.551 45.455 0.00 0.00 43.00 2.32
5664 5843 3.140623 GTGGCATTTTCCAGTGCATTTT 58.859 40.909 0.00 0.00 43.00 1.82
5665 5844 3.187022 GTGGCATTTTCCAGTGCATTTTC 59.813 43.478 0.00 0.00 43.00 2.29
5666 5845 3.071312 TGGCATTTTCCAGTGCATTTTCT 59.929 39.130 0.00 0.00 43.00 2.52
5667 5846 4.282957 TGGCATTTTCCAGTGCATTTTCTA 59.717 37.500 0.00 0.00 43.00 2.10
5668 5847 4.627035 GGCATTTTCCAGTGCATTTTCTAC 59.373 41.667 0.00 0.00 43.00 2.59
5669 5848 4.627035 GCATTTTCCAGTGCATTTTCTACC 59.373 41.667 0.00 0.00 40.94 3.18
5670 5849 4.864704 TTTTCCAGTGCATTTTCTACCC 57.135 40.909 0.00 0.00 0.00 3.69
5671 5850 2.507407 TCCAGTGCATTTTCTACCCC 57.493 50.000 0.00 0.00 0.00 4.95
5672 5851 1.707989 TCCAGTGCATTTTCTACCCCA 59.292 47.619 0.00 0.00 0.00 4.96
5673 5852 1.818674 CCAGTGCATTTTCTACCCCAC 59.181 52.381 0.00 0.00 0.00 4.61
5674 5853 1.818674 CAGTGCATTTTCTACCCCACC 59.181 52.381 0.00 0.00 0.00 4.61
5675 5854 1.710809 AGTGCATTTTCTACCCCACCT 59.289 47.619 0.00 0.00 0.00 4.00
5676 5855 2.110011 AGTGCATTTTCTACCCCACCTT 59.890 45.455 0.00 0.00 0.00 3.50
5677 5856 3.332485 AGTGCATTTTCTACCCCACCTTA 59.668 43.478 0.00 0.00 0.00 2.69
5678 5857 4.017499 AGTGCATTTTCTACCCCACCTTAT 60.017 41.667 0.00 0.00 0.00 1.73
5679 5858 5.192923 AGTGCATTTTCTACCCCACCTTATA 59.807 40.000 0.00 0.00 0.00 0.98
5680 5859 5.889289 GTGCATTTTCTACCCCACCTTATAA 59.111 40.000 0.00 0.00 0.00 0.98
5681 5860 6.549736 GTGCATTTTCTACCCCACCTTATAAT 59.450 38.462 0.00 0.00 0.00 1.28
5682 5861 7.069455 GTGCATTTTCTACCCCACCTTATAATT 59.931 37.037 0.00 0.00 0.00 1.40
5683 5862 7.621683 TGCATTTTCTACCCCACCTTATAATTT 59.378 33.333 0.00 0.00 0.00 1.82
5684 5863 7.926018 GCATTTTCTACCCCACCTTATAATTTG 59.074 37.037 0.00 0.00 0.00 2.32
5685 5864 8.977412 CATTTTCTACCCCACCTTATAATTTGT 58.023 33.333 0.00 0.00 0.00 2.83
5686 5865 8.584063 TTTTCTACCCCACCTTATAATTTGTC 57.416 34.615 0.00 0.00 0.00 3.18
5687 5866 7.519347 TTCTACCCCACCTTATAATTTGTCT 57.481 36.000 0.00 0.00 0.00 3.41
5688 5867 7.519347 TCTACCCCACCTTATAATTTGTCTT 57.481 36.000 0.00 0.00 0.00 3.01
5689 5868 8.626917 TCTACCCCACCTTATAATTTGTCTTA 57.373 34.615 0.00 0.00 0.00 2.10
5690 5869 9.060137 TCTACCCCACCTTATAATTTGTCTTAA 57.940 33.333 0.00 0.00 0.00 1.85
5691 5870 9.689501 CTACCCCACCTTATAATTTGTCTTAAA 57.310 33.333 0.00 0.00 0.00 1.52
5692 5871 8.959676 ACCCCACCTTATAATTTGTCTTAAAA 57.040 30.769 0.00 0.00 0.00 1.52
5693 5872 9.382307 ACCCCACCTTATAATTTGTCTTAAAAA 57.618 29.630 0.00 0.00 0.00 1.94
5707 5886 7.443259 TGTCTTAAAAATTTTACTCCCTCCG 57.557 36.000 3.34 0.00 0.00 4.63
5708 5887 6.999871 TGTCTTAAAAATTTTACTCCCTCCGT 59.000 34.615 3.34 0.00 0.00 4.69
5709 5888 7.173735 TGTCTTAAAAATTTTACTCCCTCCGTC 59.826 37.037 3.34 0.00 0.00 4.79
5710 5889 7.389884 GTCTTAAAAATTTTACTCCCTCCGTCT 59.610 37.037 3.34 0.00 0.00 4.18
5711 5890 8.596293 TCTTAAAAATTTTACTCCCTCCGTCTA 58.404 33.333 3.34 0.00 0.00 2.59
5712 5891 8.782339 TTAAAAATTTTACTCCCTCCGTCTAG 57.218 34.615 3.34 0.00 0.00 2.43
5713 5892 5.354842 AAATTTTACTCCCTCCGTCTAGG 57.645 43.478 0.00 0.00 42.97 3.02
5714 5893 3.463048 TTTTACTCCCTCCGTCTAGGT 57.537 47.619 0.00 0.00 41.99 3.08
5715 5894 2.431954 TTACTCCCTCCGTCTAGGTG 57.568 55.000 0.00 0.00 41.99 4.00
5716 5895 1.293062 TACTCCCTCCGTCTAGGTGT 58.707 55.000 0.00 0.00 41.99 4.16
5717 5896 1.293062 ACTCCCTCCGTCTAGGTGTA 58.707 55.000 0.00 0.00 41.99 2.90
5718 5897 1.851653 ACTCCCTCCGTCTAGGTGTAT 59.148 52.381 0.00 0.00 41.99 2.29
5719 5898 3.051581 ACTCCCTCCGTCTAGGTGTATA 58.948 50.000 0.00 0.00 41.99 1.47
5720 5899 3.461085 ACTCCCTCCGTCTAGGTGTATAA 59.539 47.826 0.00 0.00 41.99 0.98
5721 5900 4.073549 CTCCCTCCGTCTAGGTGTATAAG 58.926 52.174 0.00 0.00 41.99 1.73
5722 5901 3.461085 TCCCTCCGTCTAGGTGTATAAGT 59.539 47.826 0.00 0.00 41.99 2.24
5723 5902 3.819902 CCCTCCGTCTAGGTGTATAAGTC 59.180 52.174 0.00 0.00 41.99 3.01
5724 5903 4.458397 CCTCCGTCTAGGTGTATAAGTCA 58.542 47.826 0.00 0.00 41.99 3.41
5725 5904 4.885907 CCTCCGTCTAGGTGTATAAGTCAA 59.114 45.833 0.00 0.00 41.99 3.18
5726 5905 5.535406 CCTCCGTCTAGGTGTATAAGTCAAT 59.465 44.000 0.00 0.00 41.99 2.57
5727 5906 6.040616 CCTCCGTCTAGGTGTATAAGTCAATT 59.959 42.308 0.00 0.00 41.99 2.32
5728 5907 7.414222 TCCGTCTAGGTGTATAAGTCAATTT 57.586 36.000 0.00 0.00 41.99 1.82
5729 5908 8.523915 TCCGTCTAGGTGTATAAGTCAATTTA 57.476 34.615 0.00 0.00 41.99 1.40
5730 5909 8.627403 TCCGTCTAGGTGTATAAGTCAATTTAG 58.373 37.037 0.00 0.00 41.99 1.85
5731 5910 7.866393 CCGTCTAGGTGTATAAGTCAATTTAGG 59.134 40.741 0.00 0.00 34.51 2.69
5732 5911 8.411683 CGTCTAGGTGTATAAGTCAATTTAGGT 58.588 37.037 0.00 0.00 0.00 3.08
5735 5914 9.886132 CTAGGTGTATAAGTCAATTTAGGTTGT 57.114 33.333 0.00 0.00 0.00 3.32
5736 5915 8.561738 AGGTGTATAAGTCAATTTAGGTTGTG 57.438 34.615 0.00 0.00 0.00 3.33
5737 5916 7.120726 AGGTGTATAAGTCAATTTAGGTTGTGC 59.879 37.037 0.00 0.00 0.00 4.57
5738 5917 7.094549 GGTGTATAAGTCAATTTAGGTTGTGCA 60.095 37.037 0.00 0.00 0.00 4.57
5739 5918 8.458843 GTGTATAAGTCAATTTAGGTTGTGCAT 58.541 33.333 0.00 0.00 0.00 3.96
5740 5919 8.673711 TGTATAAGTCAATTTAGGTTGTGCATC 58.326 33.333 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
391 392 2.430382 TTCCTCTGCACCGACGGTTC 62.430 60.000 19.02 14.16 31.02 3.62
570 571 3.467803 ACTCTTGTTTTCGACTTCCAGG 58.532 45.455 0.00 0.00 0.00 4.45
617 618 8.565896 TGCTAATCAACTGAGAATTGTTATGT 57.434 30.769 0.00 0.00 0.00 2.29
813 817 5.010282 AGTTGTGCCCTTTCTGGTTATTAG 58.990 41.667 0.00 0.00 0.00 1.73
819 823 0.550914 TGAGTTGTGCCCTTTCTGGT 59.449 50.000 0.00 0.00 0.00 4.00
831 835 6.379988 ACAATAAAAGGTGGAAGTTGAGTTGT 59.620 34.615 0.00 0.00 0.00 3.32
860 864 8.954950 AATCCATGTATGAAAACACAAAAACA 57.045 26.923 0.00 0.00 30.75 2.83
1030 1060 1.608966 CGATGATCGCGGGTCATTCG 61.609 60.000 22.52 21.13 36.49 3.34
1380 1414 7.793927 AGAGAAAACTTCTTTTACAGTGGAG 57.206 36.000 0.00 0.00 40.87 3.86
1498 1532 3.678289 AGTTAGCTGTGTGCATCAATCA 58.322 40.909 0.00 0.00 45.94 2.57
1638 1672 5.030874 AGTAGCGCACACTATTTTTCAAC 57.969 39.130 11.47 0.00 0.00 3.18
1856 1891 1.839424 AATGGTTGGCAGGAGTTAGC 58.161 50.000 0.00 0.00 0.00 3.09
1877 1912 3.869246 GCTTTTTCTCGGATATGTTCGGA 59.131 43.478 0.00 0.00 33.16 4.55
1878 1913 3.002348 GGCTTTTTCTCGGATATGTTCGG 59.998 47.826 0.00 0.00 0.00 4.30
1879 1914 3.621268 TGGCTTTTTCTCGGATATGTTCG 59.379 43.478 0.00 0.00 0.00 3.95
1880 1915 5.066505 ACATGGCTTTTTCTCGGATATGTTC 59.933 40.000 0.00 0.00 0.00 3.18
1881 1916 4.949856 ACATGGCTTTTTCTCGGATATGTT 59.050 37.500 0.00 0.00 0.00 2.71
1882 1917 4.336433 CACATGGCTTTTTCTCGGATATGT 59.664 41.667 0.00 0.00 0.00 2.29
1883 1918 4.336433 ACACATGGCTTTTTCTCGGATATG 59.664 41.667 0.00 0.00 0.00 1.78
1884 1919 4.526970 ACACATGGCTTTTTCTCGGATAT 58.473 39.130 0.00 0.00 0.00 1.63
1885 1920 3.938963 GACACATGGCTTTTTCTCGGATA 59.061 43.478 0.00 0.00 0.00 2.59
1886 1921 2.749621 GACACATGGCTTTTTCTCGGAT 59.250 45.455 0.00 0.00 0.00 4.18
2412 2447 8.211629 AGGTGTGAGAAGTAACTCTTTAACATT 58.788 33.333 0.00 0.00 36.40 2.71
2599 2634 2.159467 GCGTTTTGCTATTGACGAGG 57.841 50.000 0.00 0.00 41.73 4.63
2652 2687 7.153985 ACCCAACAATGTTGAATTAATCACAG 58.846 34.615 25.93 5.77 37.92 3.66
2806 2841 7.938140 TTATCTTTCCAAACTTACCATGGAG 57.062 36.000 21.47 9.06 43.69 3.86
2893 2928 6.042093 TGAAAAACCTTGCATTTACCATGGTA 59.958 34.615 21.05 21.05 39.11 3.25
2933 2968 2.092753 AGGAAACTGCCATCATCACGAT 60.093 45.455 0.00 0.00 41.13 3.73
3015 3050 1.826096 GAGGAGGAGTGGGTTACAGTC 59.174 57.143 0.00 0.00 46.70 3.51
3016 3051 1.552719 GGAGGAGGAGTGGGTTACAGT 60.553 57.143 0.00 0.00 34.77 3.55
3017 3052 1.196012 GGAGGAGGAGTGGGTTACAG 58.804 60.000 0.00 0.00 0.00 2.74
3018 3053 0.252558 GGGAGGAGGAGTGGGTTACA 60.253 60.000 0.00 0.00 0.00 2.41
3019 3054 0.981801 GGGGAGGAGGAGTGGGTTAC 60.982 65.000 0.00 0.00 0.00 2.50
3020 3055 1.394963 GGGGAGGAGGAGTGGGTTA 59.605 63.158 0.00 0.00 0.00 2.85
3021 3056 2.125225 GGGGAGGAGGAGTGGGTT 59.875 66.667 0.00 0.00 0.00 4.11
3022 3057 4.400251 CGGGGAGGAGGAGTGGGT 62.400 72.222 0.00 0.00 0.00 4.51
3023 3058 4.075793 TCGGGGAGGAGGAGTGGG 62.076 72.222 0.00 0.00 0.00 4.61
3024 3059 2.443016 CTCGGGGAGGAGGAGTGG 60.443 72.222 0.00 0.00 0.00 4.00
3025 3060 1.454847 CTCTCGGGGAGGAGGAGTG 60.455 68.421 0.00 0.00 38.35 3.51
3026 3061 3.011885 CTCTCGGGGAGGAGGAGT 58.988 66.667 0.00 0.00 38.35 3.85
3037 3072 1.726533 GAACCCTAGTCGCCTCTCGG 61.727 65.000 0.00 0.00 39.05 4.63
3038 3073 1.726533 GGAACCCTAGTCGCCTCTCG 61.727 65.000 0.00 0.00 40.15 4.04
3101 3166 3.961414 GGGAAGGGAACGGTGGCA 61.961 66.667 0.00 0.00 0.00 4.92
3110 3175 1.396594 GAAGGAGGAGGGGAAGGGA 59.603 63.158 0.00 0.00 0.00 4.20
3182 3254 3.522731 CACGGGAGAGGAGCTCGG 61.523 72.222 7.83 0.00 44.91 4.63
3198 3270 2.693017 GAGGGAGGAGAGAGCCCA 59.307 66.667 0.00 0.00 44.55 5.36
3205 3277 2.691779 GGGGAGACGAGGGAGGAGA 61.692 68.421 0.00 0.00 0.00 3.71
3339 3414 2.032071 ACCGAAGCCAAACCGAGG 59.968 61.111 0.00 0.00 0.00 4.63
3425 3501 4.052518 GCCACCCAGCTCCACCAT 62.053 66.667 0.00 0.00 0.00 3.55
3536 3616 2.681778 CCGCACCTCCTCCTCACT 60.682 66.667 0.00 0.00 0.00 3.41
3596 3677 2.682494 TAAAGCTCCCGCCCTCGT 60.682 61.111 0.00 0.00 36.60 4.18
3656 3737 1.379642 GCAATAGCAGGAGCACACCC 61.380 60.000 0.00 0.00 45.49 4.61
3761 3842 3.114616 CGAGGACAGCACGGCAAG 61.115 66.667 0.00 0.00 0.00 4.01
3791 3872 2.646175 CCCCACGTCGTCTCACCAT 61.646 63.158 0.00 0.00 0.00 3.55
3871 3952 3.995506 CTGATCCCAACCCGCACCC 62.996 68.421 0.00 0.00 0.00 4.61
4077 4158 1.573108 TCTTCCACTAGGCTCCAAGG 58.427 55.000 0.00 0.00 33.74 3.61
4192 4275 1.356624 GAAGCAGCACAAACACGCT 59.643 52.632 0.00 0.00 39.66 5.07
4293 4377 9.878599 CGTCAGATTTTTATACCATGGTAAATC 57.121 33.333 28.44 28.44 33.22 2.17
4294 4378 9.403583 ACGTCAGATTTTTATACCATGGTAAAT 57.596 29.630 27.93 22.88 33.99 1.40
4295 4379 8.795842 ACGTCAGATTTTTATACCATGGTAAA 57.204 30.769 27.93 19.33 33.99 2.01
4296 4380 8.795842 AACGTCAGATTTTTATACCATGGTAA 57.204 30.769 27.93 13.91 33.99 2.85
4377 4461 7.763528 ACAAAACAAACAAAGCATCAACTATCA 59.236 29.630 0.00 0.00 0.00 2.15
4378 4462 8.130307 ACAAAACAAACAAAGCATCAACTATC 57.870 30.769 0.00 0.00 0.00 2.08
4379 4463 8.491331 AACAAAACAAACAAAGCATCAACTAT 57.509 26.923 0.00 0.00 0.00 2.12
4380 4464 7.897575 AACAAAACAAACAAAGCATCAACTA 57.102 28.000 0.00 0.00 0.00 2.24
4381 4465 6.799926 AACAAAACAAACAAAGCATCAACT 57.200 29.167 0.00 0.00 0.00 3.16
4382 4466 7.850268 AAAACAAAACAAACAAAGCATCAAC 57.150 28.000 0.00 0.00 0.00 3.18
4533 4617 1.684450 GGTTTGTTCATCAACCCCGTT 59.316 47.619 0.00 0.00 33.29 4.44
4535 4619 0.601057 GGGTTTGTTCATCAACCCCG 59.399 55.000 8.70 0.00 46.15 5.73
4546 4657 2.281276 GCGTCCCTCGGGTTTGTT 60.281 61.111 1.18 0.00 40.26 2.83
4642 4753 4.085546 GGGAGGGGAGTACGGGGT 62.086 72.222 0.00 0.00 0.00 4.95
4689 4800 2.657237 GACTGGTGGACCTCGTGG 59.343 66.667 0.99 0.99 36.82 4.94
4751 4863 6.068010 TGATGAATACAATCCACAATACCCC 58.932 40.000 0.00 0.00 0.00 4.95
4816 4928 2.025727 GTCCGGACGTATGAGGCG 59.974 66.667 20.85 0.00 0.00 5.52
4825 4937 1.226974 CAGGCAGTATGTCCGGACG 60.227 63.158 28.70 15.48 46.31 4.79
4829 4941 0.460284 GTGACCAGGCAGTATGTCCG 60.460 60.000 0.00 0.00 46.31 4.79
4836 4948 3.184736 AAAAACGTGACCAGGCAGT 57.815 47.368 0.00 0.00 0.00 4.40
4905 5065 4.329545 CCCGGGTGCCCCATATCG 62.330 72.222 14.18 0.00 45.83 2.92
4937 5098 4.692475 CAACGTGGACCGGGACCC 62.692 72.222 13.02 0.00 42.24 4.46
4969 5130 3.817647 AGCGGATGAAGAGGAATTTATGC 59.182 43.478 0.00 0.00 0.00 3.14
4994 5155 0.177373 GTGGCTAGGGTTTAGTCCGG 59.823 60.000 0.00 0.00 0.00 5.14
5024 5185 4.379243 ACGAGCTTGGGTGGCGAG 62.379 66.667 5.79 0.00 34.52 5.03
5043 5204 2.052690 GCTGGCTCACCGGACTCTA 61.053 63.158 9.46 0.00 46.41 2.43
5044 5205 3.386237 GCTGGCTCACCGGACTCT 61.386 66.667 9.46 0.00 46.41 3.24
5051 5212 2.433318 GACACGAGCTGGCTCACC 60.433 66.667 20.39 4.59 42.86 4.02
5077 5238 1.065928 CGCCGGCAAGGTAGAGTAG 59.934 63.158 28.98 0.37 43.70 2.57
5078 5239 2.420568 CCGCCGGCAAGGTAGAGTA 61.421 63.158 28.98 0.00 43.70 2.59
5079 5240 3.771160 CCGCCGGCAAGGTAGAGT 61.771 66.667 28.98 0.00 43.70 3.24
5184 5345 2.607187 ACGTGAAACCAGATCTAAGCG 58.393 47.619 0.00 0.00 0.00 4.68
5231 5392 6.765989 CCACATCCGAATACCTCAAATTAGAA 59.234 38.462 0.00 0.00 0.00 2.10
5232 5393 6.099125 TCCACATCCGAATACCTCAAATTAGA 59.901 38.462 0.00 0.00 0.00 2.10
5233 5394 6.288294 TCCACATCCGAATACCTCAAATTAG 58.712 40.000 0.00 0.00 0.00 1.73
5234 5395 6.241882 TCCACATCCGAATACCTCAAATTA 57.758 37.500 0.00 0.00 0.00 1.40
5235 5396 5.110814 TCCACATCCGAATACCTCAAATT 57.889 39.130 0.00 0.00 0.00 1.82
5236 5397 4.771114 TCCACATCCGAATACCTCAAAT 57.229 40.909 0.00 0.00 0.00 2.32
5237 5398 4.561500 TTCCACATCCGAATACCTCAAA 57.438 40.909 0.00 0.00 0.00 2.69
5238 5399 4.771114 ATTCCACATCCGAATACCTCAA 57.229 40.909 0.00 0.00 0.00 3.02
5239 5400 4.651962 TGTATTCCACATCCGAATACCTCA 59.348 41.667 14.78 0.00 46.06 3.86
5240 5401 5.209818 TGTATTCCACATCCGAATACCTC 57.790 43.478 14.78 0.00 46.06 3.85
5241 5402 5.825593 ATGTATTCCACATCCGAATACCT 57.174 39.130 14.78 5.76 44.99 3.08
5332 5493 1.981256 ACAGTCGGACTTGGCAAATT 58.019 45.000 8.18 0.00 0.00 1.82
5353 5514 3.506844 TGGTGTACGTGTGTAAGAGCATA 59.493 43.478 0.00 0.00 30.94 3.14
5393 5554 2.726912 CGCTTGTTGGTTGCGCAG 60.727 61.111 11.31 0.00 43.08 5.18
5417 5578 1.938585 AATCTTGGTCACTCCGGAGA 58.061 50.000 37.69 14.48 39.52 3.71
5420 5581 1.482593 AGCTAATCTTGGTCACTCCGG 59.517 52.381 0.00 0.00 39.52 5.14
5554 5733 4.044426 GTGTCAAATGTTCTTGGTCTTGC 58.956 43.478 0.00 0.00 0.00 4.01
5621 5800 7.213678 CCACCATCTCTCTCCTCTTTAATTAC 58.786 42.308 0.00 0.00 0.00 1.89
5649 5828 3.576550 GGGGTAGAAAATGCACTGGAAAA 59.423 43.478 0.00 0.00 0.00 2.29
5659 5838 8.977412 ACAAATTATAAGGTGGGGTAGAAAATG 58.023 33.333 0.00 0.00 0.00 2.32
5660 5839 9.197306 GACAAATTATAAGGTGGGGTAGAAAAT 57.803 33.333 0.00 0.00 0.00 1.82
5661 5840 8.395605 AGACAAATTATAAGGTGGGGTAGAAAA 58.604 33.333 0.00 0.00 0.00 2.29
5662 5841 7.935405 AGACAAATTATAAGGTGGGGTAGAAA 58.065 34.615 0.00 0.00 0.00 2.52
5663 5842 7.519347 AGACAAATTATAAGGTGGGGTAGAA 57.481 36.000 0.00 0.00 0.00 2.10
5664 5843 7.519347 AAGACAAATTATAAGGTGGGGTAGA 57.481 36.000 0.00 0.00 0.00 2.59
5665 5844 9.689501 TTTAAGACAAATTATAAGGTGGGGTAG 57.310 33.333 0.00 0.00 0.00 3.18
5667 5846 8.959676 TTTTAAGACAAATTATAAGGTGGGGT 57.040 30.769 0.00 0.00 0.00 4.95
5681 5860 8.354426 CGGAGGGAGTAAAATTTTTAAGACAAA 58.646 33.333 9.06 0.00 0.00 2.83
5682 5861 7.503230 ACGGAGGGAGTAAAATTTTTAAGACAA 59.497 33.333 9.06 0.00 0.00 3.18
5683 5862 6.999871 ACGGAGGGAGTAAAATTTTTAAGACA 59.000 34.615 9.06 0.00 0.00 3.41
5684 5863 7.389884 AGACGGAGGGAGTAAAATTTTTAAGAC 59.610 37.037 9.06 1.02 0.00 3.01
5685 5864 7.455891 AGACGGAGGGAGTAAAATTTTTAAGA 58.544 34.615 9.06 0.00 0.00 2.10
5686 5865 7.683437 AGACGGAGGGAGTAAAATTTTTAAG 57.317 36.000 9.06 0.00 0.00 1.85
5687 5866 7.825761 CCTAGACGGAGGGAGTAAAATTTTTAA 59.174 37.037 9.06 0.00 32.39 1.52
5688 5867 7.038088 ACCTAGACGGAGGGAGTAAAATTTTTA 60.038 37.037 9.06 0.00 41.36 1.52
5689 5868 6.178324 CCTAGACGGAGGGAGTAAAATTTTT 58.822 40.000 9.06 0.00 32.39 1.94
5690 5869 5.250082 ACCTAGACGGAGGGAGTAAAATTTT 59.750 40.000 8.75 8.75 41.36 1.82
5691 5870 4.781621 ACCTAGACGGAGGGAGTAAAATTT 59.218 41.667 5.42 0.00 41.36 1.82
5692 5871 4.161754 CACCTAGACGGAGGGAGTAAAATT 59.838 45.833 5.42 0.00 41.36 1.82
5693 5872 3.705072 CACCTAGACGGAGGGAGTAAAAT 59.295 47.826 5.42 0.00 41.36 1.82
5694 5873 3.094572 CACCTAGACGGAGGGAGTAAAA 58.905 50.000 5.42 0.00 41.36 1.52
5695 5874 2.042162 ACACCTAGACGGAGGGAGTAAA 59.958 50.000 5.42 0.00 41.36 2.01
5696 5875 1.637553 ACACCTAGACGGAGGGAGTAA 59.362 52.381 5.42 0.00 41.36 2.24
5697 5876 1.293062 ACACCTAGACGGAGGGAGTA 58.707 55.000 5.42 0.00 41.36 2.59
5698 5877 1.293062 TACACCTAGACGGAGGGAGT 58.707 55.000 5.42 5.82 41.36 3.85
5699 5878 2.660670 ATACACCTAGACGGAGGGAG 57.339 55.000 5.42 0.78 41.36 4.30
5700 5879 3.461085 ACTTATACACCTAGACGGAGGGA 59.539 47.826 5.42 0.00 41.36 4.20
5701 5880 3.819902 GACTTATACACCTAGACGGAGGG 59.180 52.174 5.42 0.00 41.36 4.30
5702 5881 4.458397 TGACTTATACACCTAGACGGAGG 58.542 47.826 0.00 0.00 42.89 4.30
5703 5882 6.636562 ATTGACTTATACACCTAGACGGAG 57.363 41.667 0.00 0.00 36.31 4.63
5704 5883 7.414222 AAATTGACTTATACACCTAGACGGA 57.586 36.000 0.00 0.00 36.31 4.69
5705 5884 7.866393 CCTAAATTGACTTATACACCTAGACGG 59.134 40.741 0.00 0.00 39.35 4.79
5706 5885 8.411683 ACCTAAATTGACTTATACACCTAGACG 58.588 37.037 0.00 0.00 0.00 4.18
5709 5888 9.886132 ACAACCTAAATTGACTTATACACCTAG 57.114 33.333 0.00 0.00 33.57 3.02
5710 5889 9.661563 CACAACCTAAATTGACTTATACACCTA 57.338 33.333 0.00 0.00 33.57 3.08
5711 5890 7.120726 GCACAACCTAAATTGACTTATACACCT 59.879 37.037 0.00 0.00 33.57 4.00
5712 5891 7.094549 TGCACAACCTAAATTGACTTATACACC 60.095 37.037 0.00 0.00 33.57 4.16
5713 5892 7.812648 TGCACAACCTAAATTGACTTATACAC 58.187 34.615 0.00 0.00 33.57 2.90
5714 5893 7.987750 TGCACAACCTAAATTGACTTATACA 57.012 32.000 0.00 0.00 33.57 2.29


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

AutoCloner maintained by Alex Coulton.