Multiple sequence alignment - TraesCS2D01G277200

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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 TraesCS2D01G277200 chr2D 100.000 3522 0 0 1 3522 347462812 347466333 0.000000e+00 6505.0
1 TraesCS2D01G277200 chr2D 95.167 269 9 4 2284 2551 532435127 532435392 4.200000e-114 422.0
2 TraesCS2D01G277200 chr2D 90.173 173 8 6 2542 2711 532436376 532436542 2.130000e-52 217.0
3 TraesCS2D01G277200 chr2D 93.333 105 3 1 2989 3093 532436540 532436640 6.090000e-33 152.0
4 TraesCS2D01G277200 chr2D 95.946 74 3 0 2899 2972 376701188 376701261 1.720000e-23 121.0
5 TraesCS2D01G277200 chr2D 96.774 62 2 0 3121 3182 532436638 532436699 1.730000e-18 104.0
6 TraesCS2D01G277200 chr2D 85.556 90 12 1 220 308 623270047 623269958 3.740000e-15 93.5
7 TraesCS2D01G277200 chr2B 90.414 2128 95 46 639 2719 412767617 412769682 0.000000e+00 2699.0
8 TraesCS2D01G277200 chr2B 89.527 592 41 11 1 590 412767032 412767604 0.000000e+00 730.0
9 TraesCS2D01G277200 chr2B 94.737 285 11 1 2972 3256 412776707 412776987 1.160000e-119 440.0
10 TraesCS2D01G277200 chr2B 91.781 292 11 3 3241 3522 412776998 412777286 9.160000e-106 394.0
11 TraesCS2D01G277200 chr2A 91.004 2012 84 41 708 2687 461153178 461155124 0.000000e+00 2623.0
12 TraesCS2D01G277200 chr2A 94.142 239 6 4 3284 3522 461160900 461161130 1.200000e-94 357.0
13 TraesCS2D01G277200 chr2A 86.347 271 12 6 2970 3235 461155170 461155420 4.480000e-69 272.0
14 TraesCS2D01G277200 chr2A 82.779 331 23 12 407 720 461151396 461151709 7.500000e-67 265.0
15 TraesCS2D01G277200 chr2A 92.982 171 11 1 2712 2882 570190648 570190479 7.550000e-62 248.0
16 TraesCS2D01G277200 chr2A 89.655 87 6 3 2895 2980 601612883 601612799 1.340000e-19 108.0
17 TraesCS2D01G277200 chr3B 89.362 564 39 8 2970 3520 207727752 207728307 0.000000e+00 689.0
18 TraesCS2D01G277200 chr3B 86.731 309 35 4 1 308 69617637 69617940 4.350000e-89 339.0
19 TraesCS2D01G277200 chr3B 88.966 145 13 1 2531 2672 207725596 207725740 3.610000e-40 176.0
20 TraesCS2D01G277200 chr5D 84.839 310 22 11 1 308 488836646 488836932 4.450000e-74 289.0
21 TraesCS2D01G277200 chr5D 93.491 169 11 0 2714 2882 117350445 117350613 5.840000e-63 252.0
22 TraesCS2D01G277200 chr5D 96.053 76 2 1 2897 2972 549851356 549851430 4.770000e-24 122.0
23 TraesCS2D01G277200 chr5D 95.890 73 1 1 2900 2972 415263953 415263883 2.220000e-22 117.0
24 TraesCS2D01G277200 chr3D 98.171 164 3 0 2719 2882 64757392 64757555 1.600000e-73 287.0
25 TraesCS2D01G277200 chr3D 93.491 169 11 0 2715 2883 545912166 545912334 5.840000e-63 252.0
26 TraesCS2D01G277200 chr3D 92.982 171 11 1 2713 2883 250054188 250054019 7.550000e-62 248.0
27 TraesCS2D01G277200 chr3D 92.593 81 6 0 2893 2973 555598324 555598244 2.220000e-22 117.0
28 TraesCS2D01G277200 chr7D 93.976 166 10 0 2718 2883 312574128 312574293 5.840000e-63 252.0
29 TraesCS2D01G277200 chr7D 92.683 82 5 1 2898 2978 615904344 615904263 2.220000e-22 117.0
30 TraesCS2D01G277200 chr7A 93.976 166 10 0 2718 2883 547092339 547092504 5.840000e-63 252.0
31 TraesCS2D01G277200 chr7A 93.023 172 10 2 2718 2889 709731230 709731061 2.100000e-62 250.0
32 TraesCS2D01G277200 chr3A 92.941 170 12 0 2714 2883 64291112 64290943 7.550000e-62 248.0
33 TraesCS2D01G277200 chr1D 92.857 84 5 1 2898 2981 257365447 257365365 1.720000e-23 121.0
34 TraesCS2D01G277200 chr1A 93.671 79 4 1 2899 2976 440885274 440885352 2.220000e-22 117.0
35 TraesCS2D01G277200 chrUn 93.590 78 4 1 2895 2972 31324874 31324798 7.990000e-22 115.0
36 TraesCS2D01G277200 chr6A 88.235 68 6 2 220 286 77058028 77058094 2.910000e-11 80.5


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 TraesCS2D01G277200 chr2D 347462812 347466333 3521 False 6505.000000 6505 100.00000 1 3522 1 chr2D.!!$F1 3521
1 TraesCS2D01G277200 chr2D 532435127 532436699 1572 False 223.750000 422 93.86175 2284 3182 4 chr2D.!!$F3 898
2 TraesCS2D01G277200 chr2B 412767032 412769682 2650 False 1714.500000 2699 89.97050 1 2719 2 chr2B.!!$F1 2718
3 TraesCS2D01G277200 chr2B 412776707 412777286 579 False 417.000000 440 93.25900 2972 3522 2 chr2B.!!$F2 550
4 TraesCS2D01G277200 chr2A 461151396 461155420 4024 False 1053.333333 2623 86.71000 407 3235 3 chr2A.!!$F2 2828
5 TraesCS2D01G277200 chr3B 207725596 207728307 2711 False 432.500000 689 89.16400 2531 3520 2 chr3B.!!$F2 989

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
308 310 0.320771 CTACGTCCACAAAGCAGGCT 60.321 55.0 0.00 0.00 0.00 4.58 F
313 315 0.395586 TCCACAAAGCAGGCTGTTGT 60.396 50.0 17.16 16.18 35.91 3.32 F
1633 3148 0.244721 ATCCCGAAGCAAAGCAAAGC 59.755 50.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 3146 0.107165 GATTAGTCGGGGGCTTTGCT 60.107 55.0 0.00 0.0 0.00 3.91 R
1838 3364 0.174845 TACGCTGCAGGCTACGAATT 59.825 50.0 17.12 0.0 39.13 2.17 R
2869 7404 0.251653 TGAGTGCTACTCCCTCCGTT 60.252 55.0 11.99 0.0 44.44 4.44 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
31 32 7.784037 TCCCATTTACTCTGCGTATAACTTTA 58.216 34.615 0.00 0.00 0.00 1.85
54 55 6.594788 ATGCCAAAATATCCGCAATATTCT 57.405 33.333 2.70 0.00 39.21 2.40
62 63 4.882671 ATCCGCAATATTCTGTGTGTTC 57.117 40.909 0.00 0.00 0.00 3.18
67 68 5.496387 CGCAATATTCTGTGTGTTCAGATC 58.504 41.667 0.00 0.00 42.84 2.75
70 71 6.965500 GCAATATTCTGTGTGTTCAGATCTTG 59.035 38.462 0.00 0.00 42.84 3.02
83 84 8.121708 GTGTTCAGATCTTGAGCATATTCTTTC 58.878 37.037 12.32 0.00 46.65 2.62
84 85 8.045507 TGTTCAGATCTTGAGCATATTCTTTCT 58.954 33.333 0.00 0.00 41.40 2.52
97 98 9.262358 AGCATATTCTTTCTAGAAATACCGTTC 57.738 33.333 18.02 6.66 43.32 3.95
105 106 1.206371 AGAAATACCGTTCCACCTCCG 59.794 52.381 0.00 0.00 0.00 4.63
166 167 2.634453 TCAGAGAGACAACCATGCAGAA 59.366 45.455 0.00 0.00 0.00 3.02
168 169 3.436015 CAGAGAGACAACCATGCAGAAAG 59.564 47.826 0.00 0.00 0.00 2.62
218 220 0.533032 GGGGAGAACGAAGAGGACAG 59.467 60.000 0.00 0.00 0.00 3.51
258 260 1.547372 GCATGGGGCATTTATAGCTGG 59.453 52.381 0.00 0.00 43.97 4.85
259 261 2.880443 CATGGGGCATTTATAGCTGGT 58.120 47.619 0.00 0.00 0.00 4.00
260 262 2.363306 TGGGGCATTTATAGCTGGTG 57.637 50.000 0.00 0.00 0.00 4.17
276 278 1.105759 GGTGCTTCTCCCATCCATGC 61.106 60.000 0.00 0.00 0.00 4.06
308 310 0.320771 CTACGTCCACAAAGCAGGCT 60.321 55.000 0.00 0.00 0.00 4.58
310 312 1.893808 CGTCCACAAAGCAGGCTGT 60.894 57.895 17.16 0.00 0.00 4.40
313 315 0.395586 TCCACAAAGCAGGCTGTTGT 60.396 50.000 17.16 16.18 35.91 3.32
324 326 1.068333 AGGCTGTTGTTTATGCGCAAG 60.068 47.619 17.11 5.49 43.44 4.01
361 364 7.071196 TCGGAGGGAGTACTACTAAGTGTTATA 59.929 40.741 4.77 0.00 36.36 0.98
472 475 1.373570 CTCGGGCTCTGGAAAATGAC 58.626 55.000 0.00 0.00 0.00 3.06
811 2317 9.196552 TCATATTATGAGACGAGCAATTACTTG 57.803 33.333 2.14 0.00 33.59 3.16
816 2322 6.505044 TGAGACGAGCAATTACTTGTAGTA 57.495 37.500 0.00 0.00 34.29 1.82
817 2323 6.552629 TGAGACGAGCAATTACTTGTAGTAG 58.447 40.000 0.00 0.00 34.29 2.57
818 2324 6.150641 TGAGACGAGCAATTACTTGTAGTAGT 59.849 38.462 0.00 0.00 34.29 2.73
819 2325 7.335171 TGAGACGAGCAATTACTTGTAGTAGTA 59.665 37.037 0.00 0.00 34.29 1.82
820 2326 8.048534 AGACGAGCAATTACTTGTAGTAGTAA 57.951 34.615 0.00 0.00 42.87 2.24
902 2409 2.280524 CCCGAGCACCGAAACACA 60.281 61.111 0.00 0.00 41.76 3.72
937 2444 4.157607 GGTTCACACCACACCAGG 57.842 61.111 0.00 0.00 43.61 4.45
1630 3145 1.000731 CCAAATCCCGAAGCAAAGCAA 59.999 47.619 0.00 0.00 0.00 3.91
1631 3146 2.547642 CCAAATCCCGAAGCAAAGCAAA 60.548 45.455 0.00 0.00 0.00 3.68
1632 3147 2.730550 AATCCCGAAGCAAAGCAAAG 57.269 45.000 0.00 0.00 0.00 2.77
1633 3148 0.244721 ATCCCGAAGCAAAGCAAAGC 59.755 50.000 0.00 0.00 0.00 3.51
1634 3149 1.106351 TCCCGAAGCAAAGCAAAGCA 61.106 50.000 0.00 0.00 0.00 3.91
1635 3150 0.249405 CCCGAAGCAAAGCAAAGCAA 60.249 50.000 0.00 0.00 0.00 3.91
1721 3242 8.144478 ACATACTCCTACTACTACATGCATTTG 58.856 37.037 0.00 0.00 0.00 2.32
1730 3251 4.559153 ACTACATGCATTTGTGGCTTTTC 58.441 39.130 0.00 0.00 31.82 2.29
1733 3254 5.212532 ACATGCATTTGTGGCTTTTCTTA 57.787 34.783 0.00 0.00 0.00 2.10
1734 3255 5.609423 ACATGCATTTGTGGCTTTTCTTAA 58.391 33.333 0.00 0.00 0.00 1.85
1776 3297 2.612212 ACTCCACAAAACGCTGTTACTG 59.388 45.455 0.00 0.00 0.00 2.74
1777 3298 2.612212 CTCCACAAAACGCTGTTACTGT 59.388 45.455 0.00 0.00 0.00 3.55
1778 3299 2.353269 TCCACAAAACGCTGTTACTGTG 59.647 45.455 18.68 18.68 35.14 3.66
1779 3300 2.096819 CCACAAAACGCTGTTACTGTGT 59.903 45.455 21.10 2.65 33.86 3.72
1780 3301 3.350912 CACAAAACGCTGTTACTGTGTC 58.649 45.455 8.76 0.00 31.65 3.67
1781 3302 3.063452 CACAAAACGCTGTTACTGTGTCT 59.937 43.478 8.76 0.00 31.65 3.41
1817 3343 3.980775 CCGTGGTTTTAGCTGTTTCATTG 59.019 43.478 0.00 0.00 0.00 2.82
1819 3345 4.306600 GTGGTTTTAGCTGTTTCATTGGG 58.693 43.478 0.00 0.00 0.00 4.12
1820 3346 3.964031 TGGTTTTAGCTGTTTCATTGGGT 59.036 39.130 0.00 0.00 0.00 4.51
1823 3349 4.599047 TTTAGCTGTTTCATTGGGTTGG 57.401 40.909 0.00 0.00 0.00 3.77
1824 3350 0.681175 AGCTGTTTCATTGGGTTGGC 59.319 50.000 0.00 0.00 0.00 4.52
1825 3351 0.667184 GCTGTTTCATTGGGTTGGCG 60.667 55.000 0.00 0.00 0.00 5.69
1827 3353 0.958091 TGTTTCATTGGGTTGGCGAG 59.042 50.000 0.00 0.00 0.00 5.03
1829 3355 1.531739 TTTCATTGGGTTGGCGAGCC 61.532 55.000 16.26 16.26 46.43 4.70
2044 3582 2.151172 GTCGCATCGTCAAAAGCAAAAC 59.849 45.455 0.00 0.00 0.00 2.43
2164 3708 0.388134 GCAACAGCAGCAATCCTGTG 60.388 55.000 0.00 0.00 43.71 3.66
2165 3709 1.241165 CAACAGCAGCAATCCTGTGA 58.759 50.000 0.00 0.00 43.71 3.58
2228 3772 5.181245 CACTTTTAACGTCACCCTGATGATT 59.819 40.000 0.00 0.00 36.89 2.57
2235 3779 3.126831 GTCACCCTGATGATTGATCGAC 58.873 50.000 0.00 0.00 33.17 4.20
2259 3823 3.998913 TCATTGTCCACCATTCTGCTA 57.001 42.857 0.00 0.00 0.00 3.49
2270 3834 8.129211 GTCCACCATTCTGCTAAACATTATTAC 58.871 37.037 0.00 0.00 0.00 1.89
2272 3836 8.131100 CCACCATTCTGCTAAACATTATTACTG 58.869 37.037 0.00 0.00 0.00 2.74
2273 3837 8.677300 CACCATTCTGCTAAACATTATTACTGT 58.323 33.333 0.00 0.00 0.00 3.55
2274 3838 9.899661 ACCATTCTGCTAAACATTATTACTGTA 57.100 29.630 0.00 0.00 0.00 2.74
2582 5168 3.505184 CACCGCCCGGCAACATAC 61.505 66.667 10.77 0.00 39.32 2.39
2633 5222 1.541670 GCACACGGAAGGAACACCTAA 60.542 52.381 0.00 0.00 33.17 2.69
2687 7221 9.198475 AGCTTACTACTGTAGTTGGTACATTAT 57.802 33.333 24.09 0.00 40.99 1.28
2695 7229 9.754382 ACTGTAGTTGGTACATTATTAATACCG 57.246 33.333 0.00 0.00 40.99 4.02
2696 7230 9.970395 CTGTAGTTGGTACATTATTAATACCGA 57.030 33.333 0.00 0.00 40.99 4.69
2726 7261 8.602472 ATCTATTCATCTTATGTACTCCCTCC 57.398 38.462 0.00 0.00 0.00 4.30
2727 7262 5.730296 ATTCATCTTATGTACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
2728 7263 4.180377 TCATCTTATGTACTCCCTCCGT 57.820 45.455 0.00 0.00 0.00 4.69
2729 7264 4.543689 TCATCTTATGTACTCCCTCCGTT 58.456 43.478 0.00 0.00 0.00 4.44
2730 7265 4.583489 TCATCTTATGTACTCCCTCCGTTC 59.417 45.833 0.00 0.00 0.00 3.95
2731 7266 3.294214 TCTTATGTACTCCCTCCGTTCC 58.706 50.000 0.00 0.00 0.00 3.62
2732 7267 3.053095 TCTTATGTACTCCCTCCGTTCCT 60.053 47.826 0.00 0.00 0.00 3.36
2733 7268 4.166725 TCTTATGTACTCCCTCCGTTCCTA 59.833 45.833 0.00 0.00 0.00 2.94
2734 7269 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2735 7270 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
2736 7271 3.716431 TGTACTCCCTCCGTTCCTAAAT 58.284 45.455 0.00 0.00 0.00 1.40
2737 7272 4.870636 TGTACTCCCTCCGTTCCTAAATA 58.129 43.478 0.00 0.00 0.00 1.40
2738 7273 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
2739 7274 6.613699 TGTACTCCCTCCGTTCCTAAATATA 58.386 40.000 0.00 0.00 0.00 0.86
2740 7275 7.068702 TGTACTCCCTCCGTTCCTAAATATAA 58.931 38.462 0.00 0.00 0.00 0.98
2741 7276 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2742 7277 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2743 7278 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2744 7279 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2745 7280 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2746 7281 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2747 7282 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
2748 7283 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
2789 7324 9.909644 AATTACAACATACGGATGTATCTAGAC 57.090 33.333 15.10 0.00 45.93 2.59
2790 7325 6.954487 ACAACATACGGATGTATCTAGACA 57.046 37.500 15.10 0.00 45.93 3.41
2791 7326 7.526142 ACAACATACGGATGTATCTAGACAT 57.474 36.000 15.10 0.00 45.93 3.06
2792 7327 8.631480 ACAACATACGGATGTATCTAGACATA 57.369 34.615 15.10 0.00 45.93 2.29
2793 7328 9.244292 ACAACATACGGATGTATCTAGACATAT 57.756 33.333 15.10 0.00 45.93 1.78
2823 7358 7.907214 AGTGTGTATTCACTCATTTTACTCC 57.093 36.000 4.01 0.00 44.07 3.85
2824 7359 6.590292 AGTGTGTATTCACTCATTTTACTCCG 59.410 38.462 4.01 0.00 44.07 4.63
2825 7360 6.367969 GTGTGTATTCACTCATTTTACTCCGT 59.632 38.462 4.01 0.00 44.14 4.69
2826 7361 7.543172 GTGTGTATTCACTCATTTTACTCCGTA 59.457 37.037 4.01 0.00 44.14 4.02
2827 7362 8.255206 TGTGTATTCACTCATTTTACTCCGTAT 58.745 33.333 4.01 0.00 44.14 3.06
2828 7363 8.540492 GTGTATTCACTCATTTTACTCCGTATG 58.460 37.037 0.00 0.00 40.98 2.39
2829 7364 8.255206 TGTATTCACTCATTTTACTCCGTATGT 58.745 33.333 0.00 0.00 0.00 2.29
2830 7365 9.740239 GTATTCACTCATTTTACTCCGTATGTA 57.260 33.333 0.00 0.00 0.00 2.29
2831 7366 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2832 7367 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2833 7368 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2834 7369 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2835 7370 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2836 7371 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2837 7372 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2838 7373 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
2839 7374 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2840 7375 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2841 7376 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
2842 7377 4.174009 CTCCGTATGTAGTCACTTGTTGG 58.826 47.826 0.00 0.00 0.00 3.77
2843 7378 2.671396 CCGTATGTAGTCACTTGTTGGC 59.329 50.000 0.00 0.00 0.00 4.52
2844 7379 3.322369 CGTATGTAGTCACTTGTTGGCA 58.678 45.455 0.00 0.00 29.07 4.92
2845 7380 3.932710 CGTATGTAGTCACTTGTTGGCAT 59.067 43.478 0.00 0.00 29.07 4.40
2846 7381 4.032900 CGTATGTAGTCACTTGTTGGCATC 59.967 45.833 0.00 0.00 29.07 3.91
2847 7382 3.769739 TGTAGTCACTTGTTGGCATCT 57.230 42.857 0.00 0.00 29.07 2.90
2848 7383 4.085357 TGTAGTCACTTGTTGGCATCTT 57.915 40.909 0.00 0.00 29.07 2.40
2849 7384 4.460263 TGTAGTCACTTGTTGGCATCTTT 58.540 39.130 0.00 0.00 29.07 2.52
2850 7385 5.616270 TGTAGTCACTTGTTGGCATCTTTA 58.384 37.500 0.00 0.00 29.07 1.85
2851 7386 6.058833 TGTAGTCACTTGTTGGCATCTTTAA 58.941 36.000 0.00 0.00 29.07 1.52
2852 7387 6.544197 TGTAGTCACTTGTTGGCATCTTTAAA 59.456 34.615 0.00 0.00 29.07 1.52
2853 7388 6.463995 AGTCACTTGTTGGCATCTTTAAAA 57.536 33.333 0.00 0.00 29.07 1.52
2854 7389 6.872920 AGTCACTTGTTGGCATCTTTAAAAA 58.127 32.000 0.00 0.00 29.07 1.94
2855 7390 6.980397 AGTCACTTGTTGGCATCTTTAAAAAG 59.020 34.615 0.00 0.00 32.62 2.27
2857 7392 6.978080 TCACTTGTTGGCATCTTTAAAAAGAC 59.022 34.615 7.29 0.00 46.80 3.01
2858 7393 6.980397 CACTTGTTGGCATCTTTAAAAAGACT 59.020 34.615 7.29 0.00 46.80 3.24
2859 7394 7.492344 CACTTGTTGGCATCTTTAAAAAGACTT 59.508 33.333 7.29 0.00 46.80 3.01
2860 7395 8.691797 ACTTGTTGGCATCTTTAAAAAGACTTA 58.308 29.630 7.29 0.00 46.80 2.24
2861 7396 8.865590 TTGTTGGCATCTTTAAAAAGACTTAC 57.134 30.769 7.29 3.64 46.80 2.34
2862 7397 8.001881 TGTTGGCATCTTTAAAAAGACTTACA 57.998 30.769 7.29 5.75 46.80 2.41
2863 7398 8.637986 TGTTGGCATCTTTAAAAAGACTTACAT 58.362 29.630 7.29 0.00 46.80 2.29
2864 7399 9.476202 GTTGGCATCTTTAAAAAGACTTACATT 57.524 29.630 7.29 0.00 46.80 2.71
2874 7409 9.558396 TTAAAAAGACTTACATTTAGGAACGGA 57.442 29.630 0.00 0.00 0.00 4.69
2875 7410 7.668525 AAAAGACTTACATTTAGGAACGGAG 57.331 36.000 0.00 0.00 0.00 4.63
2876 7411 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
2877 7412 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
2878 7413 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2883 7418 1.772836 TTAGGAACGGAGGGAGTAGC 58.227 55.000 0.00 0.00 0.00 3.58
2901 7436 9.075678 GGGAGTAGCACTCACTTTTATATAGTA 57.924 37.037 15.22 0.00 45.03 1.82
2902 7437 9.896263 GGAGTAGCACTCACTTTTATATAGTAC 57.104 37.037 15.22 0.00 46.79 2.73
2905 7440 9.896263 GTAGCACTCACTTTTATATAGTACTCC 57.104 37.037 0.00 0.00 0.00 3.85
2906 7441 7.953752 AGCACTCACTTTTATATAGTACTCCC 58.046 38.462 0.00 0.00 0.00 4.30
2907 7442 7.785506 AGCACTCACTTTTATATAGTACTCCCT 59.214 37.037 0.00 0.00 0.00 4.20
2908 7443 8.083462 GCACTCACTTTTATATAGTACTCCCTC 58.917 40.741 0.00 0.00 0.00 4.30
2909 7444 8.578151 CACTCACTTTTATATAGTACTCCCTCC 58.422 40.741 0.00 0.00 0.00 4.30
2910 7445 7.447853 ACTCACTTTTATATAGTACTCCCTCCG 59.552 40.741 0.00 0.00 0.00 4.63
2911 7446 7.293073 TCACTTTTATATAGTACTCCCTCCGT 58.707 38.462 0.00 0.00 0.00 4.69
2912 7447 8.439971 TCACTTTTATATAGTACTCCCTCCGTA 58.560 37.037 0.00 0.00 0.00 4.02
2913 7448 9.071276 CACTTTTATATAGTACTCCCTCCGTAA 57.929 37.037 0.00 0.00 0.00 3.18
2914 7449 9.646522 ACTTTTATATAGTACTCCCTCCGTAAA 57.353 33.333 0.00 0.00 0.00 2.01
2916 7451 9.866655 TTTTATATAGTACTCCCTCCGTAAAGA 57.133 33.333 0.00 0.00 0.00 2.52
2917 7452 9.866655 TTTATATAGTACTCCCTCCGTAAAGAA 57.133 33.333 0.00 0.00 0.00 2.52
2918 7453 9.866655 TTATATAGTACTCCCTCCGTAAAGAAA 57.133 33.333 0.00 0.00 0.00 2.52
2919 7454 8.953223 ATATAGTACTCCCTCCGTAAAGAAAT 57.047 34.615 0.00 0.00 0.00 2.17
2921 7456 8.953223 ATAGTACTCCCTCCGTAAAGAAATAT 57.047 34.615 0.00 0.00 0.00 1.28
2923 7458 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
2924 7459 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2925 7460 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2926 7461 8.315220 ACTCCCTCCGTAAAGAAATATAAGAA 57.685 34.615 0.00 0.00 0.00 2.52
2927 7462 8.202811 ACTCCCTCCGTAAAGAAATATAAGAAC 58.797 37.037 0.00 0.00 0.00 3.01
2928 7463 7.205297 TCCCTCCGTAAAGAAATATAAGAACG 58.795 38.462 0.00 0.00 0.00 3.95
2929 7464 6.982724 CCCTCCGTAAAGAAATATAAGAACGT 59.017 38.462 0.00 0.00 0.00 3.99
2930 7465 7.493645 CCCTCCGTAAAGAAATATAAGAACGTT 59.506 37.037 0.00 0.00 0.00 3.99
2931 7466 8.876790 CCTCCGTAAAGAAATATAAGAACGTTT 58.123 33.333 0.46 0.00 0.00 3.60
2949 7484 7.819900 AGAACGTTTAGTGATCTAAATGCTCTT 59.180 33.333 0.46 6.86 45.83 2.85
2966 7501 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
2967 7502 6.522054 TGCTCTTATATTTCTTTACGGAGGG 58.478 40.000 0.00 0.00 0.00 4.30
2968 7503 6.325545 TGCTCTTATATTTCTTTACGGAGGGA 59.674 38.462 0.00 0.00 0.00 4.20
2984 7519 3.134262 GGAGGGAGTATCTTGGTACCAAC 59.866 52.174 23.69 14.52 33.73 3.77
3023 7558 1.477553 AGCATATGCAACCAACAGGG 58.522 50.000 28.62 0.00 45.16 4.45
3026 7561 2.431782 GCATATGCAACCAACAGGGATT 59.568 45.455 22.84 0.00 39.75 3.01
3059 7594 2.091885 GGCCCCATCTTGTTGAATCCTA 60.092 50.000 0.00 0.00 0.00 2.94
3067 7602 6.825213 CCATCTTGTTGAATCCTAGACATTCA 59.175 38.462 11.20 11.20 38.27 2.57
3167 7707 5.420739 TCAGGAATTACATTTGGGCCTTTAC 59.579 40.000 4.53 0.00 0.00 2.01
3187 7727 4.819105 ACCTACAACTCATGGAATTCGA 57.181 40.909 0.00 0.00 0.00 3.71
3188 7728 5.160607 ACCTACAACTCATGGAATTCGAA 57.839 39.130 0.00 0.00 0.00 3.71
3189 7729 5.178797 ACCTACAACTCATGGAATTCGAAG 58.821 41.667 3.35 0.00 0.00 3.79
3306 7885 1.661112 CGTACTGCTGCTTTTAGCCTC 59.339 52.381 0.00 0.00 41.51 4.70
3307 7886 2.010497 GTACTGCTGCTTTTAGCCTCC 58.990 52.381 0.00 0.00 41.51 4.30
3310 7889 0.401738 TGCTGCTTTTAGCCTCCTGT 59.598 50.000 0.00 0.00 41.51 4.00
3312 7891 2.039746 TGCTGCTTTTAGCCTCCTGTTA 59.960 45.455 0.00 0.00 41.51 2.41
3313 7892 3.282885 GCTGCTTTTAGCCTCCTGTTAT 58.717 45.455 0.00 0.00 41.51 1.89
3314 7893 3.065925 GCTGCTTTTAGCCTCCTGTTATG 59.934 47.826 0.00 0.00 41.51 1.90
3315 7894 3.620488 TGCTTTTAGCCTCCTGTTATGG 58.380 45.455 0.00 0.00 41.51 2.74
3342 7921 6.370442 TGGTTCTTTACACCACGAATATGAAG 59.630 38.462 0.00 0.00 39.53 3.02
3357 7936 3.951775 ATGAAGGGATCAGCGATAGTC 57.048 47.619 0.00 0.00 42.53 2.59
3361 7940 2.790433 AGGGATCAGCGATAGTCTCTC 58.210 52.381 0.00 0.00 39.35 3.20
3377 7956 0.040646 TCTCCACCTGTATGTCCGGT 59.959 55.000 0.00 0.00 33.95 5.28
3445 8024 2.392662 TCCTCTGAGGATGATGGTGTC 58.607 52.381 22.30 0.00 40.06 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 8.293867 GGATATTTTGGCATAAAGTTATACGCA 58.706 33.333 0.00 0.00 0.00 5.24
31 32 6.015180 ACAGAATATTGCGGATATTTTGGCAT 60.015 34.615 18.82 4.72 42.67 4.40
54 55 3.473923 TGCTCAAGATCTGAACACACA 57.526 42.857 0.00 0.00 32.17 3.72
62 63 9.761504 TTCTAGAAAGAATATGCTCAAGATCTG 57.238 33.333 1.68 0.00 36.80 2.90
70 71 8.819643 ACGGTATTTCTAGAAAGAATATGCTC 57.180 34.615 21.75 5.18 41.36 4.26
83 84 3.490419 CGGAGGTGGAACGGTATTTCTAG 60.490 52.174 0.00 0.00 38.12 2.43
84 85 2.428171 CGGAGGTGGAACGGTATTTCTA 59.572 50.000 0.00 0.00 38.12 2.10
132 133 0.249447 TCTCTGACACAACCTGCACG 60.249 55.000 0.00 0.00 0.00 5.34
166 167 3.580193 GCATGCGCGGATGCTCTT 61.580 61.111 45.08 11.06 44.57 2.85
187 189 4.143333 CTCCCCTACCCACGCACG 62.143 72.222 0.00 0.00 0.00 5.34
258 260 1.442526 CGCATGGATGGGAGAAGCAC 61.443 60.000 0.00 0.00 42.66 4.40
259 261 1.153107 CGCATGGATGGGAGAAGCA 60.153 57.895 0.00 0.00 42.66 3.91
260 262 2.550101 GCGCATGGATGGGAGAAGC 61.550 63.158 0.30 0.00 42.66 3.86
286 288 2.002586 CCTGCTTTGTGGACGTAGATG 58.997 52.381 0.00 0.00 0.00 2.90
291 293 1.893808 CAGCCTGCTTTGTGGACGT 60.894 57.895 0.00 0.00 0.00 4.34
308 310 3.717400 TTTCCTTGCGCATAAACAACA 57.283 38.095 12.75 0.00 0.00 3.33
332 335 5.239087 CACTTAGTAGTACTCCCTCCGATTC 59.761 48.000 5.96 0.00 31.96 2.52
419 422 4.324099 CCTCACTCCATCTCTTTGTTCCAT 60.324 45.833 0.00 0.00 0.00 3.41
422 425 3.006247 GCCTCACTCCATCTCTTTGTTC 58.994 50.000 0.00 0.00 0.00 3.18
532 535 9.769093 GCACTTACGTAGAATACATTTCAAATT 57.231 29.630 0.00 0.00 43.24 1.82
533 536 8.941977 TGCACTTACGTAGAATACATTTCAAAT 58.058 29.630 0.00 0.00 43.24 2.32
534 537 8.312896 TGCACTTACGTAGAATACATTTCAAA 57.687 30.769 0.00 0.00 43.24 2.69
535 538 7.892778 TGCACTTACGTAGAATACATTTCAA 57.107 32.000 0.00 0.00 43.24 2.69
536 539 7.892778 TTGCACTTACGTAGAATACATTTCA 57.107 32.000 0.00 0.00 43.24 2.69
537 540 9.601971 TTTTTGCACTTACGTAGAATACATTTC 57.398 29.630 0.00 0.00 43.24 2.17
628 631 8.859236 ATGAGCATATCTGTATGTTTGCTATT 57.141 30.769 0.00 0.00 40.29 1.73
704 729 3.119495 TGTGTACACGAGGATGTCATCTG 60.119 47.826 20.61 5.63 33.85 2.90
761 2267 7.961827 TGAACACGAAACTACGTAAAATTTTGT 59.038 29.630 13.76 6.42 44.76 2.83
770 2276 9.442033 CTCATAATATGAACACGAAACTACGTA 57.558 33.333 4.37 0.00 40.65 3.57
771 2277 8.186163 TCTCATAATATGAACACGAAACTACGT 58.814 33.333 4.37 0.00 42.11 3.57
772 2278 8.469902 GTCTCATAATATGAACACGAAACTACG 58.530 37.037 4.37 0.00 39.11 3.51
773 2279 8.469902 CGTCTCATAATATGAACACGAAACTAC 58.530 37.037 20.93 0.00 43.24 2.73
811 2317 7.202315 GTGCTCACACGTAAATTACTACTAC 57.798 40.000 1.42 0.00 36.98 2.73
836 2342 4.695455 TGCAGAAAGGCATACTCTACAAAC 59.305 41.667 0.00 0.00 39.25 2.93
902 2409 1.106944 CCTTTGGTGGTTTGCTCGGT 61.107 55.000 0.00 0.00 0.00 4.69
937 2444 0.518764 CGCGTACTGTCGAGTCAGTC 60.519 60.000 11.57 4.39 45.79 3.51
1107 2616 3.321648 ACCCACATGAGGAGCGCA 61.322 61.111 11.47 0.00 0.00 6.09
1630 3145 0.331616 ATTAGTCGGGGGCTTTGCTT 59.668 50.000 0.00 0.00 0.00 3.91
1631 3146 0.107165 GATTAGTCGGGGGCTTTGCT 60.107 55.000 0.00 0.00 0.00 3.91
1632 3147 0.393808 TGATTAGTCGGGGGCTTTGC 60.394 55.000 0.00 0.00 0.00 3.68
1633 3148 2.348411 ATGATTAGTCGGGGGCTTTG 57.652 50.000 0.00 0.00 0.00 2.77
1634 3149 3.071167 GTCTATGATTAGTCGGGGGCTTT 59.929 47.826 0.00 0.00 0.00 3.51
1635 3150 2.633481 GTCTATGATTAGTCGGGGGCTT 59.367 50.000 0.00 0.00 0.00 4.35
1721 3242 5.974751 TGTTTTCATCGTTAAGAAAAGCCAC 59.025 36.000 0.00 0.00 42.43 5.01
1733 3254 9.620660 GGAGTAATAAAACATGTTTTCATCGTT 57.379 29.630 33.71 23.06 41.39 3.85
1734 3255 8.788806 TGGAGTAATAAAACATGTTTTCATCGT 58.211 29.630 33.71 19.70 41.39 3.73
1777 3298 2.691526 ACGGAGTAACTGTGTGAAGACA 59.308 45.455 0.00 0.00 41.94 3.41
1778 3299 3.366440 ACGGAGTAACTGTGTGAAGAC 57.634 47.619 0.00 0.00 41.94 3.01
1788 3314 3.070590 ACAGCTAAAACCACGGAGTAACT 59.929 43.478 0.00 0.00 41.61 2.24
1789 3315 3.396560 ACAGCTAAAACCACGGAGTAAC 58.603 45.455 0.00 0.00 41.61 2.50
1796 3322 3.980775 CCAATGAAACAGCTAAAACCACG 59.019 43.478 0.00 0.00 0.00 4.94
1817 3343 4.832608 CCTACGGCTCGCCAACCC 62.833 72.222 8.87 0.00 35.37 4.11
1819 3345 1.883084 CATCCTACGGCTCGCCAAC 60.883 63.158 8.87 0.00 35.37 3.77
1820 3346 1.609635 TTCATCCTACGGCTCGCCAA 61.610 55.000 8.87 0.00 35.37 4.52
1823 3349 1.140816 GAATTCATCCTACGGCTCGC 58.859 55.000 0.00 0.00 0.00 5.03
1824 3350 1.269102 ACGAATTCATCCTACGGCTCG 60.269 52.381 6.22 0.00 0.00 5.03
1825 3351 2.510768 ACGAATTCATCCTACGGCTC 57.489 50.000 6.22 0.00 0.00 4.70
1827 3353 2.059541 GCTACGAATTCATCCTACGGC 58.940 52.381 6.22 0.00 0.00 5.68
1829 3355 3.309388 CAGGCTACGAATTCATCCTACG 58.691 50.000 6.22 0.00 0.00 3.51
1830 3356 3.060602 GCAGGCTACGAATTCATCCTAC 58.939 50.000 6.22 0.00 0.00 3.18
1832 3358 1.486310 TGCAGGCTACGAATTCATCCT 59.514 47.619 6.22 2.90 0.00 3.24
1833 3359 1.869767 CTGCAGGCTACGAATTCATCC 59.130 52.381 5.57 0.56 0.00 3.51
1835 3361 1.303309 GCTGCAGGCTACGAATTCAT 58.697 50.000 17.12 0.00 38.06 2.57
1838 3364 0.174845 TACGCTGCAGGCTACGAATT 59.825 50.000 17.12 0.00 39.13 2.17
1839 3365 0.249073 CTACGCTGCAGGCTACGAAT 60.249 55.000 17.12 0.00 39.13 3.34
1840 3366 1.138883 CTACGCTGCAGGCTACGAA 59.861 57.895 17.12 0.00 39.13 3.85
1841 3367 2.771639 CCTACGCTGCAGGCTACGA 61.772 63.158 17.12 0.35 39.13 3.43
1842 3368 2.278857 CCTACGCTGCAGGCTACG 60.279 66.667 17.12 12.83 39.13 3.51
1844 3370 2.127869 CCTCCTACGCTGCAGGCTA 61.128 63.158 17.12 2.34 39.13 3.93
2235 3779 2.615447 CAGAATGGTGGACAATGATCGG 59.385 50.000 0.00 0.00 0.00 4.18
2282 3846 8.792633 GCACCAATACATACATACATGGTTAAT 58.207 33.333 0.00 0.00 37.59 1.40
2283 3847 7.775561 TGCACCAATACATACATACATGGTTAA 59.224 33.333 0.00 0.00 37.59 2.01
2284 3848 7.283329 TGCACCAATACATACATACATGGTTA 58.717 34.615 0.00 0.00 37.59 2.85
2285 3849 6.125719 TGCACCAATACATACATACATGGTT 58.874 36.000 0.00 0.00 37.59 3.67
2286 3850 5.689835 TGCACCAATACATACATACATGGT 58.310 37.500 0.00 0.00 40.16 3.55
2287 3851 5.181811 CCTGCACCAATACATACATACATGG 59.818 44.000 0.00 0.00 0.00 3.66
2288 3852 5.997129 TCCTGCACCAATACATACATACATG 59.003 40.000 0.00 0.00 0.00 3.21
2289 3853 6.186420 TCCTGCACCAATACATACATACAT 57.814 37.500 0.00 0.00 0.00 2.29
2290 3854 5.454613 CCTCCTGCACCAATACATACATACA 60.455 44.000 0.00 0.00 0.00 2.29
2291 3855 4.997395 CCTCCTGCACCAATACATACATAC 59.003 45.833 0.00 0.00 0.00 2.39
2443 4007 1.488957 GTTGACGAGCAGCTTCACG 59.511 57.895 0.00 1.26 0.00 4.35
2582 5168 2.000447 GCTAGCTAGTTTGGTGAACCG 59.000 52.381 21.62 0.00 39.13 4.44
2584 5170 4.626172 GTGTAGCTAGCTAGTTTGGTGAAC 59.374 45.833 24.78 11.92 38.58 3.18
2633 5222 5.946377 AGTTTCAAAAAGAGAGGTGAACACT 59.054 36.000 4.96 0.00 30.00 3.55
2706 7241 4.543689 ACGGAGGGAGTACATAAGATGAA 58.456 43.478 0.00 0.00 0.00 2.57
2713 7248 4.524802 TTAGGAACGGAGGGAGTACATA 57.475 45.455 0.00 0.00 0.00 2.29
2714 7249 3.393426 TTAGGAACGGAGGGAGTACAT 57.607 47.619 0.00 0.00 0.00 2.29
2715 7250 2.905415 TTAGGAACGGAGGGAGTACA 57.095 50.000 0.00 0.00 0.00 2.90
2716 7251 7.232330 ACTTATATTTAGGAACGGAGGGAGTAC 59.768 40.741 0.00 0.00 0.00 2.73
2717 7252 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2718 7253 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2719 7254 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2720 7255 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2721 7256 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2722 7257 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
2763 7298 9.909644 GTCTAGATACATCCGTATGTTGTAATT 57.090 33.333 0.00 0.00 44.07 1.40
2764 7299 9.074576 TGTCTAGATACATCCGTATGTTGTAAT 57.925 33.333 0.00 0.00 44.07 1.89
2765 7300 8.454570 TGTCTAGATACATCCGTATGTTGTAA 57.545 34.615 0.00 0.00 44.07 2.41
2766 7301 8.631480 ATGTCTAGATACATCCGTATGTTGTA 57.369 34.615 0.00 0.00 44.07 2.41
2767 7302 6.954487 TGTCTAGATACATCCGTATGTTGT 57.046 37.500 0.00 0.00 44.07 3.32
2800 7335 6.367969 ACGGAGTAAAATGAGTGAATACACAC 59.632 38.462 0.00 0.00 44.82 3.82
2801 7336 6.460781 ACGGAGTAAAATGAGTGAATACACA 58.539 36.000 0.00 0.00 44.82 3.72
2802 7337 6.963049 ACGGAGTAAAATGAGTGAATACAC 57.037 37.500 0.00 0.00 41.94 2.90
2820 7355 4.174009 CCAACAAGTGACTACATACGGAG 58.826 47.826 0.00 0.00 0.00 4.63
2821 7356 3.615592 GCCAACAAGTGACTACATACGGA 60.616 47.826 0.00 0.00 0.00 4.69
2822 7357 2.671396 GCCAACAAGTGACTACATACGG 59.329 50.000 0.00 0.00 0.00 4.02
2823 7358 3.322369 TGCCAACAAGTGACTACATACG 58.678 45.455 0.00 0.00 0.00 3.06
2824 7359 5.178797 AGATGCCAACAAGTGACTACATAC 58.821 41.667 0.00 0.00 0.00 2.39
2825 7360 5.420725 AGATGCCAACAAGTGACTACATA 57.579 39.130 0.00 0.00 0.00 2.29
2826 7361 4.292186 AGATGCCAACAAGTGACTACAT 57.708 40.909 0.00 0.00 0.00 2.29
2827 7362 3.769739 AGATGCCAACAAGTGACTACA 57.230 42.857 0.00 0.00 0.00 2.74
2828 7363 6.554334 TTAAAGATGCCAACAAGTGACTAC 57.446 37.500 0.00 0.00 0.00 2.73
2829 7364 7.575414 TTTTAAAGATGCCAACAAGTGACTA 57.425 32.000 0.00 0.00 0.00 2.59
2830 7365 6.463995 TTTTAAAGATGCCAACAAGTGACT 57.536 33.333 0.00 0.00 0.00 3.41
2831 7366 6.978080 TCTTTTTAAAGATGCCAACAAGTGAC 59.022 34.615 0.89 0.00 39.95 3.67
2832 7367 6.978080 GTCTTTTTAAAGATGCCAACAAGTGA 59.022 34.615 8.07 0.00 45.83 3.41
2833 7368 6.980397 AGTCTTTTTAAAGATGCCAACAAGTG 59.020 34.615 8.07 0.00 45.83 3.16
2834 7369 7.112452 AGTCTTTTTAAAGATGCCAACAAGT 57.888 32.000 8.07 0.00 45.83 3.16
2835 7370 8.968242 GTAAGTCTTTTTAAAGATGCCAACAAG 58.032 33.333 8.07 0.00 45.83 3.16
2836 7371 8.470805 TGTAAGTCTTTTTAAAGATGCCAACAA 58.529 29.630 8.07 0.00 45.83 2.83
2837 7372 8.001881 TGTAAGTCTTTTTAAAGATGCCAACA 57.998 30.769 8.07 6.51 45.83 3.33
2838 7373 9.476202 AATGTAAGTCTTTTTAAAGATGCCAAC 57.524 29.630 8.07 4.50 45.83 3.77
2848 7383 9.558396 TCCGTTCCTAAATGTAAGTCTTTTTAA 57.442 29.630 0.00 0.00 0.00 1.52
2849 7384 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
2850 7385 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
2851 7386 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
2852 7387 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
2853 7388 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
2854 7389 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
2855 7390 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
2856 7391 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
2857 7392 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
2858 7393 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
2859 7394 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
2860 7395 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
2861 7396 3.492829 GCTACTCCCTCCGTTCCTAAATG 60.493 52.174 0.00 0.00 0.00 2.32
2862 7397 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
2863 7398 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
2864 7399 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
2865 7400 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
2866 7401 0.971447 GTGCTACTCCCTCCGTTCCT 60.971 60.000 0.00 0.00 0.00 3.36
2867 7402 0.971447 AGTGCTACTCCCTCCGTTCC 60.971 60.000 0.00 0.00 0.00 3.62
2868 7403 0.456628 GAGTGCTACTCCCTCCGTTC 59.543 60.000 5.33 0.00 39.28 3.95
2869 7404 0.251653 TGAGTGCTACTCCCTCCGTT 60.252 55.000 11.99 0.00 44.44 4.44
2870 7405 0.966370 GTGAGTGCTACTCCCTCCGT 60.966 60.000 11.99 0.00 44.44 4.69
2871 7406 0.681564 AGTGAGTGCTACTCCCTCCG 60.682 60.000 11.99 0.00 44.44 4.63
2872 7407 1.562783 AAGTGAGTGCTACTCCCTCC 58.437 55.000 11.99 1.33 44.44 4.30
2873 7408 3.686916 AAAAGTGAGTGCTACTCCCTC 57.313 47.619 11.99 5.17 44.44 4.30
2874 7409 7.785506 ACTATATAAAAGTGAGTGCTACTCCCT 59.214 37.037 11.99 5.08 44.44 4.20
2875 7410 7.953752 ACTATATAAAAGTGAGTGCTACTCCC 58.046 38.462 11.99 3.15 44.44 4.30
2876 7411 9.896263 GTACTATATAAAAGTGAGTGCTACTCC 57.104 37.037 11.99 5.67 44.44 3.85
2883 7418 8.578151 GGAGGGAGTACTATATAAAAGTGAGTG 58.422 40.741 0.00 0.00 0.00 3.51
2899 7434 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
2901 7436 7.909485 TCTTATATTTCTTTACGGAGGGAGT 57.091 36.000 0.00 0.00 0.00 3.85
2902 7437 7.381678 CGTTCTTATATTTCTTTACGGAGGGAG 59.618 40.741 0.00 0.00 0.00 4.30
2905 7440 7.998753 ACGTTCTTATATTTCTTTACGGAGG 57.001 36.000 0.00 0.00 32.54 4.30
2920 7455 9.601217 AGCATTTAGATCACTAAACGTTCTTAT 57.399 29.630 0.00 0.00 46.74 1.73
2921 7456 8.997621 AGCATTTAGATCACTAAACGTTCTTA 57.002 30.769 0.00 0.00 46.74 2.10
2922 7457 7.819900 AGAGCATTTAGATCACTAAACGTTCTT 59.180 33.333 0.00 0.00 43.83 2.52
2923 7458 7.324178 AGAGCATTTAGATCACTAAACGTTCT 58.676 34.615 0.00 8.48 46.74 3.01
2924 7459 7.527084 AGAGCATTTAGATCACTAAACGTTC 57.473 36.000 0.00 0.00 46.74 3.95
2925 7460 7.907214 AAGAGCATTTAGATCACTAAACGTT 57.093 32.000 0.00 0.00 46.74 3.99
2940 7475 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
2941 7476 7.661847 CCCTCCGTAAAGAAATATAAGAGCATT 59.338 37.037 0.00 0.00 0.00 3.56
2942 7477 7.016268 TCCCTCCGTAAAGAAATATAAGAGCAT 59.984 37.037 0.00 0.00 0.00 3.79
2943 7478 6.325545 TCCCTCCGTAAAGAAATATAAGAGCA 59.674 38.462 0.00 0.00 0.00 4.26
2944 7479 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2945 7480 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2946 7481 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2947 7482 9.857957 GATACTCCCTCCGTAAAGAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
2948 7483 9.597681 AGATACTCCCTCCGTAAAGAAATATAA 57.402 33.333 0.00 0.00 0.00 0.98
2949 7484 9.597681 AAGATACTCCCTCCGTAAAGAAATATA 57.402 33.333 0.00 0.00 0.00 0.86
2950 7485 8.368668 CAAGATACTCCCTCCGTAAAGAAATAT 58.631 37.037 0.00 0.00 0.00 1.28
2951 7486 7.201974 CCAAGATACTCCCTCCGTAAAGAAATA 60.202 40.741 0.00 0.00 0.00 1.40
2952 7487 6.408206 CCAAGATACTCCCTCCGTAAAGAAAT 60.408 42.308 0.00 0.00 0.00 2.17
2953 7488 5.105064 CCAAGATACTCCCTCCGTAAAGAAA 60.105 44.000 0.00 0.00 0.00 2.52
2954 7489 4.404715 CCAAGATACTCCCTCCGTAAAGAA 59.595 45.833 0.00 0.00 0.00 2.52
2955 7490 3.958798 CCAAGATACTCCCTCCGTAAAGA 59.041 47.826 0.00 0.00 0.00 2.52
2956 7491 3.705072 ACCAAGATACTCCCTCCGTAAAG 59.295 47.826 0.00 0.00 0.00 1.85
2957 7492 3.716431 ACCAAGATACTCCCTCCGTAAA 58.284 45.455 0.00 0.00 0.00 2.01
2958 7493 3.393426 ACCAAGATACTCCCTCCGTAA 57.607 47.619 0.00 0.00 0.00 3.18
2959 7494 3.435601 GGTACCAAGATACTCCCTCCGTA 60.436 52.174 7.15 0.00 0.00 4.02
2960 7495 2.664015 GTACCAAGATACTCCCTCCGT 58.336 52.381 0.00 0.00 0.00 4.69
2961 7496 1.962100 GGTACCAAGATACTCCCTCCG 59.038 57.143 7.15 0.00 0.00 4.63
2962 7497 3.042059 TGGTACCAAGATACTCCCTCC 57.958 52.381 13.60 0.00 0.00 4.30
2963 7498 4.031611 AGTTGGTACCAAGATACTCCCTC 58.968 47.826 27.77 11.59 36.52 4.30
2964 7499 3.775316 CAGTTGGTACCAAGATACTCCCT 59.225 47.826 27.77 15.09 36.52 4.20
2965 7500 3.773119 TCAGTTGGTACCAAGATACTCCC 59.227 47.826 27.77 13.02 36.52 4.30
2966 7501 4.222145 TGTCAGTTGGTACCAAGATACTCC 59.778 45.833 27.77 13.76 36.52 3.85
2967 7502 5.401531 TGTCAGTTGGTACCAAGATACTC 57.598 43.478 27.77 14.48 36.52 2.59
2968 7503 5.338381 CCATGTCAGTTGGTACCAAGATACT 60.338 44.000 27.77 18.61 36.52 2.12
2984 7519 5.347342 TGCTTTGTTGTTTTACCATGTCAG 58.653 37.500 0.00 0.00 0.00 3.51
3059 7594 8.909923 TGCATATCAGATGAATTTTGAATGTCT 58.090 29.630 0.00 0.00 0.00 3.41
3067 7602 9.491675 TTTGTTTGTGCATATCAGATGAATTTT 57.508 25.926 0.00 0.00 0.00 1.82
3167 7707 5.063944 CACTTCGAATTCCATGAGTTGTAGG 59.936 44.000 0.00 0.00 0.00 3.18
3187 7727 0.466543 TACGGTTGGCACTGTCACTT 59.533 50.000 5.08 0.00 41.99 3.16
3188 7728 0.685097 ATACGGTTGGCACTGTCACT 59.315 50.000 5.08 0.00 41.99 3.41
3189 7729 0.796312 CATACGGTTGGCACTGTCAC 59.204 55.000 5.08 0.00 41.99 3.67
3253 7823 1.417890 ACTGTAGCTCAAACAGGCAGT 59.582 47.619 17.32 5.90 46.97 4.40
3306 7885 5.048294 GGTGTAAAGAACCAACCATAACAGG 60.048 44.000 0.00 0.00 37.65 4.00
3307 7886 5.533154 TGGTGTAAAGAACCAACCATAACAG 59.467 40.000 0.00 0.00 44.72 3.16
3342 7921 1.816224 GGAGAGACTATCGCTGATCCC 59.184 57.143 0.00 0.00 0.00 3.85
3357 7936 0.747255 CCGGACATACAGGTGGAGAG 59.253 60.000 0.00 0.00 0.00 3.20
3377 7956 1.254026 CAGAGGAGGTCGTACAACCA 58.746 55.000 5.62 0.00 42.12 3.67
3445 8024 2.286559 GGCGTCGTCATCGTCATCG 61.287 63.158 0.00 0.00 38.33 3.84
3479 8058 1.024271 GCAAGACAAGCTGACAACCA 58.976 50.000 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.