Multiple sequence alignment - TraesCS7B01G302300

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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 TraesCS7B01G302300 chr7B 100.000 5460 0 0 1 5460 539215523 539220982 0.000000e+00 10083.0
1 TraesCS7B01G302300 chr7B 89.320 206 19 1 378 580 681948893 681948688 7.020000e-64 255.0
2 TraesCS7B01G302300 chr7B 100.000 34 0 0 5427 5460 659732871 659732904 4.570000e-06 63.9
3 TraesCS7B01G302300 chr7D 95.361 4247 140 31 645 4848 510611307 510615539 0.000000e+00 6698.0
4 TraesCS7B01G302300 chr7D 84.921 630 40 19 1 603 510610700 510611301 2.190000e-163 586.0
5 TraesCS7B01G302300 chr7D 90.625 448 23 10 4876 5317 510615531 510615965 1.320000e-160 577.0
6 TraesCS7B01G302300 chr7D 95.918 49 2 0 2278 2326 120323589 120323637 4.530000e-11 80.5
7 TraesCS7B01G302300 chr7D 94.340 53 0 3 2281 2333 213784805 213784756 1.630000e-10 78.7
8 TraesCS7B01G302300 chr7D 100.000 28 0 0 5214 5241 32673297 32673324 1.000000e-02 52.8
9 TraesCS7B01G302300 chr7A 94.262 3677 130 31 645 4270 581372119 581375765 0.000000e+00 5546.0
10 TraesCS7B01G302300 chr7A 93.884 981 49 8 4308 5280 581375752 581376729 0.000000e+00 1469.0
11 TraesCS7B01G302300 chr7A 87.619 630 26 20 1 606 581371516 581372117 0.000000e+00 684.0
12 TraesCS7B01G302300 chr7A 100.000 35 0 0 5426 5460 125769707 125769741 1.270000e-06 65.8
13 TraesCS7B01G302300 chr2B 89.712 243 16 1 338 580 632573616 632573849 8.890000e-78 302.0
14 TraesCS7B01G302300 chr2B 92.308 104 5 2 2754 2857 206114721 206114821 1.590000e-30 145.0
15 TraesCS7B01G302300 chr2B 94.231 52 3 0 2277 2328 375174364 375174313 4.530000e-11 80.5
16 TraesCS7B01G302300 chr1A 89.712 243 16 1 338 580 31697892 31697659 8.890000e-78 302.0
17 TraesCS7B01G302300 chr1A 88.017 242 20 1 339 580 439488244 439488012 1.500000e-70 278.0
18 TraesCS7B01G302300 chr1A 97.297 37 1 0 5424 5460 13091125 13091089 4.570000e-06 63.9
19 TraesCS7B01G302300 chr3B 89.627 241 16 1 340 580 685089921 685090152 1.150000e-76 298.0
20 TraesCS7B01G302300 chr3B 88.115 244 18 3 338 580 615703821 615704054 4.160000e-71 279.0
21 TraesCS7B01G302300 chr3B 97.143 35 1 0 5426 5460 498408750 498408716 5.910000e-05 60.2
22 TraesCS7B01G302300 chr3A 90.909 209 19 0 372 580 591694723 591694931 1.160000e-71 281.0
23 TraesCS7B01G302300 chr3A 93.814 97 6 0 2761 2857 589797203 589797299 4.410000e-31 147.0
24 TraesCS7B01G302300 chr3A 97.222 36 1 0 5214 5249 21428337 21428302 1.640000e-05 62.1
25 TraesCS7B01G302300 chr1D 90.909 209 16 1 375 580 418606636 418606428 1.500000e-70 278.0
26 TraesCS7B01G302300 chr1D 92.857 98 7 0 2761 2858 392556677 392556580 5.700000e-30 143.0
27 TraesCS7B01G302300 chr6B 89.320 206 22 0 375 580 304065750 304065545 5.430000e-65 259.0
28 TraesCS7B01G302300 chr4B 94.000 100 6 0 2760 2859 642195650 642195551 9.470000e-33 152.0
29 TraesCS7B01G302300 chr1B 94.845 97 5 0 2761 2857 411568789 411568693 9.470000e-33 152.0
30 TraesCS7B01G302300 chr3D 93.814 97 6 0 2761 2857 305448661 305448565 4.410000e-31 147.0
31 TraesCS7B01G302300 chr3D 94.231 52 3 0 2281 2332 217588811 217588760 4.530000e-11 80.5
32 TraesCS7B01G302300 chr3D 92.857 42 1 2 5419 5460 600128118 600128157 5.910000e-05 60.2
33 TraesCS7B01G302300 chr3D 100.000 28 0 0 595 622 343450313 343450340 1.000000e-02 52.8
34 TraesCS7B01G302300 chr5B 91.837 98 7 1 2760 2857 34252184 34252088 9.540000e-28 135.0
35 TraesCS7B01G302300 chr5B 96.000 50 0 2 2281 2330 243411154 243411201 4.530000e-11 80.5
36 TraesCS7B01G302300 chr5B 100.000 29 0 0 592 620 406876381 406876353 3.000000e-03 54.7
37 TraesCS7B01G302300 chr2D 91.781 73 5 1 292 364 645284911 645284982 3.480000e-17 100.0
38 TraesCS7B01G302300 chr2D 100.000 37 0 0 5424 5460 572048835 572048799 9.810000e-08 69.4
39 TraesCS7B01G302300 chr2D 76.190 126 15 9 5226 5349 17208535 17208647 1.000000e-02 52.8
40 TraesCS7B01G302300 chr4D 97.917 48 1 0 2281 2328 482703583 482703630 3.500000e-12 84.2
41 TraesCS7B01G302300 chr4D 100.000 34 0 0 5427 5460 415302927 415302894 4.570000e-06 63.9
42 TraesCS7B01G302300 chr6D 95.918 49 2 0 2278 2326 4632425 4632473 4.530000e-11 80.5
43 TraesCS7B01G302300 chr6D 82.927 82 10 4 5207 5287 8138015 8137937 2.730000e-08 71.3
44 TraesCS7B01G302300 chr5A 88.679 53 6 0 5209 5261 456072317 456072265 1.270000e-06 65.8
45 TraesCS7B01G302300 chr2A 100.000 35 0 0 5426 5460 768317037 768317071 1.270000e-06 65.8
46 TraesCS7B01G302300 chr2A 97.297 37 1 0 5214 5250 7702098 7702134 4.570000e-06 63.9
47 TraesCS7B01G302300 chrUn 100.000 34 0 0 5427 5460 93003659 93003692 4.570000e-06 63.9


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 TraesCS7B01G302300 chr7B 539215523 539220982 5459 False 10083.000000 10083 100.000000 1 5460 1 chr7B.!!$F1 5459
1 TraesCS7B01G302300 chr7D 510610700 510615965 5265 False 2620.333333 6698 90.302333 1 5317 3 chr7D.!!$F3 5316
2 TraesCS7B01G302300 chr7A 581371516 581376729 5213 False 2566.333333 5546 91.921667 1 5280 3 chr7A.!!$F2 5279

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
422 436 0.028110 GCGGCTTCGATCAAATGGTC 59.972 55.000 0.00 0.0 35.61 4.02 F
699 730 0.603569 GTGTCCGGAGCAGAGAAAGA 59.396 55.000 3.06 0.0 0.00 2.52 F
850 888 0.888619 GACCAGGATCCGCGATGATA 59.111 55.000 8.23 0.0 0.00 2.15 F
1383 1455 1.191425 CGCGTCGTTTGAATCAGTTGA 59.809 47.619 0.00 0.0 0.00 3.18 F
1409 1481 1.202915 TCCATGTTTTGCTGCCTCAGA 60.203 47.619 0.00 0.0 32.44 3.27 F
3314 3391 1.065854 GGAGTTGGCACTGTAGCATCT 60.066 52.381 0.00 0.0 35.83 2.90 F
3457 3535 1.543429 GCCCTGTATGGACATAGGCAC 60.543 57.143 13.24 0.0 46.77 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1455 0.314935 CAGCAAAACATGGAACCGCT 59.685 50.000 0.00 0.0 0.00 5.52 R
1805 1880 1.899814 TCTGTGCCCACTAACTACAGG 59.100 52.381 0.00 0.0 39.27 4.00 R
2358 2434 2.351350 GCGGGGCGAATTATGGTAATTG 60.351 50.000 0.05 0.0 0.00 2.32 R
3099 3176 1.000607 TGTGTGTCGTAAGTCTCCAGC 60.001 52.381 0.00 0.0 39.48 4.85 R
3404 3482 2.885135 AACACTCAATGGGCTCATCA 57.115 45.000 0.00 0.0 32.24 3.07 R
4438 4539 0.846693 AAGAGTGCCTTGACCACCTT 59.153 50.000 0.00 0.0 32.92 3.50 R
4799 4903 0.999712 AAAATCACCCGACCCATCCT 59.000 50.000 0.00 0.0 0.00 3.24 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
47 48 6.128822 GCAAATTGGAGTGCTAAAGCTTAAAC 60.129 38.462 0.00 0.00 42.66 2.01
53 54 2.418976 GTGCTAAAGCTTAAACCCGGAG 59.581 50.000 0.73 0.00 42.66 4.63
56 64 1.822506 AAAGCTTAAACCCGGAGAGC 58.177 50.000 0.73 4.62 0.00 4.09
63 71 3.864983 AACCCGGAGAGCCCAAGGA 62.865 63.158 0.73 0.00 33.33 3.36
78 86 4.536765 CCCAAGGAACTAACAGGCAATAT 58.463 43.478 0.00 0.00 38.49 1.28
150 161 6.627243 TCATACCACACAAGTACACATCTAC 58.373 40.000 0.00 0.00 0.00 2.59
186 200 4.946157 GGTAGCTACAAGTAGTACTCACCA 59.054 45.833 24.75 0.00 35.65 4.17
226 240 2.040939 CCTGAGCATGAGGATGAGAGT 58.959 52.381 0.00 0.00 45.20 3.24
227 241 2.435069 CCTGAGCATGAGGATGAGAGTT 59.565 50.000 0.00 0.00 45.20 3.01
228 242 3.459145 CTGAGCATGAGGATGAGAGTTG 58.541 50.000 0.00 0.00 0.00 3.16
229 243 3.102204 TGAGCATGAGGATGAGAGTTGA 58.898 45.455 0.00 0.00 0.00 3.18
230 244 3.132467 TGAGCATGAGGATGAGAGTTGAG 59.868 47.826 0.00 0.00 0.00 3.02
231 245 3.372897 AGCATGAGGATGAGAGTTGAGA 58.627 45.455 0.00 0.00 0.00 3.27
232 246 3.385433 AGCATGAGGATGAGAGTTGAGAG 59.615 47.826 0.00 0.00 0.00 3.20
319 333 2.510238 CCTTCTCCTTGGCGAGCG 60.510 66.667 0.00 0.00 0.00 5.03
364 378 2.025767 CTCCTCCATCCTCACCTGCG 62.026 65.000 0.00 0.00 0.00 5.18
365 379 2.503061 CTCCATCCTCACCTGCGG 59.497 66.667 0.00 0.00 0.00 5.69
366 380 3.083349 TCCATCCTCACCTGCGGG 61.083 66.667 11.02 11.02 38.88 6.13
367 381 4.864334 CCATCCTCACCTGCGGGC 62.864 72.222 12.89 0.00 35.63 6.13
392 406 0.660300 GCACGACAAAGAAAAGCGGG 60.660 55.000 0.00 0.00 0.00 6.13
393 407 0.040425 CACGACAAAGAAAAGCGGGG 60.040 55.000 0.00 0.00 0.00 5.73
418 432 2.823829 GCCGCGGCTTCGATCAAAT 61.824 57.895 41.71 0.00 38.26 2.32
419 433 1.010797 CCGCGGCTTCGATCAAATG 60.011 57.895 14.67 0.00 35.61 2.32
421 435 1.705337 CGCGGCTTCGATCAAATGGT 61.705 55.000 0.00 0.00 35.61 3.55
422 436 0.028110 GCGGCTTCGATCAAATGGTC 59.972 55.000 0.00 0.00 35.61 4.02
423 437 0.657840 CGGCTTCGATCAAATGGTCC 59.342 55.000 0.00 0.00 35.61 4.46
424 438 1.750193 GGCTTCGATCAAATGGTCCA 58.250 50.000 0.00 0.00 0.00 4.02
427 442 2.096496 GCTTCGATCAAATGGTCCACAG 59.904 50.000 0.00 0.00 0.00 3.66
440 455 0.968901 TCCACAGATCGCGGTAGGTT 60.969 55.000 6.13 0.00 0.00 3.50
444 459 0.806102 CAGATCGCGGTAGGTTGGTG 60.806 60.000 6.13 0.00 0.00 4.17
452 467 1.914764 GTAGGTTGGTGGGACGGGA 60.915 63.158 0.00 0.00 0.00 5.14
550 581 3.785189 GATCCGCACGTACGCCCAT 62.785 63.158 16.72 0.03 0.00 4.00
597 628 2.273179 ACTGACCTTGCTACGCCGA 61.273 57.895 0.00 0.00 0.00 5.54
638 669 3.155167 CCCGTAGAGGTGGAGGGC 61.155 72.222 0.00 0.00 38.74 5.19
639 670 3.155167 CCGTAGAGGTGGAGGGCC 61.155 72.222 0.00 0.00 34.51 5.80
640 671 3.528370 CGTAGAGGTGGAGGGCCG 61.528 72.222 0.00 0.00 36.79 6.13
641 672 2.363925 GTAGAGGTGGAGGGCCGT 60.364 66.667 0.00 0.00 36.79 5.68
642 673 2.043248 TAGAGGTGGAGGGCCGTC 60.043 66.667 17.33 17.33 36.79 4.79
643 674 3.674050 TAGAGGTGGAGGGCCGTCC 62.674 68.421 33.30 33.30 36.79 4.79
695 726 2.680352 GGGTGTCCGGAGCAGAGA 60.680 66.667 3.06 0.00 0.00 3.10
699 730 0.603569 GTGTCCGGAGCAGAGAAAGA 59.396 55.000 3.06 0.00 0.00 2.52
769 804 1.692519 GGTGGAGTGGAAGTGTACTGT 59.307 52.381 0.00 0.00 0.00 3.55
850 888 0.888619 GACCAGGATCCGCGATGATA 59.111 55.000 8.23 0.00 0.00 2.15
865 906 2.043248 ATAGGTCGTCGTGGGCCT 60.043 61.111 4.53 6.82 35.28 5.19
870 911 3.379445 TCGTCGTGGGCCTCTTCC 61.379 66.667 4.53 0.00 0.00 3.46
887 928 2.575461 CGTGGACGGGTAAGGGTC 59.425 66.667 0.00 0.00 35.37 4.46
973 1037 2.206515 CTCTGCTTCGCTCGGTCACT 62.207 60.000 0.00 0.00 0.00 3.41
975 1039 2.876645 GCTTCGCTCGGTCACTCG 60.877 66.667 0.00 0.00 0.00 4.18
1008 1072 1.278172 CGACGGCGATAATGCTCCTG 61.278 60.000 16.62 0.00 40.82 3.86
1099 1170 1.204467 CGCTTGCTCTCTTTCTCCTCT 59.796 52.381 0.00 0.00 0.00 3.69
1358 1430 3.829577 GATTGGGGATCCTTGGTCC 57.170 57.895 12.58 4.22 34.92 4.46
1367 1439 4.143333 CCTTGGTCCGATCCGCGT 62.143 66.667 4.92 0.00 38.67 6.01
1383 1455 1.191425 CGCGTCGTTTGAATCAGTTGA 59.809 47.619 0.00 0.00 0.00 3.18
1409 1481 1.202915 TCCATGTTTTGCTGCCTCAGA 60.203 47.619 0.00 0.00 32.44 3.27
1621 1695 8.310382 CCAACATGTAGGATTTCCAATTTTACA 58.690 33.333 0.00 0.00 38.89 2.41
1712 1787 8.671921 CACATCATTACTTTCTGCTACATTTCT 58.328 33.333 0.00 0.00 0.00 2.52
1805 1880 5.403466 GGTGAATTGATCAGTTCTTTTGCAC 59.597 40.000 25.68 16.92 39.19 4.57
2186 2262 5.324409 TGGGAATGTTCTCACTAGCATTTT 58.676 37.500 0.00 0.00 31.45 1.82
2322 2398 4.506255 GCACCGGGCTGCCCTTAT 62.506 66.667 33.39 16.93 42.67 1.73
2358 2434 6.000219 ACACAATATACATGAGGAAGCATCC 59.000 40.000 0.00 0.00 46.98 3.51
2378 2454 2.227865 CCAATTACCATAATTCGCCCCG 59.772 50.000 0.00 0.00 0.00 5.73
2829 2905 2.453521 TGGACGTTGTATAGAGGCTGT 58.546 47.619 0.00 0.00 0.00 4.40
2847 2923 4.335315 GGCTGTGTCAATTAATTCGGATCA 59.665 41.667 0.00 0.00 0.00 2.92
2863 2939 3.816523 CGGATCAGAGGGAGTAGTTAGTC 59.183 52.174 0.00 0.00 0.00 2.59
2882 2958 9.654663 AGTTAGTCTGTGTAAACTGGAATTATC 57.345 33.333 0.00 0.00 31.20 1.75
2964 3041 4.955811 TCTTAGAAGCAAACACTCCTGA 57.044 40.909 0.00 0.00 0.00 3.86
2966 3043 6.605471 TCTTAGAAGCAAACACTCCTGATA 57.395 37.500 0.00 0.00 0.00 2.15
3099 3176 2.295909 TCCAAATTGGCGAGGAAAGTTG 59.704 45.455 7.24 0.00 37.47 3.16
3135 3212 3.436704 ACACACACGCTGATATTTTCCAG 59.563 43.478 0.00 0.00 0.00 3.86
3240 3317 5.121811 AGCTACATATTCAGCCTCTTTGTG 58.878 41.667 0.00 0.00 38.61 3.33
3314 3391 1.065854 GGAGTTGGCACTGTAGCATCT 60.066 52.381 0.00 0.00 35.83 2.90
3326 3403 2.840038 TGTAGCATCTGGGTCAACTGAT 59.160 45.455 0.00 0.00 0.00 2.90
3457 3535 1.543429 GCCCTGTATGGACATAGGCAC 60.543 57.143 13.24 0.00 46.77 5.01
3461 3539 4.102524 CCCTGTATGGACATAGGCACTAAA 59.897 45.833 0.00 0.00 41.19 1.85
3508 3586 7.206981 TGGTTCAGTCTGATCTTCAAAATTC 57.793 36.000 2.68 0.00 0.00 2.17
3573 3651 7.547227 AGGTTTTCATTATGCAATAGGACAAC 58.453 34.615 0.00 0.00 30.46 3.32
3612 3697 5.985781 GACTTGTTGTCATCGTGTATGTTT 58.014 37.500 0.00 0.00 44.73 2.83
3687 3772 2.849880 GCGAATTGCACCATGTGTAT 57.150 45.000 0.00 0.00 45.45 2.29
3876 3966 6.423776 AAATGATTTTTCTTCCTTCTGGCA 57.576 33.333 0.00 0.00 0.00 4.92
3890 3980 6.581712 TCCTTCTGGCAATTTTAATAATGGC 58.418 36.000 1.32 1.32 38.68 4.40
3952 4046 8.969267 AGTTCGAGAAATATTAAGAGCATTACG 58.031 33.333 0.00 0.00 0.00 3.18
3953 4047 8.965172 GTTCGAGAAATATTAAGAGCATTACGA 58.035 33.333 0.00 0.00 0.00 3.43
3954 4048 8.729529 TCGAGAAATATTAAGAGCATTACGAG 57.270 34.615 0.00 0.00 0.00 4.18
3956 4050 8.420945 CGAGAAATATTAAGAGCATTACGAGTG 58.579 37.037 0.00 0.00 0.00 3.51
3957 4051 9.250624 GAGAAATATTAAGAGCATTACGAGTGT 57.749 33.333 0.00 0.00 0.00 3.55
4001 4102 7.506971 ACTTTGCTAGTTAACTAACTGTTCCT 58.493 34.615 15.95 0.00 45.44 3.36
4295 4396 7.439381 ACCTTCATGAATGAAATAATGGCATC 58.561 34.615 16.48 0.00 45.26 3.91
4423 4524 2.614013 AAGCCCCGGGTCTTCCAT 60.614 61.111 21.85 0.00 34.36 3.41
4463 4564 2.040278 TGGTCAAGGCACTCTTAGCATT 59.960 45.455 0.00 0.00 38.49 3.56
4467 4568 5.363939 GTCAAGGCACTCTTAGCATTATCT 58.636 41.667 0.00 0.00 38.49 1.98
4481 4582 8.635765 TTAGCATTATCTTTTTCCTGTCTTGT 57.364 30.769 0.00 0.00 0.00 3.16
4540 4642 3.328382 TGGTCACACCAGCACTTATAC 57.672 47.619 0.00 0.00 44.79 1.47
4548 4650 2.365617 ACCAGCACTTATACGATCCCAG 59.634 50.000 0.00 0.00 0.00 4.45
4623 4725 4.207165 CCACGGGTGATTCAGGATTATTT 58.793 43.478 0.00 0.00 0.00 1.40
4721 4825 7.990886 GGTAGATTCATTGTTGGTTCATACCTA 59.009 37.037 0.00 0.00 45.27 3.08
4734 4838 7.466804 TGGTTCATACCTAACCTCTGAAATTT 58.533 34.615 6.56 0.00 45.53 1.82
4799 4903 2.624364 TCAGAGGCGTTGTGTACACTAA 59.376 45.455 25.60 15.39 0.00 2.24
4801 4905 2.029290 AGAGGCGTTGTGTACACTAAGG 60.029 50.000 25.60 21.21 0.00 2.69
4802 4906 1.965643 AGGCGTTGTGTACACTAAGGA 59.034 47.619 25.60 3.12 0.00 3.36
4803 4907 2.565834 AGGCGTTGTGTACACTAAGGAT 59.434 45.455 25.60 12.73 0.00 3.24
4816 4920 1.768870 CTAAGGATGGGTCGGGTGATT 59.231 52.381 0.00 0.00 0.00 2.57
4855 4959 7.459795 TTGCAATGTTGTGTCTGGAAATATA 57.540 32.000 0.00 0.00 0.00 0.86
5012 5116 2.358957 TCATCCAAAACCTGAGCATCG 58.641 47.619 0.00 0.00 38.61 3.84
5059 5163 3.671008 TGTCCATTTACTAGCGTGTGT 57.329 42.857 0.00 0.00 0.00 3.72
5063 5167 2.415168 CCATTTACTAGCGTGTGTGGTG 59.585 50.000 0.00 0.00 0.00 4.17
5167 5273 9.023967 GTGAAAATCATATGCTTGGATTTGTAC 57.976 33.333 11.96 10.67 40.17 2.90
5222 5332 3.055602 GGTTGTTGTATTACCTCCGTCCT 60.056 47.826 0.00 0.00 0.00 3.85
5255 5368 6.925211 TGTCTTAGATTTGTCTAGACACAGG 58.075 40.000 25.13 10.92 41.67 4.00
5262 5375 7.680730 AGATTTGTCTAGACACAGGTGTATTT 58.319 34.615 25.13 1.10 45.05 1.40
5263 5376 8.812972 AGATTTGTCTAGACACAGGTGTATTTA 58.187 33.333 25.13 3.21 45.05 1.40
5323 5436 9.922477 TTCATCTCTATCTAGACAAACCTAAGA 57.078 33.333 0.00 0.00 0.00 2.10
5324 5437 9.344772 TCATCTCTATCTAGACAAACCTAAGAC 57.655 37.037 0.00 0.00 0.00 3.01
5325 5438 9.126151 CATCTCTATCTAGACAAACCTAAGACA 57.874 37.037 0.00 0.00 0.00 3.41
5326 5439 9.702253 ATCTCTATCTAGACAAACCTAAGACAA 57.298 33.333 0.00 0.00 0.00 3.18
5327 5440 9.529823 TCTCTATCTAGACAAACCTAAGACAAA 57.470 33.333 0.00 0.00 0.00 2.83
5335 5448 8.166422 AGACAAACCTAAGACAAATAGTTTGG 57.834 34.615 15.42 0.00 44.81 3.28
5336 5449 7.230712 AGACAAACCTAAGACAAATAGTTTGGG 59.769 37.037 15.42 1.45 44.81 4.12
5337 5450 7.064229 ACAAACCTAAGACAAATAGTTTGGGA 58.936 34.615 15.42 0.00 44.81 4.37
5338 5451 7.013942 ACAAACCTAAGACAAATAGTTTGGGAC 59.986 37.037 15.42 0.00 44.81 4.46
5339 5452 6.195600 ACCTAAGACAAATAGTTTGGGACA 57.804 37.500 7.28 0.00 44.81 4.02
5340 5453 6.238648 ACCTAAGACAAATAGTTTGGGACAG 58.761 40.000 7.28 0.34 44.81 3.51
5341 5454 6.043938 ACCTAAGACAAATAGTTTGGGACAGA 59.956 38.462 7.28 0.00 44.81 3.41
5342 5455 6.940298 CCTAAGACAAATAGTTTGGGACAGAA 59.060 38.462 7.28 0.00 44.81 3.02
5343 5456 6.884280 AAGACAAATAGTTTGGGACAGAAG 57.116 37.500 7.28 0.00 44.81 2.85
5344 5457 5.316987 AGACAAATAGTTTGGGACAGAAGG 58.683 41.667 7.28 0.00 44.81 3.46
5345 5458 5.073144 AGACAAATAGTTTGGGACAGAAGGA 59.927 40.000 7.28 0.00 44.81 3.36
5346 5459 5.316987 ACAAATAGTTTGGGACAGAAGGAG 58.683 41.667 7.28 0.00 44.81 3.69
5347 5460 5.163088 ACAAATAGTTTGGGACAGAAGGAGT 60.163 40.000 7.28 0.00 44.81 3.85
5348 5461 6.043938 ACAAATAGTTTGGGACAGAAGGAGTA 59.956 38.462 7.28 0.00 44.81 2.59
5349 5462 5.941555 ATAGTTTGGGACAGAAGGAGTAG 57.058 43.478 0.00 0.00 42.39 2.57
5350 5463 3.588569 AGTTTGGGACAGAAGGAGTAGT 58.411 45.455 0.00 0.00 42.39 2.73
5351 5464 4.748701 AGTTTGGGACAGAAGGAGTAGTA 58.251 43.478 0.00 0.00 42.39 1.82
5352 5465 4.773149 AGTTTGGGACAGAAGGAGTAGTAG 59.227 45.833 0.00 0.00 42.39 2.57
5353 5466 4.669866 TTGGGACAGAAGGAGTAGTAGA 57.330 45.455 0.00 0.00 42.39 2.59
5354 5467 4.669866 TGGGACAGAAGGAGTAGTAGAA 57.330 45.455 0.00 0.00 0.00 2.10
5355 5468 5.006896 TGGGACAGAAGGAGTAGTAGAAA 57.993 43.478 0.00 0.00 0.00 2.52
5356 5469 4.771054 TGGGACAGAAGGAGTAGTAGAAAC 59.229 45.833 0.00 0.00 0.00 2.78
5357 5470 5.018149 GGGACAGAAGGAGTAGTAGAAACT 58.982 45.833 0.00 0.00 39.91 2.66
5358 5471 5.105675 GGGACAGAAGGAGTAGTAGAAACTG 60.106 48.000 0.00 0.00 36.36 3.16
5359 5472 5.711036 GGACAGAAGGAGTAGTAGAAACTGA 59.289 44.000 0.00 0.00 36.36 3.41
5360 5473 6.208994 GGACAGAAGGAGTAGTAGAAACTGAA 59.791 42.308 0.00 0.00 36.36 3.02
5361 5474 7.222000 ACAGAAGGAGTAGTAGAAACTGAAG 57.778 40.000 0.00 0.00 36.36 3.02
5362 5475 6.778559 ACAGAAGGAGTAGTAGAAACTGAAGT 59.221 38.462 0.00 0.00 36.36 3.01
5363 5476 7.288158 ACAGAAGGAGTAGTAGAAACTGAAGTT 59.712 37.037 0.00 0.00 40.50 2.66
5364 5477 8.794553 CAGAAGGAGTAGTAGAAACTGAAGTTA 58.205 37.037 0.00 0.00 37.25 2.24
5365 5478 8.795513 AGAAGGAGTAGTAGAAACTGAAGTTAC 58.204 37.037 0.00 0.00 37.25 2.50
5366 5479 8.474710 AAGGAGTAGTAGAAACTGAAGTTACA 57.525 34.615 0.00 0.00 37.25 2.41
5367 5480 8.653036 AGGAGTAGTAGAAACTGAAGTTACAT 57.347 34.615 0.00 0.00 37.25 2.29
5368 5481 9.091220 AGGAGTAGTAGAAACTGAAGTTACATT 57.909 33.333 0.00 0.00 37.25 2.71
5369 5482 9.708092 GGAGTAGTAGAAACTGAAGTTACATTT 57.292 33.333 0.00 0.00 37.25 2.32
5375 5488 9.665264 GTAGAAACTGAAGTTACATTTCAAAGG 57.335 33.333 0.00 0.00 37.25 3.11
5376 5489 7.203218 AGAAACTGAAGTTACATTTCAAAGGC 58.797 34.615 0.00 0.00 37.25 4.35
5377 5490 6.463995 AACTGAAGTTACATTTCAAAGGCA 57.536 33.333 0.00 0.00 36.32 4.75
5378 5491 6.655078 ACTGAAGTTACATTTCAAAGGCAT 57.345 33.333 0.00 0.00 34.41 4.40
5379 5492 6.449698 ACTGAAGTTACATTTCAAAGGCATG 58.550 36.000 0.00 0.00 34.41 4.06
5380 5493 6.040842 ACTGAAGTTACATTTCAAAGGCATGT 59.959 34.615 0.00 0.00 34.41 3.21
5381 5494 6.446318 TGAAGTTACATTTCAAAGGCATGTC 58.554 36.000 0.00 0.00 33.19 3.06
5382 5495 6.040278 TGAAGTTACATTTCAAAGGCATGTCA 59.960 34.615 0.00 0.00 33.19 3.58
5383 5496 6.403866 AGTTACATTTCAAAGGCATGTCAA 57.596 33.333 0.00 0.00 33.19 3.18
5384 5497 6.996509 AGTTACATTTCAAAGGCATGTCAAT 58.003 32.000 0.00 0.00 33.19 2.57
5385 5498 8.121305 AGTTACATTTCAAAGGCATGTCAATA 57.879 30.769 0.00 0.00 33.19 1.90
5386 5499 8.752187 AGTTACATTTCAAAGGCATGTCAATAT 58.248 29.630 0.00 0.00 33.19 1.28
5387 5500 9.023967 GTTACATTTCAAAGGCATGTCAATATC 57.976 33.333 0.00 0.00 33.19 1.63
5388 5501 6.267817 ACATTTCAAAGGCATGTCAATATCG 58.732 36.000 0.00 0.00 0.00 2.92
5389 5502 6.095300 ACATTTCAAAGGCATGTCAATATCGA 59.905 34.615 0.00 0.00 0.00 3.59
5390 5503 6.507958 TTTCAAAGGCATGTCAATATCGAA 57.492 33.333 0.00 0.00 0.00 3.71
5391 5504 6.507958 TTCAAAGGCATGTCAATATCGAAA 57.492 33.333 0.00 0.00 0.00 3.46
5392 5505 6.122850 TCAAAGGCATGTCAATATCGAAAG 57.877 37.500 0.00 0.00 0.00 2.62
5393 5506 5.647658 TCAAAGGCATGTCAATATCGAAAGT 59.352 36.000 0.00 0.00 0.00 2.66
5394 5507 5.741388 AAGGCATGTCAATATCGAAAGTC 57.259 39.130 0.00 0.00 0.00 3.01
5395 5508 5.028549 AGGCATGTCAATATCGAAAGTCT 57.971 39.130 0.00 0.00 0.00 3.24
5396 5509 5.053145 AGGCATGTCAATATCGAAAGTCTC 58.947 41.667 0.00 0.00 0.00 3.36
5397 5510 4.212214 GGCATGTCAATATCGAAAGTCTCC 59.788 45.833 0.00 0.00 0.00 3.71
5398 5511 5.053145 GCATGTCAATATCGAAAGTCTCCT 58.947 41.667 0.00 0.00 0.00 3.69
5399 5512 5.525378 GCATGTCAATATCGAAAGTCTCCTT 59.475 40.000 0.00 0.00 0.00 3.36
5400 5513 6.701841 GCATGTCAATATCGAAAGTCTCCTTA 59.298 38.462 0.00 0.00 0.00 2.69
5401 5514 7.224753 GCATGTCAATATCGAAAGTCTCCTTAA 59.775 37.037 0.00 0.00 0.00 1.85
5402 5515 9.265901 CATGTCAATATCGAAAGTCTCCTTAAT 57.734 33.333 0.00 0.00 0.00 1.40
5417 5530 8.903820 AGTCTCCTTAATAACAAATTACATGCC 58.096 33.333 0.00 0.00 0.00 4.40
5418 5531 8.903820 GTCTCCTTAATAACAAATTACATGCCT 58.096 33.333 0.00 0.00 0.00 4.75
5419 5532 9.120538 TCTCCTTAATAACAAATTACATGCCTC 57.879 33.333 0.00 0.00 0.00 4.70
5420 5533 9.125026 CTCCTTAATAACAAATTACATGCCTCT 57.875 33.333 0.00 0.00 0.00 3.69
5421 5534 9.120538 TCCTTAATAACAAATTACATGCCTCTC 57.879 33.333 0.00 0.00 0.00 3.20
5422 5535 9.125026 CCTTAATAACAAATTACATGCCTCTCT 57.875 33.333 0.00 0.00 0.00 3.10
5436 5549 8.305046 ACATGCCTCTCTATATATCTCTTTCC 57.695 38.462 0.00 0.00 0.00 3.13
5437 5550 8.121833 ACATGCCTCTCTATATATCTCTTTCCT 58.878 37.037 0.00 0.00 0.00 3.36
5438 5551 8.632679 CATGCCTCTCTATATATCTCTTTCCTC 58.367 40.741 0.00 0.00 0.00 3.71
5439 5552 7.122715 TGCCTCTCTATATATCTCTTTCCTCC 58.877 42.308 0.00 0.00 0.00 4.30
5440 5553 7.036205 TGCCTCTCTATATATCTCTTTCCTCCT 60.036 40.741 0.00 0.00 0.00 3.69
5441 5554 7.502561 GCCTCTCTATATATCTCTTTCCTCCTC 59.497 44.444 0.00 0.00 0.00 3.71
5442 5555 7.998964 CCTCTCTATATATCTCTTTCCTCCTCC 59.001 44.444 0.00 0.00 0.00 4.30
5443 5556 8.469924 TCTCTATATATCTCTTTCCTCCTCCA 57.530 38.462 0.00 0.00 0.00 3.86
5444 5557 8.333235 TCTCTATATATCTCTTTCCTCCTCCAC 58.667 40.741 0.00 0.00 0.00 4.02
5445 5558 8.001300 TCTATATATCTCTTTCCTCCTCCACA 57.999 38.462 0.00 0.00 0.00 4.17
5446 5559 8.456940 TCTATATATCTCTTTCCTCCTCCACAA 58.543 37.037 0.00 0.00 0.00 3.33
5447 5560 5.885449 ATATCTCTTTCCTCCTCCACAAG 57.115 43.478 0.00 0.00 0.00 3.16
5448 5561 3.260269 TCTCTTTCCTCCTCCACAAGA 57.740 47.619 0.00 0.00 0.00 3.02
5449 5562 3.587498 TCTCTTTCCTCCTCCACAAGAA 58.413 45.455 0.00 0.00 0.00 2.52
5450 5563 3.973973 TCTCTTTCCTCCTCCACAAGAAA 59.026 43.478 0.00 0.00 0.00 2.52
5451 5564 4.412199 TCTCTTTCCTCCTCCACAAGAAAA 59.588 41.667 0.00 0.00 0.00 2.29
5452 5565 4.718961 TCTTTCCTCCTCCACAAGAAAAG 58.281 43.478 0.00 0.00 0.00 2.27
5453 5566 2.568623 TCCTCCTCCACAAGAAAAGC 57.431 50.000 0.00 0.00 0.00 3.51
5454 5567 2.057922 TCCTCCTCCACAAGAAAAGCT 58.942 47.619 0.00 0.00 0.00 3.74
5455 5568 2.039084 TCCTCCTCCACAAGAAAAGCTC 59.961 50.000 0.00 0.00 0.00 4.09
5456 5569 2.039613 CCTCCTCCACAAGAAAAGCTCT 59.960 50.000 0.00 0.00 35.13 4.09
5457 5570 3.497584 CCTCCTCCACAAGAAAAGCTCTT 60.498 47.826 0.00 0.00 45.80 2.85
5458 5571 3.744660 TCCTCCACAAGAAAAGCTCTTC 58.255 45.455 0.00 0.00 42.84 2.87
5459 5572 3.392616 TCCTCCACAAGAAAAGCTCTTCT 59.607 43.478 0.00 0.00 42.84 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.890945 ACTCCAATTTGCCTGTGGTTAC 59.109 45.455 0.00 0.00 33.88 2.50
47 48 3.009115 TTCCTTGGGCTCTCCGGG 61.009 66.667 0.00 0.00 38.76 5.73
53 54 1.950954 GCCTGTTAGTTCCTTGGGCTC 60.951 57.143 0.00 0.00 35.73 4.70
56 64 2.286365 TTGCCTGTTAGTTCCTTGGG 57.714 50.000 0.00 0.00 0.00 4.12
63 71 7.066284 CAGAGCTGTTTATATTGCCTGTTAGTT 59.934 37.037 0.00 0.00 0.00 2.24
78 86 5.243507 TGATGCCAAAATTCAGAGCTGTTTA 59.756 36.000 0.00 0.00 0.00 2.01
150 161 2.706339 AGCTACCATGCCTCTTTGAG 57.294 50.000 0.00 0.00 0.00 3.02
186 200 2.358737 CGCCTTCCCGAGCTGTTT 60.359 61.111 0.00 0.00 0.00 2.83
208 222 3.102204 TCAACTCTCATCCTCATGCTCA 58.898 45.455 0.00 0.00 0.00 4.26
214 228 3.746792 TCCTCTCAACTCTCATCCTCA 57.253 47.619 0.00 0.00 0.00 3.86
226 240 2.094700 CGGACTCGTGATTTCCTCTCAA 60.095 50.000 0.00 0.00 0.00 3.02
227 241 1.472878 CGGACTCGTGATTTCCTCTCA 59.527 52.381 0.00 0.00 0.00 3.27
228 242 1.202313 CCGGACTCGTGATTTCCTCTC 60.202 57.143 0.00 0.00 33.95 3.20
229 243 0.818296 CCGGACTCGTGATTTCCTCT 59.182 55.000 0.00 0.00 33.95 3.69
230 244 0.806492 GCCGGACTCGTGATTTCCTC 60.806 60.000 5.05 0.00 33.95 3.71
231 245 1.218316 GCCGGACTCGTGATTTCCT 59.782 57.895 5.05 0.00 33.95 3.36
232 246 0.672401 TTGCCGGACTCGTGATTTCC 60.672 55.000 5.05 0.00 33.95 3.13
319 333 2.506438 GAGGTACGAGGCGCACAC 60.506 66.667 10.83 0.00 0.00 3.82
368 382 2.975167 TTTTCTTTGTCGTGCGCCGC 62.975 55.000 4.18 0.00 36.19 6.53
369 383 0.991770 CTTTTCTTTGTCGTGCGCCG 60.992 55.000 4.18 8.64 38.13 6.46
370 384 1.268778 GCTTTTCTTTGTCGTGCGCC 61.269 55.000 4.18 0.00 0.00 6.53
371 385 1.588305 CGCTTTTCTTTGTCGTGCGC 61.588 55.000 0.00 0.00 35.77 6.09
372 386 0.991770 CCGCTTTTCTTTGTCGTGCG 60.992 55.000 0.00 0.00 41.30 5.34
373 387 0.660300 CCCGCTTTTCTTTGTCGTGC 60.660 55.000 0.00 0.00 0.00 5.34
374 388 0.040425 CCCCGCTTTTCTTTGTCGTG 60.040 55.000 0.00 0.00 0.00 4.35
375 389 1.170290 CCCCCGCTTTTCTTTGTCGT 61.170 55.000 0.00 0.00 0.00 4.34
376 390 1.170290 ACCCCCGCTTTTCTTTGTCG 61.170 55.000 0.00 0.00 0.00 4.35
377 391 0.313987 CACCCCCGCTTTTCTTTGTC 59.686 55.000 0.00 0.00 0.00 3.18
378 392 0.106419 TCACCCCCGCTTTTCTTTGT 60.106 50.000 0.00 0.00 0.00 2.83
379 393 0.598065 CTCACCCCCGCTTTTCTTTG 59.402 55.000 0.00 0.00 0.00 2.77
380 394 1.179174 GCTCACCCCCGCTTTTCTTT 61.179 55.000 0.00 0.00 0.00 2.52
381 395 1.603739 GCTCACCCCCGCTTTTCTT 60.604 57.895 0.00 0.00 0.00 2.52
382 396 2.034221 GCTCACCCCCGCTTTTCT 59.966 61.111 0.00 0.00 0.00 2.52
383 397 3.431725 CGCTCACCCCCGCTTTTC 61.432 66.667 0.00 0.00 0.00 2.29
402 416 1.010797 CCATTTGATCGAAGCCGCG 60.011 57.895 0.00 0.00 35.37 6.46
413 427 1.737838 GCGATCTGTGGACCATTTGA 58.262 50.000 0.00 0.00 0.00 2.69
423 437 0.806102 CCAACCTACCGCGATCTGTG 60.806 60.000 8.23 0.00 0.00 3.66
424 438 1.255667 ACCAACCTACCGCGATCTGT 61.256 55.000 8.23 0.00 0.00 3.41
427 442 1.520787 CCACCAACCTACCGCGATC 60.521 63.158 8.23 0.00 0.00 3.69
452 467 0.322816 TCCTACAAGGTACGCCGACT 60.323 55.000 0.00 0.00 40.50 4.18
620 651 2.363361 CCCTCCACCTCTACGGGT 59.637 66.667 0.00 0.00 40.73 5.28
621 652 3.155167 GCCCTCCACCTCTACGGG 61.155 72.222 0.00 0.00 36.97 5.28
622 653 3.155167 GGCCCTCCACCTCTACGG 61.155 72.222 0.00 0.00 39.35 4.02
623 654 3.528370 CGGCCCTCCACCTCTACG 61.528 72.222 0.00 0.00 0.00 3.51
624 655 2.363925 ACGGCCCTCCACCTCTAC 60.364 66.667 0.00 0.00 0.00 2.59
625 656 2.043248 GACGGCCCTCCACCTCTA 60.043 66.667 0.00 0.00 0.00 2.43
630 661 3.775654 CTCTGGACGGCCCTCCAC 61.776 72.222 18.55 0.00 35.23 4.02
633 664 3.775654 CACCTCTGGACGGCCCTC 61.776 72.222 3.83 0.00 35.38 4.30
642 673 4.181010 CGCCCCATCCACCTCTGG 62.181 72.222 0.00 0.00 39.23 3.86
643 674 3.391665 GACGCCCCATCCACCTCTG 62.392 68.421 0.00 0.00 0.00 3.35
665 696 1.601419 GACACCCCATCTCCGTCGAA 61.601 60.000 0.00 0.00 0.00 3.71
695 726 2.461637 CCCCCTCCCCTCCTCTTT 59.538 66.667 0.00 0.00 0.00 2.52
719 754 2.291043 ATCCCAAGTCGCCGTCCTT 61.291 57.895 0.00 0.00 0.00 3.36
769 804 1.884075 AACCATCAGCCGTCGCTACA 61.884 55.000 0.00 0.00 46.25 2.74
787 822 2.975799 GCCGTCGTTTCAGCCCAA 60.976 61.111 0.00 0.00 0.00 4.12
850 888 4.680537 AGAGGCCCACGACGACCT 62.681 66.667 0.00 2.26 34.43 3.85
870 911 2.575461 GACCCTTACCCGTCCACG 59.425 66.667 0.00 0.00 39.44 4.94
879 920 1.448013 GTCCAGCTGCGACCCTTAC 60.448 63.158 19.08 0.64 0.00 2.34
975 1039 4.717313 GTCGGAGTTGGTGGGGGC 62.717 72.222 0.00 0.00 0.00 5.80
1071 1135 1.211969 GAGAGCAAGCGTCCACGTA 59.788 57.895 0.36 0.00 42.22 3.57
1367 1439 1.798223 CCGCTCAACTGATTCAAACGA 59.202 47.619 0.00 0.00 0.00 3.85
1383 1455 0.314935 CAGCAAAACATGGAACCGCT 59.685 50.000 0.00 0.00 0.00 5.52
1621 1695 3.939740 ATCAGGCAATCAGGTGTACAT 57.060 42.857 0.00 0.00 0.00 2.29
1712 1787 5.339200 CCCTAGGAATTAAGGCAAAGTGAGA 60.339 44.000 11.48 0.00 0.00 3.27
1805 1880 1.899814 TCTGTGCCCACTAACTACAGG 59.100 52.381 0.00 0.00 39.27 4.00
2358 2434 2.351350 GCGGGGCGAATTATGGTAATTG 60.351 50.000 0.05 0.00 0.00 2.32
2378 2454 4.038642 CCTCCAGAAGAATAGACTACCTGC 59.961 50.000 0.00 0.00 0.00 4.85
2664 2740 3.488553 CCTTCAAACGTTCCTTGTTCCAC 60.489 47.826 0.00 0.00 0.00 4.02
2829 2905 5.130311 TCCCTCTGATCCGAATTAATTGACA 59.870 40.000 5.17 0.00 0.00 3.58
2847 2923 4.661247 ACACAGACTAACTACTCCCTCT 57.339 45.455 0.00 0.00 0.00 3.69
2863 2939 4.574828 CGGGGATAATTCCAGTTTACACAG 59.425 45.833 0.00 0.00 44.60 3.66
2882 2958 5.821516 TTAAATAACTGTTACATGCGGGG 57.178 39.130 1.73 0.00 0.00 5.73
3099 3176 1.000607 TGTGTGTCGTAAGTCTCCAGC 60.001 52.381 0.00 0.00 39.48 4.85
3135 3212 3.145551 CAGCAGGCAGGGGCAATC 61.146 66.667 0.00 0.00 43.71 2.67
3240 3317 6.092807 CAGGAACAGAAGGTCAATAGTTAAGC 59.907 42.308 0.00 0.00 0.00 3.09
3269 3346 6.483307 CGTCCATGTGTCCATAGATTAACAAT 59.517 38.462 0.00 0.00 0.00 2.71
3314 3391 7.552050 AAATTTTATTGGATCAGTTGACCCA 57.448 32.000 0.00 0.00 35.45 4.51
3403 3481 3.377253 AACACTCAATGGGCTCATCAT 57.623 42.857 0.00 0.00 32.24 2.45
3404 3482 2.885135 AACACTCAATGGGCTCATCA 57.115 45.000 0.00 0.00 32.24 3.07
3457 3535 4.456911 AGCAACCTGTGTGATGTCATTTAG 59.543 41.667 0.00 0.00 0.00 1.85
3461 3539 2.574006 AGCAACCTGTGTGATGTCAT 57.426 45.000 0.00 0.00 0.00 3.06
3508 3586 4.724074 TGGTAGTTACTTCACGTATGGG 57.276 45.455 0.00 0.00 0.00 4.00
3573 3651 6.534793 ACAACAAGTCAGGCAACAATTTAAAG 59.465 34.615 0.00 0.00 41.41 1.85
3603 3681 5.067153 TGCATAGGTGGCATTAAACATACAC 59.933 40.000 0.00 0.00 36.11 2.90
3687 3772 1.559368 CCTGCCCATGAATGGTTTCA 58.441 50.000 8.49 3.05 46.65 2.69
3808 3898 2.203126 GAAGCTGGGCCAGGATCG 60.203 66.667 33.43 10.66 31.21 3.69
3876 3966 9.448438 GAGAACAAAAGGGCCATTATTAAAATT 57.552 29.630 1.49 0.00 0.00 1.82
3890 3980 3.947910 ACATGCATGAGAACAAAAGGG 57.052 42.857 32.75 1.77 0.00 3.95
3949 4043 3.822735 AGGCACAAGTACTTACACTCGTA 59.177 43.478 8.04 0.00 0.00 3.43
3950 4044 2.626743 AGGCACAAGTACTTACACTCGT 59.373 45.455 8.04 0.00 0.00 4.18
3951 4045 3.057456 AGAGGCACAAGTACTTACACTCG 60.057 47.826 8.04 0.00 0.00 4.18
3952 4046 4.522722 AGAGGCACAAGTACTTACACTC 57.477 45.455 8.04 12.90 0.00 3.51
3953 4047 4.957684 AAGAGGCACAAGTACTTACACT 57.042 40.909 8.04 4.50 0.00 3.55
3954 4048 6.221659 AGTAAAGAGGCACAAGTACTTACAC 58.778 40.000 8.04 0.11 0.00 2.90
3956 4050 7.573627 CAAAGTAAAGAGGCACAAGTACTTAC 58.426 38.462 8.04 0.86 32.83 2.34
3957 4051 6.204108 GCAAAGTAAAGAGGCACAAGTACTTA 59.796 38.462 8.04 0.00 32.83 2.24
4295 4396 9.512588 AACCATATAGCAATCTCTATTGGAAAG 57.487 33.333 13.62 0.00 42.39 2.62
4391 4492 3.951680 CGGGGCTTGTACTTTGGAAATAT 59.048 43.478 0.00 0.00 0.00 1.28
4392 4493 3.349022 CGGGGCTTGTACTTTGGAAATA 58.651 45.455 0.00 0.00 0.00 1.40
4423 4524 2.557229 CCACCTTCCATCATTGGTCCAA 60.557 50.000 6.80 6.80 44.06 3.53
4429 4530 2.756760 CCTTGACCACCTTCCATCATTG 59.243 50.000 0.00 0.00 0.00 2.82
4438 4539 0.846693 AAGAGTGCCTTGACCACCTT 59.153 50.000 0.00 0.00 32.92 3.50
4463 4564 6.778821 TGGATGACAAGACAGGAAAAAGATA 58.221 36.000 0.00 0.00 0.00 1.98
4467 4568 5.010922 CCAATGGATGACAAGACAGGAAAAA 59.989 40.000 0.00 0.00 0.00 1.94
4540 4642 1.486310 TGGAGGAAATGACTGGGATCG 59.514 52.381 0.00 0.00 0.00 3.69
4548 4650 4.261197 GCGTATGGAAATGGAGGAAATGAC 60.261 45.833 0.00 0.00 0.00 3.06
4623 4725 4.634004 CAGCATACATTTACGGAAGAACCA 59.366 41.667 0.00 0.00 38.90 3.67
4721 4825 5.278957 CCGACCAAATCAAATTTCAGAGGTT 60.279 40.000 0.00 0.00 28.51 3.50
4734 4838 4.985409 GCAAACATTTAACCGACCAAATCA 59.015 37.500 0.00 0.00 0.00 2.57
4799 4903 0.999712 AAAATCACCCGACCCATCCT 59.000 50.000 0.00 0.00 0.00 3.24
4801 4905 3.250040 CGAATAAAATCACCCGACCCATC 59.750 47.826 0.00 0.00 0.00 3.51
4802 4906 3.211045 CGAATAAAATCACCCGACCCAT 58.789 45.455 0.00 0.00 0.00 4.00
4803 4907 2.634600 CGAATAAAATCACCCGACCCA 58.365 47.619 0.00 0.00 0.00 4.51
4816 4920 4.202264 ACATTGCAAACAACCCCGAATAAA 60.202 37.500 1.71 0.00 38.99 1.40
4926 5030 2.403252 AGAATCTGTTTAGTGGGGCG 57.597 50.000 0.00 0.00 0.00 6.13
5012 5116 6.863126 CACATTTCCAAGTAGTGTCCAAATTC 59.137 38.462 0.00 0.00 0.00 2.17
5059 5163 2.596346 AGCACCATTCAAATCACACCA 58.404 42.857 0.00 0.00 0.00 4.17
5063 5167 3.378427 GGGACTAGCACCATTCAAATCAC 59.622 47.826 8.49 0.00 0.00 3.06
5167 5273 9.781834 TCGTTATTTTGCATTAGTATTTTCTGG 57.218 29.630 0.00 0.00 0.00 3.86
5191 5299 8.126700 GGAGGTAATACAACAACCATAAAATCG 58.873 37.037 0.00 0.00 35.64 3.34
5204 5312 9.551734 AATAATTTAGGACGGAGGTAATACAAC 57.448 33.333 0.00 0.00 0.00 3.32
5313 5426 7.013846 TGTCCCAAACTATTTGTCTTAGGTTTG 59.986 37.037 0.00 0.00 38.98 2.93
5317 5430 6.472887 TCTGTCCCAAACTATTTGTCTTAGG 58.527 40.000 0.97 0.00 38.98 2.69
5318 5431 7.119846 CCTTCTGTCCCAAACTATTTGTCTTAG 59.880 40.741 0.97 0.00 38.98 2.18
5319 5432 6.940298 CCTTCTGTCCCAAACTATTTGTCTTA 59.060 38.462 0.97 0.00 38.98 2.10
5320 5433 5.770162 CCTTCTGTCCCAAACTATTTGTCTT 59.230 40.000 0.97 0.00 38.98 3.01
5321 5434 5.073144 TCCTTCTGTCCCAAACTATTTGTCT 59.927 40.000 0.97 0.00 38.98 3.41
5322 5435 5.313712 TCCTTCTGTCCCAAACTATTTGTC 58.686 41.667 0.97 0.00 38.98 3.18
5323 5436 5.163088 ACTCCTTCTGTCCCAAACTATTTGT 60.163 40.000 0.97 0.00 38.98 2.83
5324 5437 5.316987 ACTCCTTCTGTCCCAAACTATTTG 58.683 41.667 0.00 0.00 40.32 2.32
5325 5438 5.584551 ACTCCTTCTGTCCCAAACTATTT 57.415 39.130 0.00 0.00 0.00 1.40
5326 5439 5.785940 ACTACTCCTTCTGTCCCAAACTATT 59.214 40.000 0.00 0.00 0.00 1.73
5327 5440 5.342866 ACTACTCCTTCTGTCCCAAACTAT 58.657 41.667 0.00 0.00 0.00 2.12
5328 5441 4.748701 ACTACTCCTTCTGTCCCAAACTA 58.251 43.478 0.00 0.00 0.00 2.24
5329 5442 3.588569 ACTACTCCTTCTGTCCCAAACT 58.411 45.455 0.00 0.00 0.00 2.66
5330 5443 4.771054 TCTACTACTCCTTCTGTCCCAAAC 59.229 45.833 0.00 0.00 0.00 2.93
5331 5444 5.006896 TCTACTACTCCTTCTGTCCCAAA 57.993 43.478 0.00 0.00 0.00 3.28
5332 5445 4.669866 TCTACTACTCCTTCTGTCCCAA 57.330 45.455 0.00 0.00 0.00 4.12
5333 5446 4.669866 TTCTACTACTCCTTCTGTCCCA 57.330 45.455 0.00 0.00 0.00 4.37
5334 5447 5.018149 AGTTTCTACTACTCCTTCTGTCCC 58.982 45.833 0.00 0.00 31.21 4.46
5335 5448 5.711036 TCAGTTTCTACTACTCCTTCTGTCC 59.289 44.000 0.00 0.00 31.96 4.02
5336 5449 6.821031 TCAGTTTCTACTACTCCTTCTGTC 57.179 41.667 0.00 0.00 31.96 3.51
5337 5450 6.778559 ACTTCAGTTTCTACTACTCCTTCTGT 59.221 38.462 0.00 0.00 31.96 3.41
5338 5451 7.222000 ACTTCAGTTTCTACTACTCCTTCTG 57.778 40.000 0.00 0.00 31.96 3.02
5339 5452 7.842887 AACTTCAGTTTCTACTACTCCTTCT 57.157 36.000 0.00 0.00 33.93 2.85
5340 5453 8.574737 TGTAACTTCAGTTTCTACTACTCCTTC 58.425 37.037 0.00 0.00 39.31 3.46
5341 5454 8.474710 TGTAACTTCAGTTTCTACTACTCCTT 57.525 34.615 0.00 0.00 39.31 3.36
5342 5455 8.653036 ATGTAACTTCAGTTTCTACTACTCCT 57.347 34.615 0.00 0.00 39.31 3.69
5343 5456 9.708092 AAATGTAACTTCAGTTTCTACTACTCC 57.292 33.333 0.00 0.00 39.31 3.85
5349 5462 9.665264 CCTTTGAAATGTAACTTCAGTTTCTAC 57.335 33.333 0.00 0.00 39.31 2.59
5350 5463 8.349983 GCCTTTGAAATGTAACTTCAGTTTCTA 58.650 33.333 0.00 0.00 39.31 2.10
5351 5464 7.147915 TGCCTTTGAAATGTAACTTCAGTTTCT 60.148 33.333 0.00 0.00 39.31 2.52
5352 5465 6.978080 TGCCTTTGAAATGTAACTTCAGTTTC 59.022 34.615 0.00 0.00 39.31 2.78
5353 5466 6.872920 TGCCTTTGAAATGTAACTTCAGTTT 58.127 32.000 0.00 0.00 39.31 2.66
5354 5467 6.463995 TGCCTTTGAAATGTAACTTCAGTT 57.536 33.333 0.00 0.00 41.73 3.16
5355 5468 6.040842 ACATGCCTTTGAAATGTAACTTCAGT 59.959 34.615 0.00 0.00 32.86 3.41
5356 5469 6.449698 ACATGCCTTTGAAATGTAACTTCAG 58.550 36.000 0.00 0.00 32.86 3.02
5357 5470 6.040278 TGACATGCCTTTGAAATGTAACTTCA 59.960 34.615 0.00 0.00 34.74 3.02
5358 5471 6.446318 TGACATGCCTTTGAAATGTAACTTC 58.554 36.000 0.00 0.00 34.74 3.01
5359 5472 6.403866 TGACATGCCTTTGAAATGTAACTT 57.596 33.333 0.00 0.00 34.74 2.66
5360 5473 6.403866 TTGACATGCCTTTGAAATGTAACT 57.596 33.333 0.00 0.00 34.74 2.24
5361 5474 8.931385 ATATTGACATGCCTTTGAAATGTAAC 57.069 30.769 0.00 0.00 34.74 2.50
5362 5475 7.914871 CGATATTGACATGCCTTTGAAATGTAA 59.085 33.333 0.00 0.00 34.74 2.41
5363 5476 7.281999 TCGATATTGACATGCCTTTGAAATGTA 59.718 33.333 0.00 0.00 34.74 2.29
5364 5477 6.095300 TCGATATTGACATGCCTTTGAAATGT 59.905 34.615 0.00 0.00 37.24 2.71
5365 5478 6.497437 TCGATATTGACATGCCTTTGAAATG 58.503 36.000 0.00 0.00 0.00 2.32
5366 5479 6.698008 TCGATATTGACATGCCTTTGAAAT 57.302 33.333 0.00 0.00 0.00 2.17
5367 5480 6.507958 TTCGATATTGACATGCCTTTGAAA 57.492 33.333 0.00 0.00 0.00 2.69
5368 5481 6.150976 ACTTTCGATATTGACATGCCTTTGAA 59.849 34.615 0.00 0.00 0.00 2.69
5369 5482 5.647658 ACTTTCGATATTGACATGCCTTTGA 59.352 36.000 0.00 0.00 0.00 2.69
5370 5483 5.883661 ACTTTCGATATTGACATGCCTTTG 58.116 37.500 0.00 0.00 0.00 2.77
5371 5484 5.882557 AGACTTTCGATATTGACATGCCTTT 59.117 36.000 0.00 0.00 0.00 3.11
5372 5485 5.431765 AGACTTTCGATATTGACATGCCTT 58.568 37.500 0.00 0.00 0.00 4.35
5373 5486 5.028549 AGACTTTCGATATTGACATGCCT 57.971 39.130 0.00 0.00 0.00 4.75
5374 5487 4.212214 GGAGACTTTCGATATTGACATGCC 59.788 45.833 0.00 0.00 0.00 4.40
5375 5488 5.053145 AGGAGACTTTCGATATTGACATGC 58.947 41.667 0.00 0.00 37.44 4.06
5392 5505 8.903820 AGGCATGTAATTTGTTATTAAGGAGAC 58.096 33.333 0.00 0.00 0.00 3.36
5393 5506 9.120538 GAGGCATGTAATTTGTTATTAAGGAGA 57.879 33.333 0.00 0.00 0.00 3.71
5394 5507 9.125026 AGAGGCATGTAATTTGTTATTAAGGAG 57.875 33.333 0.00 0.00 0.00 3.69
5395 5508 9.120538 GAGAGGCATGTAATTTGTTATTAAGGA 57.879 33.333 0.00 0.00 0.00 3.36
5396 5509 9.125026 AGAGAGGCATGTAATTTGTTATTAAGG 57.875 33.333 0.00 0.00 0.00 2.69
5410 5523 9.415008 GGAAAGAGATATATAGAGAGGCATGTA 57.585 37.037 0.00 0.00 0.00 2.29
5411 5524 8.121833 AGGAAAGAGATATATAGAGAGGCATGT 58.878 37.037 0.00 0.00 0.00 3.21
5412 5525 8.537728 AGGAAAGAGATATATAGAGAGGCATG 57.462 38.462 0.00 0.00 0.00 4.06
5413 5526 7.784550 GGAGGAAAGAGATATATAGAGAGGCAT 59.215 40.741 0.00 0.00 0.00 4.40
5414 5527 7.036205 AGGAGGAAAGAGATATATAGAGAGGCA 60.036 40.741 0.00 0.00 0.00 4.75
5415 5528 7.354312 AGGAGGAAAGAGATATATAGAGAGGC 58.646 42.308 0.00 0.00 0.00 4.70
5416 5529 7.998964 GGAGGAGGAAAGAGATATATAGAGAGG 59.001 44.444 0.00 0.00 0.00 3.69
5417 5530 8.556589 TGGAGGAGGAAAGAGATATATAGAGAG 58.443 40.741 0.00 0.00 0.00 3.20
5418 5531 8.333235 GTGGAGGAGGAAAGAGATATATAGAGA 58.667 40.741 0.00 0.00 0.00 3.10
5419 5532 8.112822 TGTGGAGGAGGAAAGAGATATATAGAG 58.887 40.741 0.00 0.00 0.00 2.43
5420 5533 8.001300 TGTGGAGGAGGAAAGAGATATATAGA 57.999 38.462 0.00 0.00 0.00 1.98
5421 5534 8.657387 TTGTGGAGGAGGAAAGAGATATATAG 57.343 38.462 0.00 0.00 0.00 1.31
5422 5535 8.456940 TCTTGTGGAGGAGGAAAGAGATATATA 58.543 37.037 0.00 0.00 0.00 0.86
5423 5536 7.309091 TCTTGTGGAGGAGGAAAGAGATATAT 58.691 38.462 0.00 0.00 0.00 0.86
5424 5537 6.683537 TCTTGTGGAGGAGGAAAGAGATATA 58.316 40.000 0.00 0.00 0.00 0.86
5425 5538 5.533112 TCTTGTGGAGGAGGAAAGAGATAT 58.467 41.667 0.00 0.00 0.00 1.63
5426 5539 4.947883 TCTTGTGGAGGAGGAAAGAGATA 58.052 43.478 0.00 0.00 0.00 1.98
5427 5540 3.796111 TCTTGTGGAGGAGGAAAGAGAT 58.204 45.455 0.00 0.00 0.00 2.75
5428 5541 3.260269 TCTTGTGGAGGAGGAAAGAGA 57.740 47.619 0.00 0.00 0.00 3.10
5429 5542 4.357918 TTTCTTGTGGAGGAGGAAAGAG 57.642 45.455 0.00 0.00 0.00 2.85
5430 5543 4.718961 CTTTTCTTGTGGAGGAGGAAAGA 58.281 43.478 0.00 0.00 0.00 2.52
5431 5544 3.254411 GCTTTTCTTGTGGAGGAGGAAAG 59.746 47.826 0.00 0.00 0.00 2.62
5432 5545 3.117512 AGCTTTTCTTGTGGAGGAGGAAA 60.118 43.478 0.00 0.00 0.00 3.13
5433 5546 2.443255 AGCTTTTCTTGTGGAGGAGGAA 59.557 45.455 0.00 0.00 0.00 3.36
5434 5547 2.039084 GAGCTTTTCTTGTGGAGGAGGA 59.961 50.000 0.00 0.00 0.00 3.71
5435 5548 2.039613 AGAGCTTTTCTTGTGGAGGAGG 59.960 50.000 0.00 0.00 29.61 4.30
5436 5549 3.415457 AGAGCTTTTCTTGTGGAGGAG 57.585 47.619 0.00 0.00 29.61 3.69
5437 5550 3.392616 AGAAGAGCTTTTCTTGTGGAGGA 59.607 43.478 13.53 0.00 46.12 3.71
5438 5551 3.749226 AGAAGAGCTTTTCTTGTGGAGG 58.251 45.455 13.53 0.00 46.12 4.30


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

AutoCloner maintained by Alex Coulton.