Multiple sequence alignment - TraesCS5D01G533900

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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 TraesCS5D01G533900 chr5D 100.000 4283 0 0 1 4283 548276744 548281026 0.000000e+00 7910
1 TraesCS5D01G533900 chr6B 87.684 2038 237 12 1527 3562 164043328 164045353 0.000000e+00 2361
2 TraesCS5D01G533900 chr6B 75.817 3395 743 69 200 3552 50337650 50341008 0.000000e+00 1650
3 TraesCS5D01G533900 chr6B 74.914 3476 778 77 117 3550 583293299 583296722 0.000000e+00 1502
4 TraesCS5D01G533900 chr4B 75.638 3604 775 85 1 3552 448807312 448810864 0.000000e+00 1696
5 TraesCS5D01G533900 chr4D 96.266 723 25 2 3558 4280 47308922 47309642 0.000000e+00 1184
6 TraesCS5D01G533900 chr4D 94.562 662 36 0 2901 3562 47308204 47308865 0.000000e+00 1024
7 TraesCS5D01G533900 chr1A 75.226 2430 536 53 206 2600 6302776 6305174 0.000000e+00 1092
8 TraesCS5D01G533900 chr7A 76.972 1559 335 19 2004 3552 644731919 644730375 0.000000e+00 869
9 TraesCS5D01G533900 chr7A 74.862 724 177 5 3558 4280 404499484 404500203 1.490000e-84 324
10 TraesCS5D01G533900 chr7A 78.281 221 36 10 1917 2131 50594198 50593984 9.660000e-27 132
11 TraesCS5D01G533900 chr5B 74.146 1756 409 40 1817 3552 257907742 257906012 0.000000e+00 686
12 TraesCS5D01G533900 chr5B 76.236 728 159 12 3561 4282 309671359 309672078 1.450000e-99 374
13 TraesCS5D01G533900 chr5B 76.264 712 153 15 3580 4283 642843261 642842558 8.750000e-97 364
14 TraesCS5D01G533900 chr1B 73.923 1764 417 38 1808 3552 279518029 279519768 0.000000e+00 669
15 TraesCS5D01G533900 chr7B 74.568 1506 353 26 2059 3552 739555809 739557296 2.170000e-177 632
16 TraesCS5D01G533900 chr4A 73.879 1673 398 34 1898 3552 565427288 565425637 2.170000e-177 632
17 TraesCS5D01G533900 chr4A 74.776 559 118 19 3679 4226 47734546 47734000 3.330000e-56 230
18 TraesCS5D01G533900 chr4A 73.703 559 124 19 3679 4226 563448312 563448858 3.380000e-46 196
19 TraesCS5D01G533900 chr7D 72.105 1373 327 47 1384 2726 113763128 113764474 3.150000e-96 363
20 TraesCS5D01G533900 chr3A 75.207 726 178 2 3558 4283 727541875 727541152 4.100000e-90 342
21 TraesCS5D01G533900 chr3A 72.291 729 167 19 3559 4278 724218305 724217603 1.220000e-45 195
22 TraesCS5D01G533900 chr2A 72.018 1308 311 47 2059 3340 492822397 492823675 1.910000e-88 337
23 TraesCS5D01G533900 chr2A 75.397 630 138 16 3646 4267 767395065 767395685 5.420000e-74 289
24 TraesCS5D01G533900 chr5A 74.240 559 121 19 3679 4226 569312894 569313440 3.350000e-51 213


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 TraesCS5D01G533900 chr5D 548276744 548281026 4282 False 7910 7910 100.000 1 4283 1 chr5D.!!$F1 4282
1 TraesCS5D01G533900 chr6B 164043328 164045353 2025 False 2361 2361 87.684 1527 3562 1 chr6B.!!$F2 2035
2 TraesCS5D01G533900 chr6B 50337650 50341008 3358 False 1650 1650 75.817 200 3552 1 chr6B.!!$F1 3352
3 TraesCS5D01G533900 chr6B 583293299 583296722 3423 False 1502 1502 74.914 117 3550 1 chr6B.!!$F3 3433
4 TraesCS5D01G533900 chr4B 448807312 448810864 3552 False 1696 1696 75.638 1 3552 1 chr4B.!!$F1 3551
5 TraesCS5D01G533900 chr4D 47308204 47309642 1438 False 1104 1184 95.414 2901 4280 2 chr4D.!!$F1 1379
6 TraesCS5D01G533900 chr1A 6302776 6305174 2398 False 1092 1092 75.226 206 2600 1 chr1A.!!$F1 2394
7 TraesCS5D01G533900 chr7A 644730375 644731919 1544 True 869 869 76.972 2004 3552 1 chr7A.!!$R2 1548
8 TraesCS5D01G533900 chr7A 404499484 404500203 719 False 324 324 74.862 3558 4280 1 chr7A.!!$F1 722
9 TraesCS5D01G533900 chr5B 257906012 257907742 1730 True 686 686 74.146 1817 3552 1 chr5B.!!$R1 1735
10 TraesCS5D01G533900 chr5B 309671359 309672078 719 False 374 374 76.236 3561 4282 1 chr5B.!!$F1 721
11 TraesCS5D01G533900 chr5B 642842558 642843261 703 True 364 364 76.264 3580 4283 1 chr5B.!!$R2 703
12 TraesCS5D01G533900 chr1B 279518029 279519768 1739 False 669 669 73.923 1808 3552 1 chr1B.!!$F1 1744
13 TraesCS5D01G533900 chr7B 739555809 739557296 1487 False 632 632 74.568 2059 3552 1 chr7B.!!$F1 1493
14 TraesCS5D01G533900 chr4A 565425637 565427288 1651 True 632 632 73.879 1898 3552 1 chr4A.!!$R2 1654
15 TraesCS5D01G533900 chr4A 47734000 47734546 546 True 230 230 74.776 3679 4226 1 chr4A.!!$R1 547
16 TraesCS5D01G533900 chr7D 113763128 113764474 1346 False 363 363 72.105 1384 2726 1 chr7D.!!$F1 1342
17 TraesCS5D01G533900 chr3A 727541152 727541875 723 True 342 342 75.207 3558 4283 1 chr3A.!!$R2 725
18 TraesCS5D01G533900 chr2A 492822397 492823675 1278 False 337 337 72.018 2059 3340 1 chr2A.!!$F1 1281
19 TraesCS5D01G533900 chr2A 767395065 767395685 620 False 289 289 75.397 3646 4267 1 chr2A.!!$F2 621
20 TraesCS5D01G533900 chr5A 569312894 569313440 546 False 213 213 74.240 3679 4226 1 chr5A.!!$F1 547

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
402 403 0.037303 CATGGGAGTGTGTTCCTGCT 59.963 55.0 0.00 0.0 37.40 4.24 F
825 827 0.039035 GTGGCCTGGTTGGGATTACA 59.961 55.0 3.32 0.0 36.00 2.41 F
1151 1162 0.179161 CGTCTACTGCCAACCGAGAG 60.179 60.0 0.00 0.0 0.00 3.20 F
1251 1262 0.252467 AGGAAGAGGACACCCAGGAG 60.252 60.0 0.00 0.0 33.88 3.69 F
1285 1296 0.475906 AGTGCCTCTGAAGCCAGTTT 59.524 50.0 0.00 0.0 41.16 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2265 2288 0.034477 CCCCACACAGAATACCACCC 60.034 60.000 0.00 0.0 0.00 4.61 R
2754 2780 0.830648 CCTCATCACCCGAGGCTAAA 59.169 55.000 0.00 0.0 43.50 1.85 R
2791 2817 3.146847 GGTCAAACCGAAATTCTCTGGT 58.853 45.455 0.00 0.0 33.92 4.00 R
2989 3015 9.593134 CTCTTCTAGCATGTATAATTCCATACC 57.407 37.037 0.00 0.0 31.52 2.73 R
3282 3308 2.206576 CTGGGCCAACTAGCTCTTTT 57.793 50.000 8.04 0.0 33.00 2.27 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
21 22 2.434359 GGCGACTCCGGGTTTGAG 60.434 66.667 0.00 0.00 36.06 3.02
23 24 1.218316 GCGACTCCGGGTTTGAGAT 59.782 57.895 0.00 0.00 36.06 2.75
30 31 2.639839 CTCCGGGTTTGAGATATGGGAT 59.360 50.000 0.00 0.00 31.26 3.85
33 34 3.557898 CCGGGTTTGAGATATGGGATGAG 60.558 52.174 0.00 0.00 0.00 2.90
45 46 3.928779 GATGAGGCGGCCGATGGA 61.929 66.667 33.48 9.91 0.00 3.41
47 48 2.738213 GATGAGGCGGCCGATGGAAT 62.738 60.000 33.48 15.06 0.00 3.01
51 52 3.957535 GCGGCCGATGGAATGCAG 61.958 66.667 33.48 0.00 0.00 4.41
52 53 3.282157 CGGCCGATGGAATGCAGG 61.282 66.667 24.07 0.00 0.00 4.85
53 54 3.599704 GGCCGATGGAATGCAGGC 61.600 66.667 2.37 2.37 46.51 4.85
54 55 2.517875 GCCGATGGAATGCAGGCT 60.518 61.111 3.76 0.00 44.06 4.58
56 57 2.719979 CGATGGAATGCAGGCTGC 59.280 61.111 31.91 31.91 45.29 5.25
57 58 1.822613 CGATGGAATGCAGGCTGCT 60.823 57.895 36.50 20.70 45.31 4.24
61 62 1.273986 TGGAATGCAGGCTGCTCCTA 61.274 55.000 34.23 23.37 45.52 2.94
71 72 1.261238 GCTGCTCCTACTCACCAGGT 61.261 60.000 0.00 0.00 34.56 4.00
73 74 1.219393 GCTCCTACTCACCAGGTGC 59.781 63.158 15.64 0.00 43.25 5.01
119 120 2.507452 CCATCCGCATGAGCCTGA 59.493 61.111 0.00 0.00 37.52 3.86
127 128 0.593618 GCATGAGCCTGATGATGCAG 59.406 55.000 1.97 0.00 40.78 4.41
137 138 1.450531 GATGATGCAGGGGGAAAGCG 61.451 60.000 0.00 0.00 0.00 4.68
138 139 1.925285 ATGATGCAGGGGGAAAGCGA 61.925 55.000 0.00 0.00 0.00 4.93
141 142 4.722700 GCAGGGGGAAAGCGAGCA 62.723 66.667 0.00 0.00 0.00 4.26
159 160 2.202676 GCTCCGCCTCGACAAGAG 60.203 66.667 0.00 0.00 46.44 2.85
160 161 2.995872 GCTCCGCCTCGACAAGAGT 61.996 63.158 0.00 0.00 45.44 3.24
162 163 1.867919 CTCCGCCTCGACAAGAGTGT 61.868 60.000 0.00 0.00 45.44 3.55
173 174 0.673985 CAAGAGTGTCGTGGTGGAGA 59.326 55.000 0.00 0.00 0.00 3.71
174 175 0.674534 AAGAGTGTCGTGGTGGAGAC 59.325 55.000 0.00 0.00 37.85 3.36
176 177 2.049433 GTGTCGTGGTGGAGACGG 60.049 66.667 0.00 0.00 40.05 4.79
177 178 3.986006 TGTCGTGGTGGAGACGGC 61.986 66.667 0.00 0.00 41.80 5.68
187 188 4.492160 GAGACGGCGGCGACATGA 62.492 66.667 38.93 0.00 0.00 3.07
196 197 3.109547 GCGACATGAACCGCGTCA 61.110 61.111 4.92 3.05 42.02 4.35
198 199 2.726691 CGACATGAACCGCGTCACC 61.727 63.158 4.92 0.00 0.00 4.02
240 241 1.730487 CGCTCGTGATCCTGCTACT 59.270 57.895 0.00 0.00 0.00 2.57
242 243 1.028905 GCTCGTGATCCTGCTACTCT 58.971 55.000 0.00 0.00 0.00 3.24
243 244 1.407258 GCTCGTGATCCTGCTACTCTT 59.593 52.381 0.00 0.00 0.00 2.85
244 245 2.542824 GCTCGTGATCCTGCTACTCTTC 60.543 54.545 0.00 0.00 0.00 2.87
254 255 3.368531 CCTGCTACTCTTCCTGGTAACAC 60.369 52.174 0.00 0.00 46.17 3.32
256 257 2.416972 GCTACTCTTCCTGGTAACACCG 60.417 54.545 0.00 0.00 46.17 4.94
257 258 0.320697 ACTCTTCCTGGTAACACCGC 59.679 55.000 0.00 0.00 46.17 5.68
262 263 1.079127 CCTGGTAACACCGCTCCTG 60.079 63.158 0.00 0.00 46.17 3.86
271 272 4.504916 CCGCTCCTGCTCGTGAGG 62.505 72.222 0.00 0.00 36.97 3.86
273 274 3.768922 GCTCCTGCTCGTGAGGCT 61.769 66.667 0.00 0.00 36.03 4.58
279 280 0.601046 CTGCTCGTGAGGCTTGTCAA 60.601 55.000 0.00 0.00 0.00 3.18
282 283 1.129437 GCTCGTGAGGCTTGTCAAATC 59.871 52.381 0.00 0.00 0.00 2.17
288 289 3.057033 GTGAGGCTTGTCAAATCTGCAAT 60.057 43.478 0.00 0.00 0.00 3.56
294 295 5.335897 GGCTTGTCAAATCTGCAATCTGTTA 60.336 40.000 0.00 0.00 0.00 2.41
297 298 5.559770 TGTCAAATCTGCAATCTGTTAGGA 58.440 37.500 0.00 0.00 0.00 2.94
303 304 4.507710 TCTGCAATCTGTTAGGACATGTC 58.492 43.478 17.91 17.91 34.72 3.06
315 316 2.158986 AGGACATGTCACTGCTAGATGC 60.159 50.000 26.47 5.30 43.25 3.91
318 319 0.471617 ATGTCACTGCTAGATGCCCC 59.528 55.000 0.00 0.00 42.00 5.80
324 325 2.203408 GCTAGATGCCCCCAAGCC 60.203 66.667 0.00 0.00 35.15 4.35
325 326 2.761465 GCTAGATGCCCCCAAGCCT 61.761 63.158 0.00 0.00 35.15 4.58
327 328 0.259938 CTAGATGCCCCCAAGCCTTT 59.740 55.000 0.00 0.00 0.00 3.11
351 352 6.681729 TGTGGTAGATGTAAGAAGAAAGGT 57.318 37.500 0.00 0.00 0.00 3.50
357 358 5.799213 AGATGTAAGAAGAAAGGTCACCTG 58.201 41.667 0.00 0.00 32.13 4.00
358 359 5.308237 AGATGTAAGAAGAAAGGTCACCTGT 59.692 40.000 0.00 0.00 32.13 4.00
363 364 5.669164 AGAAGAAAGGTCACCTGTCTATC 57.331 43.478 17.75 15.55 46.72 2.08
364 365 5.087323 AGAAGAAAGGTCACCTGTCTATCA 58.913 41.667 17.75 0.00 46.72 2.15
369 370 3.878778 AGGTCACCTGTCTATCATTTGC 58.121 45.455 0.00 0.00 29.57 3.68
372 373 4.507710 GTCACCTGTCTATCATTTGCTCA 58.492 43.478 0.00 0.00 0.00 4.26
373 374 4.937620 GTCACCTGTCTATCATTTGCTCAA 59.062 41.667 0.00 0.00 0.00 3.02
378 379 7.487189 CACCTGTCTATCATTTGCTCAAAATTC 59.513 37.037 0.00 0.00 36.28 2.17
381 382 7.541162 TGTCTATCATTTGCTCAAAATTCCTG 58.459 34.615 0.00 0.00 36.28 3.86
392 393 1.856629 AAATTCCTGCCATGGGAGTG 58.143 50.000 29.15 20.74 34.06 3.51
396 397 1.075482 CCTGCCATGGGAGTGTGTT 59.925 57.895 29.15 0.00 0.00 3.32
402 403 0.037303 CATGGGAGTGTGTTCCTGCT 59.963 55.000 0.00 0.00 37.40 4.24
418 419 2.816087 CCTGCTATGTGTGCTTTTCAGT 59.184 45.455 0.00 0.00 0.00 3.41
423 424 4.261572 GCTATGTGTGCTTTTCAGTCCAAA 60.262 41.667 0.00 0.00 0.00 3.28
426 427 2.427095 GTGTGCTTTTCAGTCCAAAGGT 59.573 45.455 0.00 0.00 32.66 3.50
444 445 7.122650 TCCAAAGGTCAAGGATTTCATTACATC 59.877 37.037 0.00 0.00 0.00 3.06
480 481 2.119495 GATAGACAGGCCAGGGAGAAA 58.881 52.381 5.01 0.00 0.00 2.52
485 486 3.333680 AGACAGGCCAGGGAGAAAATTTA 59.666 43.478 5.01 0.00 0.00 1.40
507 508 5.083533 ACAACATTGTTGTCACCATTGTT 57.916 34.783 25.66 5.18 38.47 2.83
528 529 4.265856 TGAGGGATCTGCTCCTACTAAA 57.734 45.455 0.00 0.00 44.28 1.85
546 547 9.202273 CCTACTAAAGATATTGAGCATGAACTC 57.798 37.037 0.00 0.00 37.19 3.01
552 553 6.047870 AGATATTGAGCATGAACTCAGTGTC 58.952 40.000 11.65 11.65 46.85 3.67
567 568 0.618458 GTGTCTATGTGGGGCAAGGA 59.382 55.000 0.00 0.00 0.00 3.36
613 614 2.351157 GCACCTCAGAAGTTTGTGATGC 60.351 50.000 3.00 3.00 32.05 3.91
645 646 3.768833 TAGGGAGGTGGATCGGGCC 62.769 68.421 0.00 0.00 0.00 5.80
654 655 1.304134 GGATCGGGCCCTGTTTGTT 60.304 57.895 22.43 0.00 0.00 2.83
663 664 2.365293 GGCCCTGTTTGTTGAGAATGTT 59.635 45.455 0.00 0.00 0.00 2.71
665 666 4.038642 GGCCCTGTTTGTTGAGAATGTTAA 59.961 41.667 0.00 0.00 0.00 2.01
673 674 9.698309 TGTTTGTTGAGAATGTTAAACTGAAAA 57.302 25.926 0.00 0.00 0.00 2.29
693 694 5.570234 AAAAATGTGGTGTTAGTGTTCGT 57.430 34.783 0.00 0.00 0.00 3.85
711 712 2.637872 TCGTTTTTCTCCCTGGTCTGAT 59.362 45.455 0.00 0.00 0.00 2.90
714 715 4.593956 GTTTTTCTCCCTGGTCTGATGAT 58.406 43.478 0.00 0.00 0.00 2.45
715 716 4.494091 TTTTCTCCCTGGTCTGATGATC 57.506 45.455 0.00 0.00 0.00 2.92
717 718 2.956132 TCTCCCTGGTCTGATGATCTC 58.044 52.381 0.00 0.00 0.00 2.75
726 727 3.250762 GGTCTGATGATCTCGACTCTGAG 59.749 52.174 2.45 2.45 37.33 3.35
738 739 0.768221 ACTCTGAGGGGTTGCTGGAA 60.768 55.000 9.85 0.00 0.00 3.53
741 742 0.607489 CTGAGGGGTTGCTGGAAGTG 60.607 60.000 0.00 0.00 35.30 3.16
750 751 1.973812 GCTGGAAGTGGCTTGGGTC 60.974 63.158 0.00 0.00 35.30 4.46
756 758 1.559682 GAAGTGGCTTGGGTCAGGATA 59.440 52.381 0.00 0.00 0.00 2.59
759 761 0.044092 TGGCTTGGGTCAGGATAGGA 59.956 55.000 0.00 0.00 0.00 2.94
761 763 1.564348 GGCTTGGGTCAGGATAGGAAA 59.436 52.381 0.00 0.00 0.00 3.13
788 790 5.063204 TCCGCCCAATAAAAGATGTGATAG 58.937 41.667 0.00 0.00 0.00 2.08
803 805 4.191544 TGTGATAGGACTGTTGCTTATGC 58.808 43.478 0.00 0.00 40.20 3.14
825 827 0.039035 GTGGCCTGGTTGGGATTACA 59.961 55.000 3.32 0.00 36.00 2.41
834 836 5.367945 TGGTTGGGATTACATTAGAGGTC 57.632 43.478 0.00 0.00 0.00 3.85
835 837 5.036916 TGGTTGGGATTACATTAGAGGTCT 58.963 41.667 0.00 0.00 0.00 3.85
837 839 6.099269 TGGTTGGGATTACATTAGAGGTCTAC 59.901 42.308 0.00 0.00 0.00 2.59
838 840 6.326843 GGTTGGGATTACATTAGAGGTCTACT 59.673 42.308 0.00 0.00 0.00 2.57
839 841 7.435305 GTTGGGATTACATTAGAGGTCTACTC 58.565 42.308 0.00 0.00 46.98 2.59
890 900 5.923204 AGATTGGATGTAGGTCTGTTGATC 58.077 41.667 0.00 0.00 0.00 2.92
892 902 4.471904 TGGATGTAGGTCTGTTGATCAC 57.528 45.455 0.00 0.00 0.00 3.06
895 905 3.961480 TGTAGGTCTGTTGATCACCTG 57.039 47.619 11.18 1.70 32.43 4.00
898 908 0.326264 GGTCTGTTGATCACCTGCCT 59.674 55.000 0.00 0.00 0.00 4.75
899 909 1.446907 GTCTGTTGATCACCTGCCTG 58.553 55.000 0.00 0.00 0.00 4.85
921 931 2.121963 AGCTGAGGGGGTGTTGGA 60.122 61.111 0.00 0.00 0.00 3.53
924 935 1.538876 CTGAGGGGGTGTTGGAGGA 60.539 63.158 0.00 0.00 0.00 3.71
949 960 8.997621 ACGCTTTTACAGATTTACTTATGAGA 57.002 30.769 0.00 0.00 0.00 3.27
958 969 8.428063 ACAGATTTACTTATGAGATTGAGGAGG 58.572 37.037 0.00 0.00 0.00 4.30
960 971 8.646900 AGATTTACTTATGAGATTGAGGAGGTC 58.353 37.037 0.00 0.00 0.00 3.85
977 988 4.381411 GAGGTCCTTATTCGAAATCCTGG 58.619 47.826 0.00 0.85 0.00 4.45
980 991 4.383770 GGTCCTTATTCGAAATCCTGGTGA 60.384 45.833 0.00 0.00 0.00 4.02
981 992 5.183228 GTCCTTATTCGAAATCCTGGTGAA 58.817 41.667 0.00 0.00 0.00 3.18
984 995 5.294552 CCTTATTCGAAATCCTGGTGAAGAC 59.705 44.000 0.00 0.00 0.00 3.01
991 1002 1.079543 CCTGGTGAAGACGAGGCTG 60.080 63.158 0.00 0.00 40.77 4.85
992 1003 1.668294 CTGGTGAAGACGAGGCTGT 59.332 57.895 0.00 0.00 0.00 4.40
995 1006 0.249911 GGTGAAGACGAGGCTGTTGT 60.250 55.000 0.00 0.00 0.00 3.32
1002 1013 2.093973 AGACGAGGCTGTTGTTCCTATG 60.094 50.000 0.00 0.00 31.71 2.23
1008 1019 3.352648 GGCTGTTGTTCCTATGCCTAAA 58.647 45.455 0.00 0.00 37.58 1.85
1013 1024 6.279513 TGTTGTTCCTATGCCTAAAAATGG 57.720 37.500 0.00 0.00 0.00 3.16
1024 1035 3.631250 CCTAAAAATGGCCCTGCTAAGA 58.369 45.455 0.00 0.00 0.00 2.10
1038 1049 2.501723 TGCTAAGAATGACCAGACTCCC 59.498 50.000 0.00 0.00 0.00 4.30
1042 1053 1.280421 AGAATGACCAGACTCCCAAGC 59.720 52.381 0.00 0.00 0.00 4.01
1044 1055 2.435059 GACCAGACTCCCAAGCGC 60.435 66.667 0.00 0.00 0.00 5.92
1047 1058 2.037136 CCAGACTCCCAAGCGCAAG 61.037 63.158 11.47 0.00 43.44 4.01
1050 1061 1.743252 GACTCCCAAGCGCAAGAGG 60.743 63.158 11.47 4.59 43.02 3.69
1071 1082 2.305927 GGATGACCCACAGAAAGAGGAA 59.694 50.000 0.00 0.00 34.14 3.36
1077 1088 1.270839 CCACAGAAAGAGGAAAGCCGA 60.271 52.381 0.00 0.00 39.96 5.54
1080 1091 2.284190 CAGAAAGAGGAAAGCCGATCC 58.716 52.381 0.00 0.00 39.96 3.36
1081 1092 1.909302 AGAAAGAGGAAAGCCGATCCA 59.091 47.619 3.20 0.00 39.55 3.41
1092 1103 1.139853 AGCCGATCCAAATCTCCTGAC 59.860 52.381 0.00 0.00 0.00 3.51
1101 1112 3.693085 CCAAATCTCCTGACCATGACAAG 59.307 47.826 0.00 0.00 0.00 3.16
1104 1115 0.254178 CTCCTGACCATGACAAGGGG 59.746 60.000 1.13 0.00 0.00 4.79
1105 1116 1.379044 CCTGACCATGACAAGGGGC 60.379 63.158 1.13 0.00 35.04 5.80
1106 1117 1.379916 CTGACCATGACAAGGGGCA 59.620 57.895 5.07 5.07 45.16 5.36
1110 1121 0.258774 ACCATGACAAGGGGCATACC 59.741 55.000 1.13 0.00 39.11 2.73
1118 1129 3.630289 GGGGCATACCTCTCGTGT 58.370 61.111 0.00 0.00 40.03 4.49
1119 1130 1.442148 GGGGCATACCTCTCGTGTC 59.558 63.158 0.00 0.00 40.03 3.67
1125 1136 0.456221 ATACCTCTCGTGTCGGCAAG 59.544 55.000 0.00 0.00 0.00 4.01
1144 1155 2.363788 GACATGTCGTCTACTGCCAA 57.636 50.000 10.69 0.00 41.81 4.52
1151 1162 0.179161 CGTCTACTGCCAACCGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
1156 1167 1.739562 CTGCCAACCGAGAGTGAGC 60.740 63.158 0.00 0.00 0.00 4.26
1158 1169 1.446966 GCCAACCGAGAGTGAGCTC 60.447 63.158 6.82 6.82 41.94 4.09
1159 1170 1.967535 CCAACCGAGAGTGAGCTCA 59.032 57.895 13.74 13.74 44.00 4.26
1188 1199 1.697432 TCGGAAAGTGAGGTTGATGGT 59.303 47.619 0.00 0.00 0.00 3.55
1191 1202 2.484264 GGAAAGTGAGGTTGATGGTTCG 59.516 50.000 0.00 0.00 0.00 3.95
1200 1211 1.063174 GTTGATGGTTCGCTGCTCATC 59.937 52.381 0.00 6.63 37.21 2.92
1207 1218 2.259618 GTTCGCTGCTCATCGAAACTA 58.740 47.619 9.65 0.00 44.76 2.24
1209 1220 3.982576 TCGCTGCTCATCGAAACTATA 57.017 42.857 0.00 0.00 0.00 1.31
1227 1238 1.885049 TAGCAAGAGAGCAGGGGATT 58.115 50.000 0.00 0.00 36.85 3.01
1229 1240 1.101331 GCAAGAGAGCAGGGGATTTG 58.899 55.000 0.00 0.00 0.00 2.32
1233 1244 1.558756 AGAGAGCAGGGGATTTGTGAG 59.441 52.381 0.00 0.00 0.00 3.51
1234 1245 0.622665 AGAGCAGGGGATTTGTGAGG 59.377 55.000 0.00 0.00 0.00 3.86
1235 1246 0.620556 GAGCAGGGGATTTGTGAGGA 59.379 55.000 0.00 0.00 0.00 3.71
1236 1247 1.004745 GAGCAGGGGATTTGTGAGGAA 59.995 52.381 0.00 0.00 0.00 3.36
1242 1253 2.356227 GGGGATTTGTGAGGAAGAGGAC 60.356 54.545 0.00 0.00 0.00 3.85
1245 1256 2.930826 TTTGTGAGGAAGAGGACACC 57.069 50.000 0.00 0.00 33.08 4.16
1251 1262 0.252467 AGGAAGAGGACACCCAGGAG 60.252 60.000 0.00 0.00 33.88 3.69
1264 1275 1.340114 CCCAGGAGGTTTCTAACTGGC 60.340 57.143 0.00 0.00 42.36 4.85
1285 1296 0.475906 AGTGCCTCTGAAGCCAGTTT 59.524 50.000 0.00 0.00 41.16 2.66
1287 1298 2.106511 AGTGCCTCTGAAGCCAGTTTTA 59.893 45.455 0.00 0.00 41.16 1.52
1288 1299 3.084786 GTGCCTCTGAAGCCAGTTTTAT 58.915 45.455 0.00 0.00 41.16 1.40
1290 1301 4.700213 GTGCCTCTGAAGCCAGTTTTATTA 59.300 41.667 0.00 0.00 41.16 0.98
1292 1303 4.700213 GCCTCTGAAGCCAGTTTTATTACA 59.300 41.667 0.00 0.00 41.16 2.41
1296 1307 7.337942 CCTCTGAAGCCAGTTTTATTACAGAAT 59.662 37.037 0.00 0.00 41.16 2.40
1297 1308 8.635765 TCTGAAGCCAGTTTTATTACAGAATT 57.364 30.769 0.00 0.00 41.16 2.17
1298 1309 8.730680 TCTGAAGCCAGTTTTATTACAGAATTC 58.269 33.333 0.00 0.00 41.16 2.17
1301 1312 5.034797 GCCAGTTTTATTACAGAATTCGGC 58.965 41.667 5.43 1.24 0.00 5.54
1302 1313 5.163652 GCCAGTTTTATTACAGAATTCGGCT 60.164 40.000 5.43 0.00 0.00 5.52
1306 1317 5.888691 TTTATTACAGAATTCGGCTGCAA 57.111 34.783 5.43 0.00 36.86 4.08
1337 1348 0.618458 TCCCAGGATGTGCAGGTAAC 59.382 55.000 0.00 0.00 0.00 2.50
1361 1372 8.831000 ACTAGAAACGTTGTTGTTAAATGTTC 57.169 30.769 0.00 0.00 36.08 3.18
1362 1373 6.784068 AGAAACGTTGTTGTTAAATGTTCG 57.216 33.333 0.00 0.00 36.08 3.95
1365 1376 5.918387 ACGTTGTTGTTAAATGTTCGTTG 57.082 34.783 0.00 0.00 0.00 4.10
1370 1381 7.380320 GTTGTTGTTAAATGTTCGTTGTCTTG 58.620 34.615 0.00 0.00 0.00 3.02
1373 1384 6.424176 TGTTAAATGTTCGTTGTCTTGTGA 57.576 33.333 0.00 0.00 0.00 3.58
1375 1386 7.476667 TGTTAAATGTTCGTTGTCTTGTGATT 58.523 30.769 0.00 0.00 0.00 2.57
1381 1392 1.126846 CGTTGTCTTGTGATTCGGCTC 59.873 52.381 0.00 0.00 0.00 4.70
1382 1393 2.143122 GTTGTCTTGTGATTCGGCTCA 58.857 47.619 0.00 0.00 0.00 4.26
1395 1406 1.137086 TCGGCTCAATCTAACTCTGCC 59.863 52.381 0.00 0.00 35.94 4.85
1416 1427 1.147600 GGTTGTGGAGGTTGACGGT 59.852 57.895 0.00 0.00 0.00 4.83
1425 1436 0.836400 AGGTTGACGGTGAGGTGGAT 60.836 55.000 0.00 0.00 0.00 3.41
1429 1440 1.257750 TGACGGTGAGGTGGATCCAG 61.258 60.000 16.81 3.76 39.02 3.86
1442 1453 4.041444 GGTGGATCCAGAGCTGAAGATATT 59.959 45.833 16.81 0.00 35.97 1.28
1443 1454 5.247110 GGTGGATCCAGAGCTGAAGATATTA 59.753 44.000 16.81 0.00 35.97 0.98
1449 1460 6.810911 TCCAGAGCTGAAGATATTAAGTGAC 58.189 40.000 0.00 0.00 0.00 3.67
1467 1478 3.069729 GTGACTATGTGGTACATCTCCCC 59.930 52.174 0.00 0.00 44.52 4.81
1511 1522 0.694444 ATCCATACCCCTCCGCTTGT 60.694 55.000 0.00 0.00 0.00 3.16
1512 1523 1.153168 CCATACCCCTCCGCTTGTG 60.153 63.158 0.00 0.00 0.00 3.33
1597 1608 2.750657 GCTATGAGGCTGGCCACCT 61.751 63.158 22.29 22.29 41.41 4.00
1616 1627 5.069781 CCACCTTAAGAGATCTGGAAGGTAG 59.930 48.000 22.94 16.35 44.68 3.18
1618 1629 5.659079 ACCTTAAGAGATCTGGAAGGTAGTG 59.341 44.000 22.44 5.61 44.66 2.74
1641 1653 6.787043 GTGCTCATAAAACTTGCAAAAATTCG 59.213 34.615 0.00 0.00 35.34 3.34
1643 1655 7.003648 GCTCATAAAACTTGCAAAAATTCGTC 58.996 34.615 0.00 0.00 0.00 4.20
1653 1665 3.120199 GCAAAAATTCGTCTGCTGCTCTA 60.120 43.478 0.00 0.00 0.00 2.43
1699 1711 4.632153 AGCTACTAAAATGGGAGTATGCG 58.368 43.478 0.00 0.00 32.38 4.73
1749 1761 7.750229 TGATGTGCTTAGAGAACTTGAAAAT 57.250 32.000 0.00 0.00 0.00 1.82
1770 1782 1.208293 GTGAGGGGGAACTTAGCTGAG 59.792 57.143 3.53 3.53 0.00 3.35
1957 1978 3.326588 TGTTGTCAAGCTTTCTAGGCCTA 59.673 43.478 13.09 13.09 0.00 3.93
2223 2246 5.805728 TGTCTTAGGAGAATTGACCCTTTC 58.194 41.667 0.00 0.00 32.66 2.62
2259 2282 3.244911 GGAACTGGATTCTTTCTGTGGGA 60.245 47.826 0.00 0.00 37.48 4.37
2265 2288 4.458989 TGGATTCTTTCTGTGGGAAAATCG 59.541 41.667 0.00 0.00 42.52 3.34
2286 2309 1.339727 GGTGGTATTCTGTGTGGGGTC 60.340 57.143 0.00 0.00 0.00 4.46
2290 2313 2.093447 GGTATTCTGTGTGGGGTCAGAG 60.093 54.545 0.00 0.00 40.91 3.35
2305 2328 5.762218 GGGGTCAGAGATGATACTTTTGATG 59.238 44.000 0.00 0.00 0.00 3.07
2349 2372 6.984474 GCAAGTATATACTCCAGCTTGTTGTA 59.016 38.462 15.72 0.00 36.62 2.41
2451 2475 2.297315 CCTCATCGAGCTTGCTACCATA 59.703 50.000 0.00 0.00 0.00 2.74
2754 2780 9.628500 GAAATCTCATACCATAACCCTTTACTT 57.372 33.333 0.00 0.00 0.00 2.24
2986 3012 6.326064 CCATGAGAAGAAGAGGAAAGAGGATA 59.674 42.308 0.00 0.00 0.00 2.59
2989 3015 7.790027 TGAGAAGAAGAGGAAAGAGGATATTG 58.210 38.462 0.00 0.00 0.00 1.90
3047 3073 1.597854 CCGCTCTTTCACCTGTGCA 60.598 57.895 0.00 0.00 0.00 4.57
3252 3278 0.770499 TGGTGATTGAGGGCACTGAA 59.230 50.000 0.00 0.00 35.43 3.02
3282 3308 0.613260 AGCATGCCACGGAGTTCTAA 59.387 50.000 15.66 0.00 41.61 2.10
3292 3318 4.865365 CCACGGAGTTCTAAAAAGAGCTAG 59.135 45.833 0.00 0.00 41.61 3.42
3367 3393 8.031864 CAGCTGAAGAGAAACTTACTGAATCTA 58.968 37.037 8.42 0.00 39.13 1.98
3554 3580 0.323178 CAAGGGAAGCTGGATGTGCT 60.323 55.000 0.00 0.00 43.32 4.40
3575 3662 3.011119 TGCGTTTAGGCCGATATGTTTT 58.989 40.909 0.00 0.00 0.00 2.43
3625 3712 1.000145 GTCTTGGATCGCCGAGTTTC 59.000 55.000 0.00 0.00 44.80 2.78
3748 3837 3.876914 ACTCATGTGAAAAAGCGAGTTGA 59.123 39.130 0.94 0.00 29.68 3.18
3784 3873 2.838736 TGATTTCGAGAAGGCCTATGC 58.161 47.619 5.16 0.00 0.00 3.14
3951 4041 0.552615 AGGGGTTAGGCAGGGTGATT 60.553 55.000 0.00 0.00 0.00 2.57
3952 4042 0.335019 GGGGTTAGGCAGGGTGATTT 59.665 55.000 0.00 0.00 0.00 2.17
4084 4174 4.709250 TGGAGTTGTTGTACTGCAATACA 58.291 39.130 3.42 3.42 42.47 2.29
4280 4370 3.142174 GTGATATTGGCAGCTTCCCTAC 58.858 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.545952 CCATATCTCAAACCCGGAGTCG 60.546 54.545 0.73 0.00 34.04 4.18
9 10 2.047061 TCCCATATCTCAAACCCGGAG 58.953 52.381 0.73 0.00 0.00 4.63
15 16 3.070018 CGCCTCATCCCATATCTCAAAC 58.930 50.000 0.00 0.00 0.00 2.93
21 22 1.078143 GGCCGCCTCATCCCATATC 60.078 63.158 0.71 0.00 0.00 1.63
23 24 3.625897 CGGCCGCCTCATCCCATA 61.626 66.667 14.67 0.00 0.00 2.74
30 31 3.479203 ATTCCATCGGCCGCCTCA 61.479 61.111 23.51 2.57 0.00 3.86
51 52 1.519719 CTGGTGAGTAGGAGCAGCC 59.480 63.158 0.00 0.00 32.56 4.85
52 53 1.261238 ACCTGGTGAGTAGGAGCAGC 61.261 60.000 0.00 0.00 37.57 5.25
53 54 0.534412 CACCTGGTGAGTAGGAGCAG 59.466 60.000 22.33 0.00 38.71 4.24
54 55 1.544825 GCACCTGGTGAGTAGGAGCA 61.545 60.000 30.23 0.00 46.84 4.26
56 57 0.534412 CTGCACCTGGTGAGTAGGAG 59.466 60.000 30.23 9.56 38.71 3.69
57 58 0.178932 ACTGCACCTGGTGAGTAGGA 60.179 55.000 30.23 2.92 38.71 2.94
60 61 1.480212 CCCACTGCACCTGGTGAGTA 61.480 60.000 30.23 13.87 35.23 2.59
61 62 2.822637 CCCACTGCACCTGGTGAGT 61.823 63.158 30.23 23.90 35.23 3.41
101 102 2.407440 ATCAGGCTCATGCGGATGGG 62.407 60.000 17.41 15.39 40.82 4.00
103 104 0.250166 TCATCAGGCTCATGCGGATG 60.250 55.000 11.15 11.15 45.11 3.51
104 105 0.691332 ATCATCAGGCTCATGCGGAT 59.309 50.000 0.00 0.00 40.82 4.18
106 107 1.853114 GCATCATCAGGCTCATGCGG 61.853 60.000 0.00 0.00 40.82 5.69
108 109 0.593618 CTGCATCATCAGGCTCATGC 59.406 55.000 0.00 2.08 41.75 4.06
109 110 1.239347 CCTGCATCATCAGGCTCATG 58.761 55.000 0.00 0.00 46.11 3.07
110 111 3.727738 CCTGCATCATCAGGCTCAT 57.272 52.632 0.00 0.00 46.11 2.90
119 120 1.454479 CGCTTTCCCCCTGCATCAT 60.454 57.895 0.00 0.00 0.00 2.45
153 154 0.389391 CTCCACCACGACACTCTTGT 59.611 55.000 0.00 0.00 39.32 3.16
159 160 2.049433 CCGTCTCCACCACGACAC 60.049 66.667 0.00 0.00 39.75 3.67
160 161 3.986006 GCCGTCTCCACCACGACA 61.986 66.667 0.00 0.00 39.75 4.35
201 202 1.012486 GCGGTGGAGTACGGTTTCTG 61.012 60.000 0.00 0.00 32.62 3.02
204 205 2.048877 CGCGGTGGAGTACGGTTT 60.049 61.111 0.00 0.00 32.62 3.27
240 241 0.606604 GAGCGGTGTTACCAGGAAGA 59.393 55.000 0.00 0.00 38.47 2.87
242 243 0.834687 AGGAGCGGTGTTACCAGGAA 60.835 55.000 0.00 0.00 38.47 3.36
243 244 1.229082 AGGAGCGGTGTTACCAGGA 60.229 57.895 0.00 0.00 38.47 3.86
244 245 1.079127 CAGGAGCGGTGTTACCAGG 60.079 63.158 0.00 0.00 38.47 4.45
256 257 3.308014 AAGCCTCACGAGCAGGAGC 62.308 63.158 0.00 0.00 42.56 4.70
257 258 1.447489 CAAGCCTCACGAGCAGGAG 60.447 63.158 0.00 0.00 31.91 3.69
262 263 1.129437 GATTTGACAAGCCTCACGAGC 59.871 52.381 0.00 0.00 0.00 5.03
271 272 4.170292 ACAGATTGCAGATTTGACAAGC 57.830 40.909 6.46 0.00 31.47 4.01
273 274 6.003326 TCCTAACAGATTGCAGATTTGACAA 58.997 36.000 6.46 0.00 0.00 3.18
279 280 5.503927 ACATGTCCTAACAGATTGCAGATT 58.496 37.500 0.00 0.00 39.20 2.40
282 283 4.093998 GTGACATGTCCTAACAGATTGCAG 59.906 45.833 22.85 0.00 39.20 4.41
288 289 2.899900 AGCAGTGACATGTCCTAACAGA 59.100 45.455 22.85 0.00 39.20 3.41
294 295 2.158986 GCATCTAGCAGTGACATGTCCT 60.159 50.000 22.85 15.84 44.79 3.85
315 316 3.470433 CCACAAAAGGCTTGGGGG 58.530 61.111 0.00 2.87 39.29 5.40
318 319 3.157087 ACATCTACCACAAAAGGCTTGG 58.843 45.455 0.00 0.00 36.39 3.61
324 325 8.507249 CCTTTCTTCTTACATCTACCACAAAAG 58.493 37.037 0.00 0.00 0.00 2.27
325 326 7.996644 ACCTTTCTTCTTACATCTACCACAAAA 59.003 33.333 0.00 0.00 0.00 2.44
327 328 7.074653 ACCTTTCTTCTTACATCTACCACAA 57.925 36.000 0.00 0.00 0.00 3.33
351 352 4.824479 TGAGCAAATGATAGACAGGTGA 57.176 40.909 0.00 0.00 0.00 4.02
357 358 6.474751 GCAGGAATTTTGAGCAAATGATAGAC 59.525 38.462 0.00 0.00 35.09 2.59
358 359 6.406177 GGCAGGAATTTTGAGCAAATGATAGA 60.406 38.462 0.00 0.00 35.09 1.98
360 361 5.187381 TGGCAGGAATTTTGAGCAAATGATA 59.813 36.000 0.00 0.00 35.09 2.15
363 364 3.666274 TGGCAGGAATTTTGAGCAAATG 58.334 40.909 0.00 0.00 35.09 2.32
364 365 4.258543 CATGGCAGGAATTTTGAGCAAAT 58.741 39.130 0.00 0.00 36.57 2.32
369 370 2.429610 CTCCCATGGCAGGAATTTTGAG 59.570 50.000 6.09 0.00 31.49 3.02
372 373 2.181975 CACTCCCATGGCAGGAATTTT 58.818 47.619 7.81 0.00 31.49 1.82
373 374 1.077663 ACACTCCCATGGCAGGAATTT 59.922 47.619 7.81 0.00 31.49 1.82
378 379 0.962356 GAACACACTCCCATGGCAGG 60.962 60.000 7.81 0.00 0.00 4.85
381 382 0.962356 CAGGAACACACTCCCATGGC 60.962 60.000 6.09 0.00 35.95 4.40
392 393 1.813513 AGCACACATAGCAGGAACAC 58.186 50.000 0.00 0.00 0.00 3.32
396 397 3.076621 CTGAAAAGCACACATAGCAGGA 58.923 45.455 0.00 0.00 0.00 3.86
402 403 4.278170 CCTTTGGACTGAAAAGCACACATA 59.722 41.667 0.00 0.00 34.03 2.29
418 419 6.310941 TGTAATGAAATCCTTGACCTTTGGA 58.689 36.000 0.00 0.00 0.00 3.53
423 424 5.194537 AGGGATGTAATGAAATCCTTGACCT 59.805 40.000 0.00 0.00 41.85 3.85
444 445 7.316640 CCTGTCTATCGATACTAAAATCAGGG 58.683 42.308 0.00 0.00 35.40 4.45
459 460 0.468214 TCTCCCTGGCCTGTCTATCG 60.468 60.000 3.32 0.00 0.00 2.92
474 475 8.539674 GTGACAACAATGTTGTAAATTTTCTCC 58.460 33.333 28.90 14.28 41.31 3.71
528 529 5.987098 ACACTGAGTTCATGCTCAATATCT 58.013 37.500 4.82 0.00 43.92 1.98
546 547 1.679944 CCTTGCCCCACATAGACACTG 60.680 57.143 0.00 0.00 0.00 3.66
552 553 0.825010 GCCATCCTTGCCCCACATAG 60.825 60.000 0.00 0.00 0.00 2.23
588 589 3.378112 TCACAAACTTCTGAGGTGCAAAG 59.622 43.478 0.00 0.00 0.00 2.77
613 614 0.471211 TCCCTAGGGTTAGGCATCCG 60.471 60.000 27.58 0.00 44.44 4.18
645 646 7.479980 TCAGTTTAACATTCTCAACAAACAGG 58.520 34.615 0.00 0.00 0.00 4.00
673 674 5.570234 AAACGAACACTAACACCACATTT 57.430 34.783 0.00 0.00 0.00 2.32
679 680 4.260907 GGGAGAAAAACGAACACTAACACC 60.261 45.833 0.00 0.00 0.00 4.16
680 681 4.573607 AGGGAGAAAAACGAACACTAACAC 59.426 41.667 0.00 0.00 0.00 3.32
684 685 3.135167 ACCAGGGAGAAAAACGAACACTA 59.865 43.478 0.00 0.00 0.00 2.74
691 692 2.543777 TCAGACCAGGGAGAAAAACG 57.456 50.000 0.00 0.00 0.00 3.60
693 694 4.537688 AGATCATCAGACCAGGGAGAAAAA 59.462 41.667 0.00 0.00 0.00 1.94
711 712 0.626382 ACCCCTCAGAGTCGAGATCA 59.374 55.000 11.89 0.00 34.79 2.92
714 715 1.251527 GCAACCCCTCAGAGTCGAGA 61.252 60.000 11.89 1.70 34.79 4.04
715 716 1.216710 GCAACCCCTCAGAGTCGAG 59.783 63.158 0.00 5.37 0.00 4.04
717 718 1.079543 CAGCAACCCCTCAGAGTCG 60.080 63.158 0.00 0.00 0.00 4.18
726 727 2.991540 GCCACTTCCAGCAACCCC 60.992 66.667 0.00 0.00 0.00 4.95
738 739 1.207791 CTATCCTGACCCAAGCCACT 58.792 55.000 0.00 0.00 0.00 4.00
741 742 1.213296 TTCCTATCCTGACCCAAGCC 58.787 55.000 0.00 0.00 0.00 4.35
759 761 6.371271 CACATCTTTTATTGGGCGGAATTTTT 59.629 34.615 0.00 0.00 0.00 1.94
761 763 5.186797 TCACATCTTTTATTGGGCGGAATTT 59.813 36.000 0.00 0.00 0.00 1.82
768 770 6.016777 CAGTCCTATCACATCTTTTATTGGGC 60.017 42.308 0.00 0.00 0.00 5.36
771 773 7.912250 GCAACAGTCCTATCACATCTTTTATTG 59.088 37.037 0.00 0.00 0.00 1.90
774 776 6.711277 AGCAACAGTCCTATCACATCTTTTA 58.289 36.000 0.00 0.00 0.00 1.52
804 806 0.849094 TAATCCCAACCAGGCCACCT 60.849 55.000 5.01 0.00 35.39 4.00
807 809 1.006813 ATGTAATCCCAACCAGGCCA 58.993 50.000 5.01 0.00 35.39 5.36
834 836 3.058570 CGATGAGGGTCGATTCAGAGTAG 60.059 52.174 0.00 0.00 44.06 2.57
835 837 2.879026 CGATGAGGGTCGATTCAGAGTA 59.121 50.000 0.00 0.00 44.06 2.59
837 839 1.000827 CCGATGAGGGTCGATTCAGAG 60.001 57.143 0.00 0.00 44.06 3.35
838 840 1.032794 CCGATGAGGGTCGATTCAGA 58.967 55.000 0.00 0.00 44.06 3.27
839 841 0.747255 ACCGATGAGGGTCGATTCAG 59.253 55.000 0.00 0.00 46.96 3.02
840 842 1.191535 AACCGATGAGGGTCGATTCA 58.808 50.000 0.00 0.00 46.96 2.57
874 884 3.369892 GCAGGTGATCAACAGACCTACAT 60.370 47.826 14.46 0.00 0.00 2.29
881 891 0.325933 CCAGGCAGGTGATCAACAGA 59.674 55.000 14.46 0.00 0.00 3.41
882 892 2.864114 CCAGGCAGGTGATCAACAG 58.136 57.895 14.46 6.08 0.00 3.16
892 902 1.376942 CTCAGCTGAACCAGGCAGG 60.377 63.158 18.85 0.00 45.67 4.85
895 905 2.045536 CCCTCAGCTGAACCAGGC 60.046 66.667 18.85 0.00 31.21 4.85
898 908 2.121963 ACCCCCTCAGCTGAACCA 60.122 61.111 18.85 0.00 0.00 3.67
899 909 2.069165 AACACCCCCTCAGCTGAACC 62.069 60.000 18.85 0.00 0.00 3.62
921 931 8.038944 TCATAAGTAAATCTGTAAAAGCGTCCT 58.961 33.333 0.00 0.00 0.00 3.85
924 935 8.997621 TCTCATAAGTAAATCTGTAAAAGCGT 57.002 30.769 0.00 0.00 0.00 5.07
958 969 4.766375 TCACCAGGATTTCGAATAAGGAC 58.234 43.478 0.00 0.00 0.00 3.85
960 971 5.294552 GTCTTCACCAGGATTTCGAATAAGG 59.705 44.000 0.00 0.00 0.00 2.69
963 974 4.158949 TCGTCTTCACCAGGATTTCGAATA 59.841 41.667 0.00 0.00 0.00 1.75
964 975 3.056107 TCGTCTTCACCAGGATTTCGAAT 60.056 43.478 0.00 0.00 0.00 3.34
966 977 1.890489 TCGTCTTCACCAGGATTTCGA 59.110 47.619 0.00 0.00 0.00 3.71
967 978 2.263077 CTCGTCTTCACCAGGATTTCG 58.737 52.381 0.00 0.00 0.00 3.46
968 979 2.622436 CCTCGTCTTCACCAGGATTTC 58.378 52.381 0.00 0.00 0.00 2.17
972 983 1.228894 AGCCTCGTCTTCACCAGGA 60.229 57.895 0.00 0.00 0.00 3.86
977 988 1.527311 GAACAACAGCCTCGTCTTCAC 59.473 52.381 0.00 0.00 0.00 3.18
980 991 0.759346 AGGAACAACAGCCTCGTCTT 59.241 50.000 0.00 0.00 0.00 3.01
981 992 1.629043 TAGGAACAACAGCCTCGTCT 58.371 50.000 0.00 0.00 35.73 4.18
984 995 1.009829 GCATAGGAACAACAGCCTCG 58.990 55.000 0.00 0.00 35.73 4.63
1008 1019 3.026694 GTCATTCTTAGCAGGGCCATTT 58.973 45.455 6.18 0.00 0.00 2.32
1013 1024 1.210478 TCTGGTCATTCTTAGCAGGGC 59.790 52.381 0.00 0.00 41.64 5.19
1014 1025 2.503356 AGTCTGGTCATTCTTAGCAGGG 59.497 50.000 0.00 0.00 41.64 4.45
1024 1035 0.036010 CGCTTGGGAGTCTGGTCATT 60.036 55.000 0.00 0.00 0.00 2.57
1038 1049 1.372087 GGTCATCCCTCTTGCGCTTG 61.372 60.000 9.73 0.65 0.00 4.01
1050 1061 1.909302 TCCTCTTTCTGTGGGTCATCC 59.091 52.381 0.00 0.00 0.00 3.51
1059 1070 2.355209 GGATCGGCTTTCCTCTTTCTGT 60.355 50.000 0.00 0.00 0.00 3.41
1060 1071 2.284190 GGATCGGCTTTCCTCTTTCTG 58.716 52.381 0.00 0.00 0.00 3.02
1062 1073 2.403252 TGGATCGGCTTTCCTCTTTC 57.597 50.000 4.51 0.00 34.17 2.62
1063 1074 2.879103 TTGGATCGGCTTTCCTCTTT 57.121 45.000 4.51 0.00 34.17 2.52
1065 1076 2.507471 AGATTTGGATCGGCTTTCCTCT 59.493 45.455 4.51 0.00 37.37 3.69
1068 1079 1.950216 GGAGATTTGGATCGGCTTTCC 59.050 52.381 0.00 0.00 37.37 3.13
1071 1082 1.839994 TCAGGAGATTTGGATCGGCTT 59.160 47.619 0.00 0.00 37.37 4.35
1077 1088 3.524789 TGTCATGGTCAGGAGATTTGGAT 59.475 43.478 0.00 0.00 0.00 3.41
1080 1091 3.693085 CCTTGTCATGGTCAGGAGATTTG 59.307 47.826 0.00 0.00 0.00 2.32
1081 1092 3.308688 CCCTTGTCATGGTCAGGAGATTT 60.309 47.826 4.19 0.00 0.00 2.17
1092 1103 0.552848 AGGTATGCCCCTTGTCATGG 59.447 55.000 0.00 0.00 34.57 3.66
1101 1112 1.442148 GACACGAGAGGTATGCCCC 59.558 63.158 0.00 0.00 34.57 5.80
1104 1115 1.589196 GCCGACACGAGAGGTATGC 60.589 63.158 0.00 0.00 0.00 3.14
1105 1116 0.172578 TTGCCGACACGAGAGGTATG 59.827 55.000 0.00 0.00 0.00 2.39
1106 1117 0.456221 CTTGCCGACACGAGAGGTAT 59.544 55.000 0.00 0.00 0.00 2.73
1110 1121 4.154613 GTCTTGCCGACACGAGAG 57.845 61.111 0.00 0.00 42.37 3.20
1118 1129 4.571250 GACGACATGTCTTGCCGA 57.429 55.556 22.95 0.00 44.58 5.54
1135 1146 0.888619 TCACTCTCGGTTGGCAGTAG 59.111 55.000 0.00 0.00 0.00 2.57
1137 1148 1.668294 CTCACTCTCGGTTGGCAGT 59.332 57.895 0.00 0.00 0.00 4.40
1156 1167 1.001406 ACTTTCCGAGGAAGCAGTGAG 59.999 52.381 8.06 3.64 35.38 3.51
1158 1169 1.151668 CACTTTCCGAGGAAGCAGTG 58.848 55.000 17.31 17.31 36.94 3.66
1159 1170 1.001406 CTCACTTTCCGAGGAAGCAGT 59.999 52.381 4.63 4.25 35.38 4.40
1170 1181 2.484264 CGAACCATCAACCTCACTTTCC 59.516 50.000 0.00 0.00 0.00 3.13
1182 1193 0.807275 CGATGAGCAGCGAACCATCA 60.807 55.000 1.37 2.58 43.75 3.07
1191 1202 3.384668 TGCTATAGTTTCGATGAGCAGC 58.615 45.455 0.84 0.00 35.12 5.25
1200 1211 4.047822 CCTGCTCTCTTGCTATAGTTTCG 58.952 47.826 0.84 0.00 0.00 3.46
1207 1218 2.115337 ATCCCCTGCTCTCTTGCTAT 57.885 50.000 0.00 0.00 0.00 2.97
1209 1220 0.998145 AAATCCCCTGCTCTCTTGCT 59.002 50.000 0.00 0.00 0.00 3.91
1227 1238 1.056660 GGGTGTCCTCTTCCTCACAA 58.943 55.000 0.00 0.00 33.17 3.33
1229 1240 0.610687 CTGGGTGTCCTCTTCCTCAC 59.389 60.000 0.00 0.00 0.00 3.51
1233 1244 1.268283 CCTCCTGGGTGTCCTCTTCC 61.268 65.000 0.00 0.00 0.00 3.46
1234 1245 2.291856 CCTCCTGGGTGTCCTCTTC 58.708 63.158 0.00 0.00 0.00 2.87
1235 1246 4.569214 CCTCCTGGGTGTCCTCTT 57.431 61.111 0.00 0.00 0.00 2.85
1245 1256 1.630878 AGCCAGTTAGAAACCTCCTGG 59.369 52.381 0.00 0.00 44.43 4.45
1272 1283 8.635765 AATTCTGTAATAAAACTGGCTTCAGA 57.364 30.769 0.00 0.00 40.86 3.27
1273 1284 7.693951 CGAATTCTGTAATAAAACTGGCTTCAG 59.306 37.037 3.52 0.00 43.84 3.02
1275 1286 6.967199 CCGAATTCTGTAATAAAACTGGCTTC 59.033 38.462 3.52 0.00 0.00 3.86
1276 1287 6.625081 GCCGAATTCTGTAATAAAACTGGCTT 60.625 38.462 3.52 0.00 33.62 4.35
1277 1288 5.163652 GCCGAATTCTGTAATAAAACTGGCT 60.164 40.000 3.52 0.00 33.62 4.75
1278 1289 5.034797 GCCGAATTCTGTAATAAAACTGGC 58.965 41.667 3.52 0.30 0.00 4.85
1285 1296 4.941263 AGTTGCAGCCGAATTCTGTAATAA 59.059 37.500 3.52 0.00 38.17 1.40
1287 1298 3.127548 CAGTTGCAGCCGAATTCTGTAAT 59.872 43.478 3.52 0.00 38.17 1.89
1288 1299 2.483877 CAGTTGCAGCCGAATTCTGTAA 59.516 45.455 3.52 0.00 34.58 2.41
1290 1301 0.877071 CAGTTGCAGCCGAATTCTGT 59.123 50.000 3.52 0.00 34.21 3.41
1292 1303 0.962356 CCCAGTTGCAGCCGAATTCT 60.962 55.000 3.52 0.00 0.00 2.40
1296 1307 2.281484 GTCCCAGTTGCAGCCGAA 60.281 61.111 0.00 0.00 0.00 4.30
1297 1308 3.241530 AGTCCCAGTTGCAGCCGA 61.242 61.111 0.00 0.00 0.00 5.54
1298 1309 2.809861 ATCAGTCCCAGTTGCAGCCG 62.810 60.000 0.00 0.00 0.00 5.52
1301 1312 1.457346 GGAATCAGTCCCAGTTGCAG 58.543 55.000 0.00 0.00 41.10 4.41
1302 1313 3.650647 GGAATCAGTCCCAGTTGCA 57.349 52.632 0.00 0.00 41.10 4.08
1323 1334 3.617263 CGTTTCTAGTTACCTGCACATCC 59.383 47.826 0.00 0.00 0.00 3.51
1324 1335 4.243270 ACGTTTCTAGTTACCTGCACATC 58.757 43.478 0.00 0.00 0.00 3.06
1326 1337 3.738830 ACGTTTCTAGTTACCTGCACA 57.261 42.857 0.00 0.00 0.00 4.57
1337 1348 7.637132 ACGAACATTTAACAACAACGTTTCTAG 59.363 33.333 0.00 0.00 0.00 2.43
1341 1352 6.362820 ACAACGAACATTTAACAACAACGTTT 59.637 30.769 0.00 0.00 38.90 3.60
1344 1355 5.735427 AGACAACGAACATTTAACAACAACG 59.265 36.000 0.00 0.00 0.00 4.10
1345 1356 7.061326 ACAAGACAACGAACATTTAACAACAAC 59.939 33.333 0.00 0.00 0.00 3.32
1346 1357 7.061210 CACAAGACAACGAACATTTAACAACAA 59.939 33.333 0.00 0.00 0.00 2.83
1350 1361 6.424176 TCACAAGACAACGAACATTTAACA 57.576 33.333 0.00 0.00 0.00 2.41
1356 1367 3.186409 CCGAATCACAAGACAACGAACAT 59.814 43.478 0.00 0.00 0.00 2.71
1357 1368 2.542178 CCGAATCACAAGACAACGAACA 59.458 45.455 0.00 0.00 0.00 3.18
1360 1371 1.144969 GCCGAATCACAAGACAACGA 58.855 50.000 0.00 0.00 0.00 3.85
1361 1372 1.126846 GAGCCGAATCACAAGACAACG 59.873 52.381 0.00 0.00 0.00 4.10
1362 1373 2.143122 TGAGCCGAATCACAAGACAAC 58.857 47.619 0.00 0.00 0.00 3.32
1365 1376 3.265791 AGATTGAGCCGAATCACAAGAC 58.734 45.455 7.77 0.00 35.16 3.01
1370 1381 4.505922 CAGAGTTAGATTGAGCCGAATCAC 59.494 45.833 7.77 0.00 35.16 3.06
1373 1384 3.462021 GCAGAGTTAGATTGAGCCGAAT 58.538 45.455 0.00 0.00 0.00 3.34
1375 1386 1.137086 GGCAGAGTTAGATTGAGCCGA 59.863 52.381 0.00 0.00 0.00 5.54
1381 1392 3.012518 CAACCTGGGCAGAGTTAGATTG 58.987 50.000 0.00 0.00 0.00 2.67
1382 1393 2.644798 ACAACCTGGGCAGAGTTAGATT 59.355 45.455 0.00 0.00 0.00 2.40
1395 1406 0.884704 CGTCAACCTCCACAACCTGG 60.885 60.000 0.00 0.00 42.29 4.45
1413 1424 1.819229 CTCTGGATCCACCTCACCG 59.181 63.158 11.44 0.00 39.86 4.94
1416 1427 0.041684 TCAGCTCTGGATCCACCTCA 59.958 55.000 11.44 0.00 39.86 3.86
1425 1436 6.609212 AGTCACTTAATATCTTCAGCTCTGGA 59.391 38.462 0.00 0.00 0.00 3.86
1429 1440 9.190858 CACATAGTCACTTAATATCTTCAGCTC 57.809 37.037 0.00 0.00 0.00 4.09
1442 1453 5.597182 GGGAGATGTACCACATAGTCACTTA 59.403 44.000 0.00 0.00 39.27 2.24
1443 1454 4.406003 GGGAGATGTACCACATAGTCACTT 59.594 45.833 0.00 0.00 39.27 3.16
1449 1460 3.829601 GAGAGGGGAGATGTACCACATAG 59.170 52.174 0.00 0.00 39.27 2.23
1461 1472 1.682478 TACAGTCAGGAGAGGGGAGA 58.318 55.000 0.00 0.00 0.00 3.71
1494 1505 1.153168 CACAAGCGGAGGGGTATGG 60.153 63.158 0.00 0.00 0.00 2.74
1496 1507 2.590092 GCACAAGCGGAGGGGTAT 59.410 61.111 0.00 0.00 0.00 2.73
1497 1508 3.712907 GGCACAAGCGGAGGGGTA 61.713 66.667 0.00 0.00 43.41 3.69
1515 1526 0.180406 TGAATCTAAGCGCCCCTTCC 59.820 55.000 2.29 0.00 34.95 3.46
1597 1608 5.273208 AGCACTACCTTCCAGATCTCTTAA 58.727 41.667 0.00 0.00 0.00 1.85
1616 1627 6.787043 CGAATTTTTGCAAGTTTTATGAGCAC 59.213 34.615 0.00 0.00 34.56 4.40
1618 1629 6.876804 ACGAATTTTTGCAAGTTTTATGAGC 58.123 32.000 0.00 0.00 0.00 4.26
1653 1665 9.434420 GCTCTAATCATCAACTCATTATTAGCT 57.566 33.333 0.00 0.00 30.54 3.32
1749 1761 0.984230 CAGCTAAGTTCCCCCTCACA 59.016 55.000 0.00 0.00 0.00 3.58
1932 1953 3.815401 GCCTAGAAAGCTTGACAACAGAA 59.185 43.478 0.00 0.00 0.00 3.02
2249 2272 2.235016 CACCCGATTTTCCCACAGAAA 58.765 47.619 0.00 0.00 42.82 2.52
2259 2282 3.756434 CACACAGAATACCACCCGATTTT 59.244 43.478 0.00 0.00 0.00 1.82
2265 2288 0.034477 CCCCACACAGAATACCACCC 60.034 60.000 0.00 0.00 0.00 4.61
2286 2309 8.489990 AGACAACATCAAAAGTATCATCTCTG 57.510 34.615 0.00 0.00 0.00 3.35
2290 2313 7.335422 ACAGGAGACAACATCAAAAGTATCATC 59.665 37.037 0.00 0.00 0.00 2.92
2305 2328 1.604278 GCCTTTCACACAGGAGACAAC 59.396 52.381 0.00 0.00 32.41 3.32
2451 2475 3.141398 CGGGACTTGCATATTGCTACAT 58.859 45.455 0.75 0.00 45.31 2.29
2577 2603 4.753233 TGTGAATCTCTCTAAGAGCAAGC 58.247 43.478 0.00 0.00 42.04 4.01
2720 2746 2.434336 TGGTATGAGATTTCCTGGACCG 59.566 50.000 0.00 0.00 0.00 4.79
2754 2780 0.830648 CCTCATCACCCGAGGCTAAA 59.169 55.000 0.00 0.00 43.50 1.85
2785 2811 3.977427 ACCGAAATTCTCTGGTTTTTGC 58.023 40.909 0.00 0.00 29.93 3.68
2791 2817 3.146847 GGTCAAACCGAAATTCTCTGGT 58.853 45.455 0.00 0.00 33.92 4.00
2989 3015 9.593134 CTCTTCTAGCATGTATAATTCCATACC 57.407 37.037 0.00 0.00 31.52 2.73
3252 3278 3.255725 CGTGGCATGCTCAATCAAATTT 58.744 40.909 18.92 0.00 0.00 1.82
3282 3308 2.206576 CTGGGCCAACTAGCTCTTTT 57.793 50.000 8.04 0.00 33.00 2.27
3367 3393 6.349300 ACTCTCGGCATAAGTCATTGTTATT 58.651 36.000 0.00 0.00 0.00 1.40
3554 3580 2.319136 AACATATCGGCCTAAACGCA 57.681 45.000 0.00 0.00 0.00 5.24
3575 3662 6.498303 TGATGAGCTTATAAGGGCATCTAAGA 59.502 38.462 14.28 0.00 34.70 2.10
3625 3712 2.412870 TCAACTTGTCAGCATACACCG 58.587 47.619 0.00 0.00 0.00 4.94
3748 3837 2.664402 ATCAAGTTTCAGCACCACCT 57.336 45.000 0.00 0.00 0.00 4.00
3784 3873 4.319177 CAAGAAGTCCCAGTTCACCTTAG 58.681 47.826 0.00 0.00 30.04 2.18
3951 4041 2.452600 AACAGAAAAGGGGAGTGCAA 57.547 45.000 0.00 0.00 0.00 4.08
3952 4042 2.452600 AAACAGAAAAGGGGAGTGCA 57.547 45.000 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.