Multiple sequence alignment - TraesCS4B01G105100

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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 TraesCS4B01G105100 chr4B 100.000 2541 0 0 1 2541 112500865 112498325 0.000000e+00 4693.0
1 TraesCS4B01G105100 chr4D 91.399 1372 81 22 363 1715 80222309 80220956 0.000000e+00 1845.0
2 TraesCS4B01G105100 chr4D 86.634 202 21 4 2345 2541 69135231 69135431 4.260000e-53 219.0
3 TraesCS4B01G105100 chr4A 91.747 1345 81 16 396 1719 505495055 505496390 0.000000e+00 1842.0
4 TraesCS4B01G105100 chr4A 87.273 220 24 3 6 224 505494405 505494621 5.430000e-62 248.0
5 TraesCS4B01G105100 chr4A 88.000 200 21 2 2345 2541 631641392 631641193 1.520000e-57 233.0
6 TraesCS4B01G105100 chr6D 90.536 634 54 4 1719 2346 90345280 90344647 0.000000e+00 833.0
7 TraesCS4B01G105100 chr6D 84.858 634 65 15 1713 2342 445767651 445768257 6.010000e-171 610.0
8 TraesCS4B01G105100 chr6D 87.065 201 21 3 2345 2541 144603256 144603455 3.290000e-54 222.0
9 TraesCS4B01G105100 chr1D 88.057 628 71 4 1718 2342 7410786 7410160 0.000000e+00 741.0
10 TraesCS4B01G105100 chr1D 89.894 188 16 2 2347 2532 379571560 379571746 3.270000e-59 239.0
11 TraesCS4B01G105100 chr6B 87.480 631 75 4 1718 2346 707332123 707331495 0.000000e+00 725.0
12 TraesCS4B01G105100 chr6B 85.354 635 83 7 1718 2346 707611088 707610458 0.000000e+00 649.0
13 TraesCS4B01G105100 chr6B 85.039 635 85 7 1718 2346 707665494 707664864 2.760000e-179 638.0
14 TraesCS4B01G105100 chr6A 84.015 538 68 5 1774 2310 4076311 4076831 3.770000e-138 501.0
15 TraesCS4B01G105100 chr3B 86.682 443 56 2 1716 2157 804222223 804222663 2.940000e-134 488.0
16 TraesCS4B01G105100 chr3B 87.065 201 22 3 2344 2541 55006788 55006589 9.150000e-55 224.0
17 TraesCS4B01G105100 chr3B 86.935 199 22 4 2345 2541 467905199 467905003 1.180000e-53 220.0
18 TraesCS4B01G105100 chr3B 87.000 200 21 3 2345 2541 821157180 821156983 1.180000e-53 220.0
19 TraesCS4B01G105100 chr3B 86.364 88 7 5 248 333 519067835 519067919 9.680000e-15 91.6
20 TraesCS4B01G105100 chr5D 80.055 361 61 8 1719 2077 28643016 28642665 9.020000e-65 257.0
21 TraesCS4B01G105100 chr7B 87.437 199 20 4 2345 2539 147573555 147573752 9.150000e-55 224.0
22 TraesCS4B01G105100 chr7B 87.065 201 21 3 2345 2541 605109075 605109274 3.290000e-54 222.0
23 TraesCS4B01G105100 chr3D 83.193 119 13 7 253 368 394978774 394978888 4.470000e-18 102.0
24 TraesCS4B01G105100 chr2A 86.047 86 12 0 2071 2156 101900930 101901015 2.690000e-15 93.5


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 TraesCS4B01G105100 chr4B 112498325 112500865 2540 True 4693 4693 100.000 1 2541 1 chr4B.!!$R1 2540
1 TraesCS4B01G105100 chr4D 80220956 80222309 1353 True 1845 1845 91.399 363 1715 1 chr4D.!!$R1 1352
2 TraesCS4B01G105100 chr4A 505494405 505496390 1985 False 1045 1842 89.510 6 1719 2 chr4A.!!$F1 1713
3 TraesCS4B01G105100 chr6D 90344647 90345280 633 True 833 833 90.536 1719 2346 1 chr6D.!!$R1 627
4 TraesCS4B01G105100 chr6D 445767651 445768257 606 False 610 610 84.858 1713 2342 1 chr6D.!!$F2 629
5 TraesCS4B01G105100 chr1D 7410160 7410786 626 True 741 741 88.057 1718 2342 1 chr1D.!!$R1 624
6 TraesCS4B01G105100 chr6B 707331495 707332123 628 True 725 725 87.480 1718 2346 1 chr6B.!!$R1 628
7 TraesCS4B01G105100 chr6B 707610458 707611088 630 True 649 649 85.354 1718 2346 1 chr6B.!!$R2 628
8 TraesCS4B01G105100 chr6B 707664864 707665494 630 True 638 638 85.039 1718 2346 1 chr6B.!!$R3 628
9 TraesCS4B01G105100 chr6A 4076311 4076831 520 False 501 501 84.015 1774 2310 1 chr6A.!!$F1 536

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
233 234 0.04331 GCGATGACATTTACGACGGC 60.043 55.0 0.00 0.0 0.00 5.68 F
235 236 0.04331 GATGACATTTACGACGGCGC 60.043 55.0 12.58 0.0 42.48 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1267 1576 0.250513 GCTTCCGGTTGATCTCCACT 59.749 55.0 0.00 0.0 0.00 4.00 R
1886 2207 0.251922 AACCTCCAATGTGGCATGCT 60.252 50.0 18.92 0.0 37.47 3.79 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
24 25 0.108138 AGTATGGTCGGTGCTTGAGC 60.108 55.000 0.00 0.00 42.50 4.26
51 52 2.012673 GTGCTCTTTGCGATTCCAGAT 58.987 47.619 0.00 0.00 46.63 2.90
55 56 3.539604 CTCTTTGCGATTCCAGATTCCT 58.460 45.455 0.00 0.00 0.00 3.36
68 69 6.907853 TCCAGATTCCTCACTACTCATATG 57.092 41.667 0.00 0.00 0.00 1.78
75 76 8.588290 ATTCCTCACTACTCATATGATCTACC 57.412 38.462 5.72 0.00 0.00 3.18
77 78 7.398829 TCCTCACTACTCATATGATCTACCTC 58.601 42.308 5.72 0.00 0.00 3.85
93 94 1.162698 CCTCACAAGTGTGGAGCATG 58.837 55.000 14.43 0.00 44.61 4.06
109 110 2.013563 GCATGGCTCTTTGTCGGATCA 61.014 52.381 0.00 0.00 0.00 2.92
135 136 5.350504 AGCTACTCTTCATGTGCATAAGT 57.649 39.130 0.00 0.00 0.00 2.24
137 138 4.872691 GCTACTCTTCATGTGCATAAGTGT 59.127 41.667 0.00 2.18 33.14 3.55
139 140 4.898320 ACTCTTCATGTGCATAAGTGTGA 58.102 39.130 0.00 0.00 0.00 3.58
140 141 4.934001 ACTCTTCATGTGCATAAGTGTGAG 59.066 41.667 0.00 0.00 0.00 3.51
142 143 3.979101 TCATGTGCATAAGTGTGAGGA 57.021 42.857 0.00 0.00 0.00 3.71
143 144 4.492494 TCATGTGCATAAGTGTGAGGAT 57.508 40.909 0.00 0.00 0.00 3.24
146 147 5.993441 TCATGTGCATAAGTGTGAGGATATG 59.007 40.000 0.00 0.00 0.00 1.78
150 151 6.127196 TGTGCATAAGTGTGAGGATATGTGTA 60.127 38.462 0.00 0.00 0.00 2.90
151 152 6.201044 GTGCATAAGTGTGAGGATATGTGTAC 59.799 42.308 0.00 0.00 0.00 2.90
153 154 6.761242 GCATAAGTGTGAGGATATGTGTACAA 59.239 38.462 0.00 0.00 0.00 2.41
154 155 7.279981 GCATAAGTGTGAGGATATGTGTACAAA 59.720 37.037 0.00 0.00 0.00 2.83
156 157 9.905713 ATAAGTGTGAGGATATGTGTACAAAAT 57.094 29.630 0.00 0.00 0.00 1.82
173 174 8.418662 TGTACAAAATATATGTTCTACTCCGCT 58.581 33.333 0.00 0.00 32.27 5.52
175 176 7.272978 ACAAAATATATGTTCTACTCCGCTGT 58.727 34.615 0.00 0.00 0.00 4.40
218 219 1.533469 GGGGCGATGTACTAGGCGAT 61.533 60.000 0.00 0.00 0.00 4.58
224 225 3.857383 GCGATGTACTAGGCGATGACATT 60.857 47.826 0.00 0.00 31.03 2.71
225 226 4.299155 CGATGTACTAGGCGATGACATTT 58.701 43.478 0.00 0.00 31.03 2.32
226 227 5.458015 CGATGTACTAGGCGATGACATTTA 58.542 41.667 0.00 0.00 31.03 1.40
227 228 5.342525 CGATGTACTAGGCGATGACATTTAC 59.657 44.000 0.00 0.00 31.03 2.01
228 229 4.603985 TGTACTAGGCGATGACATTTACG 58.396 43.478 0.00 0.00 0.00 3.18
229 230 4.336153 TGTACTAGGCGATGACATTTACGA 59.664 41.667 0.00 0.00 0.00 3.43
230 231 3.703420 ACTAGGCGATGACATTTACGAC 58.297 45.455 0.00 0.00 0.00 4.34
231 232 1.556564 AGGCGATGACATTTACGACG 58.443 50.000 0.00 0.00 38.87 5.12
232 233 0.575390 GGCGATGACATTTACGACGG 59.425 55.000 0.00 0.00 0.00 4.79
233 234 0.043310 GCGATGACATTTACGACGGC 60.043 55.000 0.00 0.00 0.00 5.68
234 235 0.226235 CGATGACATTTACGACGGCG 59.774 55.000 10.39 10.39 44.79 6.46
235 236 0.043310 GATGACATTTACGACGGCGC 60.043 55.000 12.58 0.00 42.48 6.53
236 237 0.738063 ATGACATTTACGACGGCGCA 60.738 50.000 12.58 0.00 42.48 6.09
237 238 1.058284 GACATTTACGACGGCGCAC 59.942 57.895 12.58 0.00 42.48 5.34
258 259 4.899239 GGTGGCGGCGAGGATGAG 62.899 72.222 12.98 0.00 0.00 2.90
259 260 4.899239 GTGGCGGCGAGGATGAGG 62.899 72.222 12.98 0.00 0.00 3.86
262 263 4.292178 GCGGCGAGGATGAGGGAG 62.292 72.222 12.98 0.00 0.00 4.30
263 264 4.292178 CGGCGAGGATGAGGGAGC 62.292 72.222 0.00 0.00 0.00 4.70
264 265 3.157252 GGCGAGGATGAGGGAGCA 61.157 66.667 0.00 0.00 0.00 4.26
265 266 2.735772 GGCGAGGATGAGGGAGCAA 61.736 63.158 0.00 0.00 0.00 3.91
266 267 1.227497 GCGAGGATGAGGGAGCAAG 60.227 63.158 0.00 0.00 0.00 4.01
267 268 1.445095 CGAGGATGAGGGAGCAAGG 59.555 63.158 0.00 0.00 0.00 3.61
268 269 1.835693 GAGGATGAGGGAGCAAGGG 59.164 63.158 0.00 0.00 0.00 3.95
269 270 0.985490 GAGGATGAGGGAGCAAGGGT 60.985 60.000 0.00 0.00 0.00 4.34
270 271 1.225704 GGATGAGGGAGCAAGGGTG 59.774 63.158 0.00 0.00 0.00 4.61
271 272 1.225704 GATGAGGGAGCAAGGGTGG 59.774 63.158 0.00 0.00 0.00 4.61
272 273 1.229951 ATGAGGGAGCAAGGGTGGA 60.230 57.895 0.00 0.00 0.00 4.02
273 274 1.277580 ATGAGGGAGCAAGGGTGGAG 61.278 60.000 0.00 0.00 0.00 3.86
274 275 2.612115 AGGGAGCAAGGGTGGAGG 60.612 66.667 0.00 0.00 0.00 4.30
275 276 2.610859 GGGAGCAAGGGTGGAGGA 60.611 66.667 0.00 0.00 0.00 3.71
276 277 2.671682 GGAGCAAGGGTGGAGGAC 59.328 66.667 0.00 0.00 0.00 3.85
277 278 2.266055 GAGCAAGGGTGGAGGACG 59.734 66.667 0.00 0.00 0.00 4.79
278 279 3.316573 GAGCAAGGGTGGAGGACGG 62.317 68.421 0.00 0.00 0.00 4.79
279 280 3.637273 GCAAGGGTGGAGGACGGT 61.637 66.667 0.00 0.00 0.00 4.83
280 281 2.347490 CAAGGGTGGAGGACGGTG 59.653 66.667 0.00 0.00 0.00 4.94
281 282 2.203182 AAGGGTGGAGGACGGTGA 59.797 61.111 0.00 0.00 0.00 4.02
282 283 2.214920 AAGGGTGGAGGACGGTGAC 61.215 63.158 0.00 0.00 0.00 3.67
299 300 4.830765 CGGCTCGGATGCGGGAAA 62.831 66.667 12.04 0.00 0.00 3.13
300 301 2.203209 GGCTCGGATGCGGGAAAT 60.203 61.111 12.04 0.00 0.00 2.17
301 302 2.546494 GGCTCGGATGCGGGAAATG 61.546 63.158 12.04 0.00 0.00 2.32
302 303 2.546494 GCTCGGATGCGGGAAATGG 61.546 63.158 12.04 0.00 0.00 3.16
303 304 1.146041 CTCGGATGCGGGAAATGGA 59.854 57.895 0.00 0.00 0.00 3.41
304 305 0.882042 CTCGGATGCGGGAAATGGAG 60.882 60.000 0.00 0.00 0.00 3.86
305 306 1.146041 CGGATGCGGGAAATGGAGA 59.854 57.895 0.00 0.00 0.00 3.71
306 307 0.463654 CGGATGCGGGAAATGGAGAA 60.464 55.000 0.00 0.00 0.00 2.87
307 308 1.025041 GGATGCGGGAAATGGAGAAC 58.975 55.000 0.00 0.00 0.00 3.01
308 309 1.408822 GGATGCGGGAAATGGAGAACT 60.409 52.381 0.00 0.00 0.00 3.01
309 310 2.158813 GGATGCGGGAAATGGAGAACTA 60.159 50.000 0.00 0.00 0.00 2.24
310 311 3.541632 GATGCGGGAAATGGAGAACTAA 58.458 45.455 0.00 0.00 0.00 2.24
311 312 2.706890 TGCGGGAAATGGAGAACTAAC 58.293 47.619 0.00 0.00 0.00 2.34
312 313 1.664151 GCGGGAAATGGAGAACTAACG 59.336 52.381 0.00 0.00 0.00 3.18
313 314 1.664151 CGGGAAATGGAGAACTAACGC 59.336 52.381 0.00 0.00 0.00 4.84
314 315 1.664151 GGGAAATGGAGAACTAACGCG 59.336 52.381 3.53 3.53 0.00 6.01
315 316 1.664151 GGAAATGGAGAACTAACGCGG 59.336 52.381 12.47 0.00 0.00 6.46
316 317 1.062148 GAAATGGAGAACTAACGCGGC 59.938 52.381 12.47 0.00 0.00 6.53
322 587 1.810030 GAACTAACGCGGCAGGAGG 60.810 63.158 12.47 0.00 0.00 4.30
333 598 2.107141 CAGGAGGGCGGTCGATTC 59.893 66.667 0.00 0.00 0.00 2.52
335 600 4.587189 GGAGGGCGGTCGATTCGG 62.587 72.222 6.18 0.00 0.00 4.30
343 609 1.079405 GGTCGATTCGGTGGCTTGA 60.079 57.895 6.18 0.00 0.00 3.02
352 618 4.448537 TTCGGTGGCTTGATTAATTTGG 57.551 40.909 0.00 0.00 0.00 3.28
354 620 3.829601 TCGGTGGCTTGATTAATTTGGTT 59.170 39.130 0.00 0.00 0.00 3.67
367 633 9.289782 TGATTAATTTGGTTAAATTTTGGGTGG 57.710 29.630 0.00 0.00 42.33 4.61
393 659 1.142262 TCTATCCGATCCGACTGGTGA 59.858 52.381 0.00 0.00 36.30 4.02
405 671 0.892358 ACTGGTGAACGCGTCTAGGA 60.892 55.000 14.44 0.00 0.00 2.94
418 694 4.398358 CGCGTCTAGGATTCCTTATATCCA 59.602 45.833 11.25 0.00 43.33 3.41
444 727 8.256605 ACCATATATGTGAGCTTGATATGAGAC 58.743 37.037 11.73 0.00 33.98 3.36
449 732 3.549471 GTGAGCTTGATATGAGACGTGTG 59.451 47.826 0.00 0.00 0.00 3.82
457 740 2.264109 ATGAGACGTGTGAGTTAGCG 57.736 50.000 0.00 0.00 0.00 4.26
459 742 0.386858 GAGACGTGTGAGTTAGCGCA 60.387 55.000 11.47 0.00 0.00 6.09
470 753 4.267928 GTGAGTTAGCGCAAACGAATAGAT 59.732 41.667 11.47 0.00 43.93 1.98
472 755 4.430007 AGTTAGCGCAAACGAATAGATCA 58.570 39.130 11.47 0.00 43.93 2.92
484 767 6.262056 ACGAATAGATCAATTTAAGGGGGT 57.738 37.500 0.00 0.00 0.00 4.95
488 771 7.717875 CGAATAGATCAATTTAAGGGGGTTGTA 59.282 37.037 0.00 0.00 0.00 2.41
490 773 8.940397 ATAGATCAATTTAAGGGGGTTGTATG 57.060 34.615 0.00 0.00 0.00 2.39
511 794 1.459592 GGTCGTGATTTTGTGACCGAG 59.540 52.381 0.00 0.00 41.26 4.63
512 795 1.136336 GTCGTGATTTTGTGACCGAGC 60.136 52.381 0.00 0.00 0.00 5.03
544 828 5.692204 CGGACATATAGGTGACATTTGAGAC 59.308 44.000 0.00 0.00 0.00 3.36
550 834 0.669318 GTGACATTTGAGACGCCCGA 60.669 55.000 0.00 0.00 0.00 5.14
553 837 0.892755 ACATTTGAGACGCCCGACTA 59.107 50.000 0.00 0.00 0.00 2.59
569 853 4.320348 CCCGACTATAGACGCTCTAAAAGG 60.320 50.000 17.45 8.12 31.96 3.11
576 860 1.198759 ACGCTCTAAAAGGCCCAGGA 61.199 55.000 0.00 0.00 0.00 3.86
589 873 3.052338 AGGCCCAGGAATTGATTTGATCT 60.052 43.478 0.00 0.00 0.00 2.75
601 885 5.892160 TGATTTGATCTGAGCTGGAAAAG 57.108 39.130 0.00 0.00 0.00 2.27
604 888 6.491062 TGATTTGATCTGAGCTGGAAAAGAAA 59.509 34.615 0.00 0.00 0.00 2.52
611 895 0.673985 GCTGGAAAAGAAAGGCGGTT 59.326 50.000 0.00 0.00 0.00 4.44
615 899 1.335964 GGAAAAGAAAGGCGGTTGAGC 60.336 52.381 0.00 0.00 0.00 4.26
678 962 7.181569 CCAAATTAAAGGCTTGAGGGAATAA 57.818 36.000 0.00 0.00 0.00 1.40
1165 1450 1.247567 CCTCGCCAACATGAAAGGTT 58.752 50.000 0.00 0.00 44.44 3.50
1166 1451 1.200020 CCTCGCCAACATGAAAGGTTC 59.800 52.381 0.00 0.00 39.78 3.62
1173 1458 4.261447 GCCAACATGAAAGGTTCGTAACTT 60.261 41.667 0.00 0.00 39.78 2.66
1181 1466 1.069668 AGGTTCGTAACTTGGCGAAGT 59.930 47.619 8.47 8.47 45.81 3.01
1182 1467 1.458445 GGTTCGTAACTTGGCGAAGTC 59.542 52.381 14.89 2.51 45.81 3.01
1210 1517 8.850156 GCCATTATTCACTATGGTTAATGAACT 58.150 33.333 11.60 0.00 42.67 3.01
1244 1551 5.777802 TGATTGCGATTGTGTTAATTGGTT 58.222 33.333 0.00 0.00 0.00 3.67
1249 1556 4.294232 CGATTGTGTTAATTGGTTGCACA 58.706 39.130 0.00 0.00 38.15 4.57
1411 1720 3.542676 CCCTACATGGCGCCGGTA 61.543 66.667 23.90 24.00 0.00 4.02
1471 1780 1.194781 AAGGTGTCATGCCGGTCTCT 61.195 55.000 1.90 0.00 0.00 3.10
1618 1931 4.508584 GGTGATTCCTACCAAAAGACCCTT 60.509 45.833 0.00 0.00 38.12 3.95
1683 1998 8.908172 AGTAGAACTACTATAACAAAACTCGC 57.092 34.615 12.07 0.00 43.98 5.03
1747 2062 8.522003 GTGAATTCCGGTTTTTACCCTTTATTA 58.478 33.333 0.00 0.00 0.00 0.98
1748 2063 9.086758 TGAATTCCGGTTTTTACCCTTTATTAA 57.913 29.630 0.00 0.00 0.00 1.40
1781 2097 7.863722 TGACACTAATTACCCTATTTAGCCAA 58.136 34.615 0.00 0.00 0.00 4.52
1853 2170 8.207545 ACCCTGTTTAAAATTTTGTGAGCATTA 58.792 29.630 13.76 0.00 0.00 1.90
1886 2207 5.304614 GGGTCATAATTGTCAGGTCTAGCTA 59.695 44.000 0.00 0.00 0.00 3.32
1896 2217 0.465705 GGTCTAGCTAGCATGCCACA 59.534 55.000 18.83 0.00 0.00 4.17
1901 2222 0.256752 AGCTAGCATGCCACATTGGA 59.743 50.000 18.83 0.00 40.96 3.53
1970 2291 1.915769 AGCTTCTCCCGACCAGCTT 60.916 57.895 0.00 0.00 39.69 3.74
2054 2378 1.447838 CGCTTCCAGCCGCTTCTAA 60.448 57.895 0.00 0.00 38.18 2.10
2066 2390 1.601903 CGCTTCTAACTTGTGTTGCCA 59.398 47.619 0.00 0.00 37.59 4.92
2113 2438 2.813908 GCTTCCGACCGAACGCAT 60.814 61.111 0.00 0.00 0.00 4.73
2157 2482 4.585879 ACGGTTAGGTATTGTCAAGCATT 58.414 39.130 0.00 0.00 0.00 3.56
2177 2502 4.986587 CGACGGCGACACCAACGA 62.987 66.667 16.62 0.00 40.82 3.85
2239 2565 2.992689 TCCACGAGCAGGCCGTAA 60.993 61.111 0.00 0.00 38.29 3.18
2240 2566 2.186903 CCACGAGCAGGCCGTAAT 59.813 61.111 0.00 0.00 38.29 1.89
2241 2567 1.038681 TCCACGAGCAGGCCGTAATA 61.039 55.000 0.00 0.00 38.29 0.98
2242 2568 0.033504 CCACGAGCAGGCCGTAATAT 59.966 55.000 0.00 0.00 38.29 1.28
2310 2640 2.650116 AAGCTCGCTGACATCGGGT 61.650 57.895 0.00 0.00 0.00 5.28
2346 2676 3.068064 TGATCCGCTGCACCGAGA 61.068 61.111 2.22 0.00 0.00 4.04
2347 2677 2.279120 GATCCGCTGCACCGAGAG 60.279 66.667 2.22 0.00 0.00 3.20
2348 2678 4.521062 ATCCGCTGCACCGAGAGC 62.521 66.667 2.22 0.00 0.00 4.09
2351 2681 3.782244 CGCTGCACCGAGAGCAAC 61.782 66.667 0.00 0.00 42.17 4.17
2352 2682 2.358003 GCTGCACCGAGAGCAACT 60.358 61.111 0.00 0.00 42.17 3.16
2353 2683 2.386660 GCTGCACCGAGAGCAACTC 61.387 63.158 0.00 1.59 42.17 3.01
2354 2684 1.739562 CTGCACCGAGAGCAACTCC 60.740 63.158 5.57 0.00 42.17 3.85
2355 2685 2.343758 GCACCGAGAGCAACTCCA 59.656 61.111 5.57 0.00 42.18 3.86
2356 2686 1.301716 GCACCGAGAGCAACTCCAA 60.302 57.895 5.57 0.00 42.18 3.53
2357 2687 1.569479 GCACCGAGAGCAACTCCAAC 61.569 60.000 5.57 0.00 42.18 3.77
2358 2688 1.006102 ACCGAGAGCAACTCCAACG 60.006 57.895 5.57 0.00 42.18 4.10
2359 2689 1.738099 CCGAGAGCAACTCCAACGG 60.738 63.158 9.70 9.70 42.18 4.44
2360 2690 1.738099 CGAGAGCAACTCCAACGGG 60.738 63.158 5.57 0.00 42.18 5.28
2361 2691 1.376037 GAGAGCAACTCCAACGGGG 60.376 63.158 0.33 0.00 39.53 5.73
2362 2692 3.056328 GAGCAACTCCAACGGGGC 61.056 66.667 0.00 0.00 36.21 5.80
2363 2693 3.842925 GAGCAACTCCAACGGGGCA 62.843 63.158 0.00 0.00 36.21 5.36
2364 2694 2.909965 GCAACTCCAACGGGGCAA 60.910 61.111 0.00 0.00 36.21 4.52
2365 2695 3.039134 CAACTCCAACGGGGCAAC 58.961 61.111 0.00 0.00 36.21 4.17
2377 2707 4.337060 GGCAACCCAAACGGACGC 62.337 66.667 0.00 0.00 34.64 5.19
2378 2708 4.676586 GCAACCCAAACGGACGCG 62.677 66.667 3.53 3.53 34.64 6.01
2379 2709 4.676586 CAACCCAAACGGACGCGC 62.677 66.667 5.73 0.00 34.64 6.86
2384 2714 4.659874 CAAACGGACGCGCGCTTT 62.660 61.111 32.58 19.12 0.00 3.51
2385 2715 4.659874 AAACGGACGCGCGCTTTG 62.660 61.111 32.58 19.69 0.00 2.77
2396 2726 4.115287 CGCTTTGTCCGCTTTTCG 57.885 55.556 0.00 0.00 38.08 3.46
2397 2727 1.278637 CGCTTTGTCCGCTTTTCGT 59.721 52.632 0.00 0.00 36.19 3.85
2398 2728 0.316689 CGCTTTGTCCGCTTTTCGTT 60.317 50.000 0.00 0.00 36.19 3.85
2399 2729 1.395670 GCTTTGTCCGCTTTTCGTTC 58.604 50.000 0.00 0.00 36.19 3.95
2400 2730 1.658968 CTTTGTCCGCTTTTCGTTCG 58.341 50.000 0.00 0.00 36.19 3.95
2401 2731 1.004292 CTTTGTCCGCTTTTCGTTCGT 60.004 47.619 0.00 0.00 36.19 3.85
2402 2732 1.008329 TTGTCCGCTTTTCGTTCGTT 58.992 45.000 0.00 0.00 36.19 3.85
2403 2733 1.008329 TGTCCGCTTTTCGTTCGTTT 58.992 45.000 0.00 0.00 36.19 3.60
2404 2734 1.267632 TGTCCGCTTTTCGTTCGTTTG 60.268 47.619 0.00 0.00 36.19 2.93
2405 2735 0.305313 TCCGCTTTTCGTTCGTTTGG 59.695 50.000 0.00 0.00 36.19 3.28
2406 2736 0.659123 CCGCTTTTCGTTCGTTTGGG 60.659 55.000 0.00 0.00 36.19 4.12
2407 2737 0.028374 CGCTTTTCGTTCGTTTGGGT 59.972 50.000 0.00 0.00 0.00 4.51
2408 2738 1.750351 GCTTTTCGTTCGTTTGGGTC 58.250 50.000 0.00 0.00 0.00 4.46
2409 2739 1.918543 GCTTTTCGTTCGTTTGGGTCG 60.919 52.381 0.00 0.00 0.00 4.79
2410 2740 0.656785 TTTTCGTTCGTTTGGGTCGG 59.343 50.000 0.00 0.00 0.00 4.79
2411 2741 1.774046 TTTCGTTCGTTTGGGTCGGC 61.774 55.000 0.00 0.00 0.00 5.54
2412 2742 3.719144 CGTTCGTTTGGGTCGGCC 61.719 66.667 0.00 0.00 0.00 6.13
2413 2743 2.592287 GTTCGTTTGGGTCGGCCA 60.592 61.111 9.07 0.00 36.17 5.36
2414 2744 2.281208 TTCGTTTGGGTCGGCCAG 60.281 61.111 9.07 0.00 36.17 4.85
2415 2745 3.835790 TTCGTTTGGGTCGGCCAGG 62.836 63.158 9.07 0.00 36.17 4.45
2422 2752 4.778143 GGTCGGCCAGGCGAACAT 62.778 66.667 24.60 0.00 34.09 2.71
2423 2753 3.499737 GTCGGCCAGGCGAACATG 61.500 66.667 18.32 0.00 0.00 3.21
2441 2771 3.164576 CGCGTCCGCATTCTGAAA 58.835 55.556 12.58 0.00 42.06 2.69
2442 2772 1.715585 CGCGTCCGCATTCTGAAAT 59.284 52.632 12.58 0.00 42.06 2.17
2443 2773 0.927537 CGCGTCCGCATTCTGAAATA 59.072 50.000 12.58 0.00 42.06 1.40
2444 2774 1.326245 CGCGTCCGCATTCTGAAATAA 59.674 47.619 12.58 0.00 42.06 1.40
2445 2775 2.597505 CGCGTCCGCATTCTGAAATAAG 60.598 50.000 12.58 0.00 42.06 1.73
2446 2776 2.351726 GCGTCCGCATTCTGAAATAAGT 59.648 45.455 6.82 0.00 41.49 2.24
2447 2777 3.181510 GCGTCCGCATTCTGAAATAAGTT 60.182 43.478 6.82 0.00 41.49 2.66
2448 2778 4.334443 CGTCCGCATTCTGAAATAAGTTG 58.666 43.478 0.00 0.00 0.00 3.16
2449 2779 4.662145 GTCCGCATTCTGAAATAAGTTGG 58.338 43.478 0.00 0.00 0.00 3.77
2450 2780 3.128589 TCCGCATTCTGAAATAAGTTGGC 59.871 43.478 0.00 0.00 0.00 4.52
2451 2781 3.129287 CCGCATTCTGAAATAAGTTGGCT 59.871 43.478 0.00 0.00 0.00 4.75
2452 2782 4.380867 CCGCATTCTGAAATAAGTTGGCTT 60.381 41.667 0.00 0.00 38.66 4.35
2453 2783 4.560035 CGCATTCTGAAATAAGTTGGCTTG 59.440 41.667 0.00 0.00 36.22 4.01
2454 2784 5.619757 CGCATTCTGAAATAAGTTGGCTTGA 60.620 40.000 0.00 0.00 36.22 3.02
2455 2785 5.574443 GCATTCTGAAATAAGTTGGCTTGAC 59.426 40.000 0.00 0.00 36.22 3.18
2456 2786 5.705609 TTCTGAAATAAGTTGGCTTGACC 57.294 39.130 0.00 0.00 36.22 4.02
2457 2787 3.751175 TCTGAAATAAGTTGGCTTGACCG 59.249 43.478 0.00 0.00 43.94 4.79
2458 2788 3.482436 TGAAATAAGTTGGCTTGACCGT 58.518 40.909 0.00 0.00 43.94 4.83
2459 2789 3.500680 TGAAATAAGTTGGCTTGACCGTC 59.499 43.478 0.00 0.00 43.94 4.79
2460 2790 2.109425 ATAAGTTGGCTTGACCGTCC 57.891 50.000 0.00 0.00 43.94 4.79
2461 2791 0.759959 TAAGTTGGCTTGACCGTCCA 59.240 50.000 0.00 0.00 43.94 4.02
2462 2792 0.818040 AAGTTGGCTTGACCGTCCAC 60.818 55.000 0.00 0.00 43.94 4.02
2463 2793 2.280524 TTGGCTTGACCGTCCACG 60.281 61.111 0.00 0.00 43.94 4.94
2474 2804 4.083862 GTCCACGGGGAGGCTGAC 62.084 72.222 6.67 0.00 46.12 3.51
2481 2811 4.344237 GGGAGGCTGACCCAAATG 57.656 61.111 6.40 0.00 46.05 2.32
2482 2812 1.384191 GGGAGGCTGACCCAAATGT 59.616 57.895 6.40 0.00 46.05 2.71
2483 2813 0.967380 GGGAGGCTGACCCAAATGTG 60.967 60.000 6.40 0.00 46.05 3.21
2484 2814 1.598701 GGAGGCTGACCCAAATGTGC 61.599 60.000 0.00 0.00 36.11 4.57
2485 2815 1.598701 GAGGCTGACCCAAATGTGCC 61.599 60.000 0.00 0.00 40.54 5.01
2486 2816 2.568090 GCTGACCCAAATGTGCCG 59.432 61.111 0.00 0.00 0.00 5.69
2487 2817 1.971167 GCTGACCCAAATGTGCCGA 60.971 57.895 0.00 0.00 0.00 5.54
2488 2818 1.875963 CTGACCCAAATGTGCCGAC 59.124 57.895 0.00 0.00 0.00 4.79
2489 2819 1.911293 CTGACCCAAATGTGCCGACG 61.911 60.000 0.00 0.00 0.00 5.12
2490 2820 1.964373 GACCCAAATGTGCCGACGT 60.964 57.895 0.00 0.00 0.00 4.34
2491 2821 2.182614 GACCCAAATGTGCCGACGTG 62.183 60.000 0.00 0.00 0.00 4.49
2492 2822 2.126888 CCAAATGTGCCGACGTGC 60.127 61.111 0.00 0.00 0.00 5.34
2493 2823 2.636462 CAAATGTGCCGACGTGCA 59.364 55.556 0.00 6.88 39.37 4.57
2494 2824 1.009108 CAAATGTGCCGACGTGCAA 60.009 52.632 11.70 4.74 44.11 4.08
2495 2825 0.593518 CAAATGTGCCGACGTGCAAA 60.594 50.000 11.70 7.90 44.11 3.68
2496 2826 0.101399 AAATGTGCCGACGTGCAAAA 59.899 45.000 11.70 5.35 44.11 2.44
2497 2827 0.101399 AATGTGCCGACGTGCAAAAA 59.899 45.000 11.70 3.28 44.11 1.94
2517 2847 3.889196 AAAGCTCGCACGAAATAAACA 57.111 38.095 0.00 0.00 0.00 2.83
2518 2848 4.419522 AAAGCTCGCACGAAATAAACAT 57.580 36.364 0.00 0.00 0.00 2.71
2519 2849 5.539582 AAAGCTCGCACGAAATAAACATA 57.460 34.783 0.00 0.00 0.00 2.29
2520 2850 5.539582 AAGCTCGCACGAAATAAACATAA 57.460 34.783 0.00 0.00 0.00 1.90
2521 2851 5.539582 AGCTCGCACGAAATAAACATAAA 57.460 34.783 0.00 0.00 0.00 1.40
2522 2852 5.933790 AGCTCGCACGAAATAAACATAAAA 58.066 33.333 0.00 0.00 0.00 1.52
2523 2853 6.551736 AGCTCGCACGAAATAAACATAAAAT 58.448 32.000 0.00 0.00 0.00 1.82
2524 2854 7.690228 AGCTCGCACGAAATAAACATAAAATA 58.310 30.769 0.00 0.00 0.00 1.40
2525 2855 8.178964 AGCTCGCACGAAATAAACATAAAATAA 58.821 29.630 0.00 0.00 0.00 1.40
2526 2856 8.790674 GCTCGCACGAAATAAACATAAAATAAA 58.209 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.829720 TCAAGCACCGACCATACTAACT 59.170 45.455 0.00 0.00 0.00 2.24
2 3 3.187700 CTCAAGCACCGACCATACTAAC 58.812 50.000 0.00 0.00 0.00 2.34
3 4 2.418197 GCTCAAGCACCGACCATACTAA 60.418 50.000 0.00 0.00 41.59 2.24
5 6 0.108138 GCTCAAGCACCGACCATACT 60.108 55.000 0.00 0.00 41.59 2.12
6 7 2.384203 GCTCAAGCACCGACCATAC 58.616 57.895 0.00 0.00 41.59 2.39
7 8 4.932789 GCTCAAGCACCGACCATA 57.067 55.556 0.00 0.00 41.59 2.74
24 25 4.398247 GAATCGCAAAGAGCACTTTACTG 58.602 43.478 8.88 0.00 43.41 2.74
34 35 3.539604 AGGAATCTGGAATCGCAAAGAG 58.460 45.455 0.00 0.00 0.00 2.85
41 42 4.339530 TGAGTAGTGAGGAATCTGGAATCG 59.660 45.833 0.00 0.00 0.00 3.34
51 52 7.760607 AGGTAGATCATATGAGTAGTGAGGAA 58.239 38.462 11.78 0.00 0.00 3.36
55 56 7.518188 TGTGAGGTAGATCATATGAGTAGTGA 58.482 38.462 11.78 0.00 0.00 3.41
77 78 0.892358 AGCCATGCTCCACACTTGTG 60.892 55.000 2.13 2.13 45.23 3.33
93 94 2.961526 TAGTGATCCGACAAAGAGCC 57.038 50.000 0.00 0.00 0.00 4.70
109 110 4.808414 TGCACATGAAGAGTAGCTTAGT 57.192 40.909 0.00 0.00 36.83 2.24
146 147 8.485591 GCGGAGTAGAACATATATTTTGTACAC 58.514 37.037 16.77 12.10 0.00 2.90
150 151 7.224753 CACAGCGGAGTAGAACATATATTTTGT 59.775 37.037 0.00 0.00 0.00 2.83
151 152 7.307396 CCACAGCGGAGTAGAACATATATTTTG 60.307 40.741 0.00 0.00 36.56 2.44
153 154 6.223852 CCACAGCGGAGTAGAACATATATTT 58.776 40.000 0.00 0.00 36.56 1.40
154 155 5.784177 CCACAGCGGAGTAGAACATATATT 58.216 41.667 0.00 0.00 36.56 1.28
156 157 3.005472 GCCACAGCGGAGTAGAACATATA 59.995 47.826 0.00 0.00 36.56 0.86
160 161 1.292223 GCCACAGCGGAGTAGAACA 59.708 57.895 0.00 0.00 36.56 3.18
170 171 1.652563 CATGGATGATGCCACAGCG 59.347 57.895 0.00 0.00 44.31 5.18
205 206 5.009310 TCGTAAATGTCATCGCCTAGTACAT 59.991 40.000 0.00 0.00 32.32 2.29
206 207 4.336153 TCGTAAATGTCATCGCCTAGTACA 59.664 41.667 0.00 0.00 0.00 2.90
212 213 1.556564 CGTCGTAAATGTCATCGCCT 58.443 50.000 0.00 0.00 0.00 5.52
218 219 1.373121 TGCGCCGTCGTAAATGTCA 60.373 52.632 4.18 0.00 38.14 3.58
224 225 4.764336 CCTCGTGCGCCGTCGTAA 62.764 66.667 16.00 0.00 38.14 3.18
241 242 4.899239 CTCATCCTCGCCGCCACC 62.899 72.222 0.00 0.00 0.00 4.61
242 243 4.899239 CCTCATCCTCGCCGCCAC 62.899 72.222 0.00 0.00 0.00 5.01
245 246 4.292178 CTCCCTCATCCTCGCCGC 62.292 72.222 0.00 0.00 0.00 6.53
246 247 4.292178 GCTCCCTCATCCTCGCCG 62.292 72.222 0.00 0.00 0.00 6.46
247 248 2.657102 CTTGCTCCCTCATCCTCGCC 62.657 65.000 0.00 0.00 0.00 5.54
248 249 1.227497 CTTGCTCCCTCATCCTCGC 60.227 63.158 0.00 0.00 0.00 5.03
249 250 1.445095 CCTTGCTCCCTCATCCTCG 59.555 63.158 0.00 0.00 0.00 4.63
250 251 0.985490 ACCCTTGCTCCCTCATCCTC 60.985 60.000 0.00 0.00 0.00 3.71
251 252 1.083706 ACCCTTGCTCCCTCATCCT 59.916 57.895 0.00 0.00 0.00 3.24
252 253 1.225704 CACCCTTGCTCCCTCATCC 59.774 63.158 0.00 0.00 0.00 3.51
253 254 1.225704 CCACCCTTGCTCCCTCATC 59.774 63.158 0.00 0.00 0.00 2.92
254 255 1.229951 TCCACCCTTGCTCCCTCAT 60.230 57.895 0.00 0.00 0.00 2.90
255 256 1.920325 CTCCACCCTTGCTCCCTCA 60.920 63.158 0.00 0.00 0.00 3.86
256 257 2.674220 CCTCCACCCTTGCTCCCTC 61.674 68.421 0.00 0.00 0.00 4.30
257 258 2.612115 CCTCCACCCTTGCTCCCT 60.612 66.667 0.00 0.00 0.00 4.20
258 259 2.610859 TCCTCCACCCTTGCTCCC 60.611 66.667 0.00 0.00 0.00 4.30
259 260 2.671682 GTCCTCCACCCTTGCTCC 59.328 66.667 0.00 0.00 0.00 4.70
260 261 2.266055 CGTCCTCCACCCTTGCTC 59.734 66.667 0.00 0.00 0.00 4.26
261 262 3.322466 CCGTCCTCCACCCTTGCT 61.322 66.667 0.00 0.00 0.00 3.91
262 263 3.637273 ACCGTCCTCCACCCTTGC 61.637 66.667 0.00 0.00 0.00 4.01
263 264 2.214216 TCACCGTCCTCCACCCTTG 61.214 63.158 0.00 0.00 0.00 3.61
264 265 2.203182 TCACCGTCCTCCACCCTT 59.797 61.111 0.00 0.00 0.00 3.95
265 266 2.603776 GTCACCGTCCTCCACCCT 60.604 66.667 0.00 0.00 0.00 4.34
266 267 4.065281 CGTCACCGTCCTCCACCC 62.065 72.222 0.00 0.00 0.00 4.61
267 268 4.065281 CCGTCACCGTCCTCCACC 62.065 72.222 0.00 0.00 0.00 4.61
268 269 4.736896 GCCGTCACCGTCCTCCAC 62.737 72.222 0.00 0.00 0.00 4.02
269 270 4.988716 AGCCGTCACCGTCCTCCA 62.989 66.667 0.00 0.00 0.00 3.86
270 271 4.131088 GAGCCGTCACCGTCCTCC 62.131 72.222 0.00 0.00 0.00 4.30
271 272 4.477975 CGAGCCGTCACCGTCCTC 62.478 72.222 0.00 0.00 0.00 3.71
274 275 3.823330 ATCCGAGCCGTCACCGTC 61.823 66.667 0.00 0.00 0.00 4.79
275 276 4.129737 CATCCGAGCCGTCACCGT 62.130 66.667 0.00 0.00 0.00 4.83
282 283 4.830765 TTTCCCGCATCCGAGCCG 62.831 66.667 0.00 0.00 36.29 5.52
283 284 2.203209 ATTTCCCGCATCCGAGCC 60.203 61.111 0.00 0.00 36.29 4.70
284 285 2.546494 CCATTTCCCGCATCCGAGC 61.546 63.158 0.00 0.00 36.29 5.03
285 286 0.882042 CTCCATTTCCCGCATCCGAG 60.882 60.000 0.00 0.00 36.29 4.63
286 287 1.146041 CTCCATTTCCCGCATCCGA 59.854 57.895 0.00 0.00 36.29 4.55
287 288 0.463654 TTCTCCATTTCCCGCATCCG 60.464 55.000 0.00 0.00 0.00 4.18
288 289 1.025041 GTTCTCCATTTCCCGCATCC 58.975 55.000 0.00 0.00 0.00 3.51
289 290 2.044123 AGTTCTCCATTTCCCGCATC 57.956 50.000 0.00 0.00 0.00 3.91
290 291 3.279434 GTTAGTTCTCCATTTCCCGCAT 58.721 45.455 0.00 0.00 0.00 4.73
291 292 2.706890 GTTAGTTCTCCATTTCCCGCA 58.293 47.619 0.00 0.00 0.00 5.69
292 293 1.664151 CGTTAGTTCTCCATTTCCCGC 59.336 52.381 0.00 0.00 0.00 6.13
293 294 1.664151 GCGTTAGTTCTCCATTTCCCG 59.336 52.381 0.00 0.00 0.00 5.14
294 295 1.664151 CGCGTTAGTTCTCCATTTCCC 59.336 52.381 0.00 0.00 0.00 3.97
295 296 1.664151 CCGCGTTAGTTCTCCATTTCC 59.336 52.381 4.92 0.00 0.00 3.13
296 297 1.062148 GCCGCGTTAGTTCTCCATTTC 59.938 52.381 4.92 0.00 0.00 2.17
297 298 1.084289 GCCGCGTTAGTTCTCCATTT 58.916 50.000 4.92 0.00 0.00 2.32
298 299 0.036765 TGCCGCGTTAGTTCTCCATT 60.037 50.000 4.92 0.00 0.00 3.16
299 300 0.460284 CTGCCGCGTTAGTTCTCCAT 60.460 55.000 4.92 0.00 0.00 3.41
300 301 1.080093 CTGCCGCGTTAGTTCTCCA 60.080 57.895 4.92 0.00 0.00 3.86
301 302 1.810030 CCTGCCGCGTTAGTTCTCC 60.810 63.158 4.92 0.00 0.00 3.71
302 303 0.802607 CTCCTGCCGCGTTAGTTCTC 60.803 60.000 4.92 0.00 0.00 2.87
303 304 1.215647 CTCCTGCCGCGTTAGTTCT 59.784 57.895 4.92 0.00 0.00 3.01
304 305 1.810030 CCTCCTGCCGCGTTAGTTC 60.810 63.158 4.92 0.00 0.00 3.01
305 306 2.264794 CCTCCTGCCGCGTTAGTT 59.735 61.111 4.92 0.00 0.00 2.24
306 307 3.771160 CCCTCCTGCCGCGTTAGT 61.771 66.667 4.92 0.00 0.00 2.24
315 316 4.162690 AATCGACCGCCCTCCTGC 62.163 66.667 0.00 0.00 0.00 4.85
316 317 2.107141 GAATCGACCGCCCTCCTG 59.893 66.667 0.00 0.00 0.00 3.86
324 589 2.125673 AAGCCACCGAATCGACCG 60.126 61.111 3.36 0.00 0.00 4.79
333 598 3.866883 ACCAAATTAATCAAGCCACCG 57.133 42.857 0.00 0.00 0.00 4.94
352 618 9.797556 GATAGATTGTACCACCCAAAATTTAAC 57.202 33.333 0.00 0.00 0.00 2.01
354 620 7.283580 CGGATAGATTGTACCACCCAAAATTTA 59.716 37.037 0.00 0.00 0.00 1.40
361 627 3.035055 TCGGATAGATTGTACCACCCA 57.965 47.619 0.00 0.00 0.00 4.51
367 633 4.379603 CCAGTCGGATCGGATAGATTGTAC 60.380 50.000 6.23 0.00 40.26 2.90
369 635 2.558795 CCAGTCGGATCGGATAGATTGT 59.441 50.000 6.23 0.00 40.26 2.71
393 659 5.105837 GGATATAAGGAATCCTAGACGCGTT 60.106 44.000 15.53 6.16 39.93 4.84
418 694 8.256605 GTCTCATATCAAGCTCACATATATGGT 58.743 37.037 16.96 0.28 33.37 3.55
444 727 0.448861 CGTTTGCGCTAACTCACACG 60.449 55.000 27.39 13.85 29.61 4.49
449 732 4.503007 TGATCTATTCGTTTGCGCTAACTC 59.497 41.667 27.39 18.11 38.14 3.01
457 740 6.918022 CCCCTTAAATTGATCTATTCGTTTGC 59.082 38.462 2.80 0.00 0.00 3.68
459 742 7.123383 ACCCCCTTAAATTGATCTATTCGTTT 58.877 34.615 2.80 0.00 0.00 3.60
470 753 4.046103 ACCCATACAACCCCCTTAAATTGA 59.954 41.667 0.00 0.00 0.00 2.57
472 755 4.616553 GACCCATACAACCCCCTTAAATT 58.383 43.478 0.00 0.00 0.00 1.82
484 767 4.214545 GTCACAAAATCACGACCCATACAA 59.785 41.667 0.00 0.00 0.00 2.41
488 771 2.159382 GGTCACAAAATCACGACCCAT 58.841 47.619 0.00 0.00 41.77 4.00
490 773 0.515564 CGGTCACAAAATCACGACCC 59.484 55.000 0.00 0.00 44.20 4.46
511 794 0.525668 CTATATGTCCGCCCGATCGC 60.526 60.000 10.32 0.00 0.00 4.58
512 795 0.100682 CCTATATGTCCGCCCGATCG 59.899 60.000 8.51 8.51 0.00 3.69
520 803 5.692204 GTCTCAAATGTCACCTATATGTCCG 59.308 44.000 0.00 0.00 0.00 4.79
521 804 5.692204 CGTCTCAAATGTCACCTATATGTCC 59.308 44.000 0.00 0.00 0.00 4.02
523 806 5.050490 GCGTCTCAAATGTCACCTATATGT 58.950 41.667 0.00 0.00 0.00 2.29
524 807 4.449068 GGCGTCTCAAATGTCACCTATATG 59.551 45.833 0.00 0.00 0.00 1.78
525 808 4.503296 GGGCGTCTCAAATGTCACCTATAT 60.503 45.833 0.00 0.00 0.00 0.86
544 828 1.207085 GAGCGTCTATAGTCGGGCG 59.793 63.158 18.69 9.33 0.00 6.13
550 834 3.321396 GGGCCTTTTAGAGCGTCTATAGT 59.679 47.826 0.84 0.00 0.00 2.12
553 837 2.103263 CTGGGCCTTTTAGAGCGTCTAT 59.897 50.000 4.53 0.00 0.00 1.98
569 853 3.956199 TCAGATCAAATCAATTCCTGGGC 59.044 43.478 0.00 0.00 0.00 5.36
576 860 6.845758 TTTCCAGCTCAGATCAAATCAATT 57.154 33.333 0.00 0.00 0.00 2.32
589 873 1.238439 CGCCTTTCTTTTCCAGCTCA 58.762 50.000 0.00 0.00 0.00 4.26
601 885 0.947180 TACACGCTCAACCGCCTTTC 60.947 55.000 0.00 0.00 0.00 2.62
604 888 0.533308 TTTTACACGCTCAACCGCCT 60.533 50.000 0.00 0.00 0.00 5.52
611 895 2.626266 TCACTCCTCTTTTACACGCTCA 59.374 45.455 0.00 0.00 0.00 4.26
615 899 2.989840 CAGCTCACTCCTCTTTTACACG 59.010 50.000 0.00 0.00 0.00 4.49
671 955 4.652822 AGATGCCTTATTCGGTTATTCCC 58.347 43.478 0.00 0.00 0.00 3.97
678 962 3.644966 TCCAAAGATGCCTTATTCGGT 57.355 42.857 0.00 0.00 31.15 4.69
771 1055 3.505680 TGCTTAACTGGCTAATGGTTGTG 59.494 43.478 0.00 0.00 0.00 3.33
976 1261 0.107361 TCACCTCGCTCGATCACCTA 60.107 55.000 0.00 0.00 0.00 3.08
1165 1450 0.387622 CGGACTTCGCCAAGTTACGA 60.388 55.000 13.95 0.00 43.37 3.43
1166 1451 2.067616 CGGACTTCGCCAAGTTACG 58.932 57.895 0.00 3.20 43.37 3.18
1181 1466 4.431416 AACCATAGTGAATAATGGCGGA 57.569 40.909 1.29 0.00 45.53 5.54
1182 1467 6.429692 TCATTAACCATAGTGAATAATGGCGG 59.570 38.462 1.29 0.00 45.53 6.13
1210 1517 9.800433 AACACAATCGCAATCATAATTCATAAA 57.200 25.926 0.00 0.00 0.00 1.40
1213 1520 9.970395 ATTAACACAATCGCAATCATAATTCAT 57.030 25.926 0.00 0.00 0.00 2.57
1214 1521 9.800433 AATTAACACAATCGCAATCATAATTCA 57.200 25.926 0.00 0.00 0.00 2.57
1216 1523 9.033481 CCAATTAACACAATCGCAATCATAATT 57.967 29.630 0.00 0.00 0.00 1.40
1217 1524 8.196771 ACCAATTAACACAATCGCAATCATAAT 58.803 29.630 0.00 0.00 0.00 1.28
1227 1534 4.148000 GTGTGCAACCAATTAACACAATCG 59.852 41.667 0.00 0.00 42.39 3.34
1231 1538 2.796383 GCGTGTGCAACCAATTAACACA 60.796 45.455 0.00 0.00 40.88 3.72
1267 1576 0.250513 GCTTCCGGTTGATCTCCACT 59.749 55.000 0.00 0.00 0.00 4.00
1411 1720 2.499685 GGAGCCCGCTTGTCGTAT 59.500 61.111 0.00 0.00 36.19 3.06
1618 1931 1.140052 TCGGTGGAGAAAGTTCAGCAA 59.860 47.619 0.00 0.00 0.00 3.91
1683 1998 4.675114 GTCTTTTGTTACAAGCATCGTTGG 59.325 41.667 0.00 0.00 0.00 3.77
1886 2207 0.251922 AACCTCCAATGTGGCATGCT 60.252 50.000 18.92 0.00 37.47 3.79
1970 2291 4.451150 GCGACCTCCATCGTGCCA 62.451 66.667 0.00 0.00 44.13 4.92
2039 2363 1.071699 ACAAGTTAGAAGCGGCTGGAA 59.928 47.619 1.81 0.00 0.00 3.53
2054 2378 2.521708 GGGGCTGGCAACACAAGT 60.522 61.111 2.88 0.00 46.17 3.16
2066 2390 0.825010 GATGCAATCGATTGGGGGCT 60.825 55.000 33.05 13.04 38.21 5.19
2113 2438 2.042259 TTCGAGCGAGCCTAACGGA 61.042 57.895 0.00 0.00 0.00 4.69
2177 2502 4.189580 AACACCCACTGCTGCCGT 62.190 61.111 0.00 0.00 0.00 5.68
2239 2565 2.231478 CCTACCTTGATGTCGCGGATAT 59.769 50.000 6.13 0.00 0.00 1.63
2240 2566 1.611977 CCTACCTTGATGTCGCGGATA 59.388 52.381 6.13 0.00 0.00 2.59
2241 2567 0.389391 CCTACCTTGATGTCGCGGAT 59.611 55.000 6.13 0.00 0.00 4.18
2242 2568 0.681887 TCCTACCTTGATGTCGCGGA 60.682 55.000 6.13 0.00 0.00 5.54
2270 2599 0.703488 TGGAGCCATTGGAATCCACA 59.297 50.000 20.48 5.11 35.92 4.17
2310 2640 1.374885 CGTACATGGACGTGCCCAA 60.375 57.895 22.63 0.00 40.04 4.12
2346 2676 3.429372 TTGCCCCGTTGGAGTTGCT 62.429 57.895 0.00 0.00 35.39 3.91
2347 2677 2.909965 TTGCCCCGTTGGAGTTGC 60.910 61.111 0.00 0.00 35.39 4.17
2348 2678 2.561037 GGTTGCCCCGTTGGAGTTG 61.561 63.158 0.00 0.00 35.39 3.16
2349 2679 2.203437 GGTTGCCCCGTTGGAGTT 60.203 61.111 0.00 0.00 35.39 3.01
2350 2680 4.280019 GGGTTGCCCCGTTGGAGT 62.280 66.667 0.00 0.00 42.41 3.85
2359 2689 3.666253 CGTCCGTTTGGGTTGCCC 61.666 66.667 0.00 0.00 45.71 5.36
2360 2690 4.337060 GCGTCCGTTTGGGTTGCC 62.337 66.667 0.00 0.00 37.00 4.52
2361 2691 4.676586 CGCGTCCGTTTGGGTTGC 62.677 66.667 0.00 0.00 37.00 4.17
2362 2692 4.676586 GCGCGTCCGTTTGGGTTG 62.677 66.667 8.43 0.00 37.00 3.77
2367 2697 4.659874 AAAGCGCGCGTCCGTTTG 62.660 61.111 32.35 0.04 36.67 2.93
2368 2698 4.659874 CAAAGCGCGCGTCCGTTT 62.660 61.111 32.35 21.22 36.67 3.60
2376 2706 4.683334 AAAGCGGACAAAGCGCGC 62.683 61.111 26.66 26.66 40.04 6.86
2377 2707 2.051345 AAAAGCGGACAAAGCGCG 60.051 55.556 0.00 0.00 40.04 6.86
2378 2708 2.074920 CGAAAAGCGGACAAAGCGC 61.075 57.895 0.00 0.00 40.04 5.92
2379 2709 0.316689 AACGAAAAGCGGACAAAGCG 60.317 50.000 0.00 0.00 46.49 4.68
2380 2710 1.395670 GAACGAAAAGCGGACAAAGC 58.604 50.000 0.00 0.00 46.49 3.51
2381 2711 1.004292 ACGAACGAAAAGCGGACAAAG 60.004 47.619 0.14 0.00 46.49 2.77
2382 2712 1.008329 ACGAACGAAAAGCGGACAAA 58.992 45.000 0.14 0.00 46.49 2.83
2383 2713 1.008329 AACGAACGAAAAGCGGACAA 58.992 45.000 0.14 0.00 46.49 3.18
2384 2714 1.008329 AAACGAACGAAAAGCGGACA 58.992 45.000 0.14 0.00 46.49 4.02
2385 2715 1.382163 CAAACGAACGAAAAGCGGAC 58.618 50.000 0.14 0.00 46.49 4.79
2386 2716 0.305313 CCAAACGAACGAAAAGCGGA 59.695 50.000 0.14 0.00 46.49 5.54
2387 2717 0.659123 CCCAAACGAACGAAAAGCGG 60.659 55.000 0.14 0.00 46.49 5.52
2389 2719 1.750351 GACCCAAACGAACGAAAAGC 58.250 50.000 0.14 0.00 0.00 3.51
2390 2720 1.333435 CCGACCCAAACGAACGAAAAG 60.333 52.381 0.14 0.00 0.00 2.27
2391 2721 0.656785 CCGACCCAAACGAACGAAAA 59.343 50.000 0.14 0.00 0.00 2.29
2392 2722 1.774046 GCCGACCCAAACGAACGAAA 61.774 55.000 0.14 0.00 0.00 3.46
2393 2723 2.246042 GCCGACCCAAACGAACGAA 61.246 57.895 0.14 0.00 0.00 3.85
2394 2724 2.662527 GCCGACCCAAACGAACGA 60.663 61.111 0.14 0.00 0.00 3.85
2395 2725 3.719144 GGCCGACCCAAACGAACG 61.719 66.667 0.00 0.00 0.00 3.95
2396 2726 2.592287 TGGCCGACCCAAACGAAC 60.592 61.111 0.00 0.00 41.82 3.95
2397 2727 2.281208 CTGGCCGACCCAAACGAA 60.281 61.111 0.00 0.00 44.81 3.85
2398 2728 4.323477 CCTGGCCGACCCAAACGA 62.323 66.667 0.00 0.00 44.81 3.85
2405 2735 4.778143 ATGTTCGCCTGGCCGACC 62.778 66.667 14.12 7.08 36.90 4.79
2406 2736 3.499737 CATGTTCGCCTGGCCGAC 61.500 66.667 14.12 12.31 36.90 4.79
2423 2753 2.309764 ATTTCAGAATGCGGACGCGC 62.310 55.000 5.73 0.00 45.51 6.86
2424 2754 0.927537 TATTTCAGAATGCGGACGCG 59.072 50.000 3.53 3.53 45.51 6.01
2425 2755 2.351726 ACTTATTTCAGAATGCGGACGC 59.648 45.455 10.13 10.13 42.35 5.19
2426 2756 4.334443 CAACTTATTTCAGAATGCGGACG 58.666 43.478 0.00 0.00 34.76 4.79
2427 2757 4.662145 CCAACTTATTTCAGAATGCGGAC 58.338 43.478 0.00 0.00 34.76 4.79
2428 2758 3.128589 GCCAACTTATTTCAGAATGCGGA 59.871 43.478 0.00 0.00 34.76 5.54
2429 2759 3.129287 AGCCAACTTATTTCAGAATGCGG 59.871 43.478 0.00 0.00 34.76 5.69
2430 2760 4.361451 AGCCAACTTATTTCAGAATGCG 57.639 40.909 0.00 0.00 34.76 4.73
2431 2761 5.574443 GTCAAGCCAACTTATTTCAGAATGC 59.426 40.000 0.00 0.00 33.74 3.56
2432 2762 6.095377 GGTCAAGCCAACTTATTTCAGAATG 58.905 40.000 0.00 0.00 33.74 2.67
2433 2763 5.106157 CGGTCAAGCCAACTTATTTCAGAAT 60.106 40.000 0.00 0.00 36.97 2.40
2434 2764 4.215399 CGGTCAAGCCAACTTATTTCAGAA 59.785 41.667 0.00 0.00 36.97 3.02
2435 2765 3.751175 CGGTCAAGCCAACTTATTTCAGA 59.249 43.478 0.00 0.00 36.97 3.27
2436 2766 3.502211 ACGGTCAAGCCAACTTATTTCAG 59.498 43.478 0.00 0.00 36.97 3.02
2437 2767 3.482436 ACGGTCAAGCCAACTTATTTCA 58.518 40.909 0.00 0.00 36.97 2.69
2438 2768 3.119955 GGACGGTCAAGCCAACTTATTTC 60.120 47.826 10.76 0.00 36.97 2.17
2439 2769 2.817844 GGACGGTCAAGCCAACTTATTT 59.182 45.455 10.76 0.00 36.97 1.40
2440 2770 2.224670 TGGACGGTCAAGCCAACTTATT 60.225 45.455 10.76 0.00 36.97 1.40
2441 2771 1.349688 TGGACGGTCAAGCCAACTTAT 59.650 47.619 10.76 0.00 36.97 1.73
2442 2772 0.759959 TGGACGGTCAAGCCAACTTA 59.240 50.000 10.76 0.00 36.97 2.24
2443 2773 0.818040 GTGGACGGTCAAGCCAACTT 60.818 55.000 10.76 0.00 36.97 2.66
2444 2774 1.227853 GTGGACGGTCAAGCCAACT 60.228 57.895 10.76 0.00 36.97 3.16
2445 2775 2.604174 CGTGGACGGTCAAGCCAAC 61.604 63.158 10.76 0.00 36.97 3.77
2446 2776 2.280524 CGTGGACGGTCAAGCCAA 60.281 61.111 10.76 0.00 36.97 4.52
2457 2787 4.083862 GTCAGCCTCCCCGTGGAC 62.084 72.222 0.00 0.00 35.03 4.02
2461 2791 4.974438 TTGGGTCAGCCTCCCCGT 62.974 66.667 0.00 0.00 44.44 5.28
2462 2792 2.983879 ATTTGGGTCAGCCTCCCCG 61.984 63.158 0.00 0.00 44.44 5.73
2463 2793 1.380380 CATTTGGGTCAGCCTCCCC 60.380 63.158 0.00 1.05 44.00 4.81
2464 2794 0.967380 CACATTTGGGTCAGCCTCCC 60.967 60.000 0.00 1.98 44.81 4.30
2465 2795 1.598701 GCACATTTGGGTCAGCCTCC 61.599 60.000 0.00 0.00 34.45 4.30
2466 2796 1.598701 GGCACATTTGGGTCAGCCTC 61.599 60.000 0.00 0.00 39.02 4.70
2467 2797 1.607467 GGCACATTTGGGTCAGCCT 60.607 57.895 0.00 0.00 39.02 4.58
2468 2798 2.973082 GGCACATTTGGGTCAGCC 59.027 61.111 0.00 0.00 34.71 4.85
2469 2799 1.971167 TCGGCACATTTGGGTCAGC 60.971 57.895 0.00 0.00 0.00 4.26
2470 2800 1.875963 GTCGGCACATTTGGGTCAG 59.124 57.895 0.00 0.00 0.00 3.51
2471 2801 1.963855 CGTCGGCACATTTGGGTCA 60.964 57.895 0.00 0.00 0.00 4.02
2472 2802 1.964373 ACGTCGGCACATTTGGGTC 60.964 57.895 0.00 0.00 0.00 4.46
2473 2803 2.112297 ACGTCGGCACATTTGGGT 59.888 55.556 0.00 0.00 0.00 4.51
2474 2804 2.560861 CACGTCGGCACATTTGGG 59.439 61.111 0.00 0.00 0.00 4.12
2475 2805 2.126888 GCACGTCGGCACATTTGG 60.127 61.111 0.00 0.00 0.00 3.28
2476 2806 0.593518 TTTGCACGTCGGCACATTTG 60.594 50.000 7.74 0.00 44.86 2.32
2477 2807 0.101399 TTTTGCACGTCGGCACATTT 59.899 45.000 7.74 0.00 44.86 2.32
2478 2808 0.101399 TTTTTGCACGTCGGCACATT 59.899 45.000 7.74 0.00 44.86 2.71
2479 2809 1.730487 TTTTTGCACGTCGGCACAT 59.270 47.368 7.74 0.00 44.86 3.21
2480 2810 3.188011 TTTTTGCACGTCGGCACA 58.812 50.000 7.74 0.02 44.86 4.57
2495 2825 4.602995 TGTTTATTTCGTGCGAGCTTTTT 58.397 34.783 0.00 0.00 0.00 1.94
2496 2826 4.217754 TGTTTATTTCGTGCGAGCTTTT 57.782 36.364 0.00 0.00 0.00 2.27
2497 2827 3.889196 TGTTTATTTCGTGCGAGCTTT 57.111 38.095 0.00 0.00 0.00 3.51
2498 2828 5.539582 TTATGTTTATTTCGTGCGAGCTT 57.460 34.783 0.00 0.00 0.00 3.74
2499 2829 5.539582 TTTATGTTTATTTCGTGCGAGCT 57.460 34.783 0.00 0.00 0.00 4.09
2500 2830 6.790336 ATTTTATGTTTATTTCGTGCGAGC 57.210 33.333 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.