Multiple sequence alignment - TraesCS3D01G534500

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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 TraesCS3D01G534500 chr3D 100.000 3712 0 0 1 3712 609288246 609284535 0.000000e+00 6855.0
1 TraesCS3D01G534500 chr3D 89.696 1281 105 13 1554 2825 609005508 609006770 0.000000e+00 1609.0
2 TraesCS3D01G534500 chr3D 86.929 1247 154 5 1569 2807 608952004 608953249 0.000000e+00 1391.0
3 TraesCS3D01G534500 chr3D 85.944 498 60 7 1000 1495 609004616 609005105 1.180000e-144 523.0
4 TraesCS3D01G534500 chr3D 85.049 515 66 6 985 1498 608950880 608951384 7.110000e-142 514.0
5 TraesCS3D01G534500 chr3A 92.840 2109 137 9 601 2700 742873357 742871254 0.000000e+00 3046.0
6 TraesCS3D01G534500 chr3A 89.758 1279 111 10 1554 2825 742356315 742357580 0.000000e+00 1618.0
7 TraesCS3D01G534500 chr3A 84.433 758 113 2 2054 2807 742333396 742334152 0.000000e+00 741.0
8 TraesCS3D01G534500 chr3A 85.156 512 65 7 988 1498 742332247 742332748 7.110000e-142 514.0
9 TraesCS3D01G534500 chr3A 85.341 498 57 9 1000 1495 742355430 742355913 5.530000e-138 501.0
10 TraesCS3D01G534500 chr3A 80.630 413 61 13 34 439 742873857 742873457 6.020000e-78 302.0
11 TraesCS3D01G534500 chr2D 87.406 1723 185 20 980 2694 623438017 623439715 0.000000e+00 1951.0
12 TraesCS3D01G534500 chr3B 86.747 1245 157 5 1569 2809 819651191 819652431 0.000000e+00 1378.0
13 TraesCS3D01G534500 chr3B 86.116 1246 164 4 1569 2809 819382290 819383531 0.000000e+00 1334.0
14 TraesCS3D01G534500 chr3B 85.212 1251 173 9 1569 2809 819523093 819524341 0.000000e+00 1275.0
15 TraesCS3D01G534500 chr3B 85.188 1249 174 8 1569 2809 819300060 819301305 0.000000e+00 1271.0
16 TraesCS3D01G534500 chr3B 85.770 513 58 9 985 1493 753164585 753164084 2.540000e-146 529.0
17 TraesCS3D01G534500 chr3B 85.433 508 64 6 985 1492 819650032 819650529 1.530000e-143 520.0
18 TraesCS3D01G534500 chr3B 84.884 516 64 10 985 1499 819522383 819522885 3.310000e-140 508.0
19 TraesCS3D01G534500 chr3B 82.229 332 55 3 2844 3173 782670548 782670219 2.180000e-72 283.0
20 TraesCS3D01G534500 chr2B 85.714 1337 134 26 980 2306 765454627 765455916 0.000000e+00 1358.0
21 TraesCS3D01G534500 chr2B 83.053 832 95 31 2810 3599 109776737 109777564 0.000000e+00 713.0
22 TraesCS3D01G534500 chr2B 83.712 792 71 28 2845 3598 44310618 44309847 0.000000e+00 695.0
23 TraesCS3D01G534500 chr2B 82.139 823 104 26 2810 3599 109149194 109150006 0.000000e+00 665.0
24 TraesCS3D01G534500 chr2B 79.976 844 94 42 2806 3599 8018917 8018099 1.510000e-153 553.0
25 TraesCS3D01G534500 chr2B 79.882 845 94 43 2806 3599 8182860 8182041 1.950000e-152 549.0
26 TraesCS3D01G534500 chr2B 81.792 692 76 22 2871 3518 109069921 109070606 5.460000e-148 534.0
27 TraesCS3D01G534500 chr2B 82.601 546 46 23 3085 3599 55696191 55695664 1.580000e-118 436.0
28 TraesCS3D01G534500 chr5D 82.192 803 116 19 2820 3599 374139816 374140614 0.000000e+00 665.0
29 TraesCS3D01G534500 chr5D 77.519 774 97 44 2973 3707 557522648 557521913 9.660000e-106 394.0
30 TraesCS3D01G534500 chr5D 94.444 36 1 1 495 530 369562085 369562051 2.000000e-03 54.7
31 TraesCS3D01G534500 chrUn 82.420 785 82 25 2833 3599 34348981 34349727 5.230000e-178 634.0
32 TraesCS3D01G534500 chrUn 81.746 126 21 2 2810 2934 49927644 49927768 1.820000e-18 104.0
33 TraesCS3D01G534500 chr5B 80.344 814 92 36 2833 3599 598437482 598436690 4.190000e-154 555.0
34 TraesCS3D01G534500 chr7D 76.584 931 123 57 2820 3709 52470632 52471508 1.230000e-114 424.0
35 TraesCS3D01G534500 chr7B 87.006 177 21 1 2846 3022 653881113 653880939 8.130000e-47 198.0
36 TraesCS3D01G534500 chr6B 83.511 188 21 6 2822 3005 30971837 30972018 2.290000e-37 167.0
37 TraesCS3D01G534500 chr6B 73.913 322 46 25 3043 3351 30972032 30972328 1.100000e-15 95.3


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 TraesCS3D01G534500 chr3D 609284535 609288246 3711 True 6855.0 6855 100.0000 1 3712 1 chr3D.!!$R1 3711
1 TraesCS3D01G534500 chr3D 609004616 609006770 2154 False 1066.0 1609 87.8200 1000 2825 2 chr3D.!!$F2 1825
2 TraesCS3D01G534500 chr3D 608950880 608953249 2369 False 952.5 1391 85.9890 985 2807 2 chr3D.!!$F1 1822
3 TraesCS3D01G534500 chr3A 742871254 742873857 2603 True 1674.0 3046 86.7350 34 2700 2 chr3A.!!$R1 2666
4 TraesCS3D01G534500 chr3A 742355430 742357580 2150 False 1059.5 1618 87.5495 1000 2825 2 chr3A.!!$F2 1825
5 TraesCS3D01G534500 chr3A 742332247 742334152 1905 False 627.5 741 84.7945 988 2807 2 chr3A.!!$F1 1819
6 TraesCS3D01G534500 chr2D 623438017 623439715 1698 False 1951.0 1951 87.4060 980 2694 1 chr2D.!!$F1 1714
7 TraesCS3D01G534500 chr3B 819382290 819383531 1241 False 1334.0 1334 86.1160 1569 2809 1 chr3B.!!$F2 1240
8 TraesCS3D01G534500 chr3B 819300060 819301305 1245 False 1271.0 1271 85.1880 1569 2809 1 chr3B.!!$F1 1240
9 TraesCS3D01G534500 chr3B 819650032 819652431 2399 False 949.0 1378 86.0900 985 2809 2 chr3B.!!$F4 1824
10 TraesCS3D01G534500 chr3B 819522383 819524341 1958 False 891.5 1275 85.0480 985 2809 2 chr3B.!!$F3 1824
11 TraesCS3D01G534500 chr3B 753164084 753164585 501 True 529.0 529 85.7700 985 1493 1 chr3B.!!$R1 508
12 TraesCS3D01G534500 chr2B 765454627 765455916 1289 False 1358.0 1358 85.7140 980 2306 1 chr2B.!!$F4 1326
13 TraesCS3D01G534500 chr2B 109776737 109777564 827 False 713.0 713 83.0530 2810 3599 1 chr2B.!!$F3 789
14 TraesCS3D01G534500 chr2B 44309847 44310618 771 True 695.0 695 83.7120 2845 3598 1 chr2B.!!$R3 753
15 TraesCS3D01G534500 chr2B 109149194 109150006 812 False 665.0 665 82.1390 2810 3599 1 chr2B.!!$F2 789
16 TraesCS3D01G534500 chr2B 8018099 8018917 818 True 553.0 553 79.9760 2806 3599 1 chr2B.!!$R1 793
17 TraesCS3D01G534500 chr2B 8182041 8182860 819 True 549.0 549 79.8820 2806 3599 1 chr2B.!!$R2 793
18 TraesCS3D01G534500 chr2B 109069921 109070606 685 False 534.0 534 81.7920 2871 3518 1 chr2B.!!$F1 647
19 TraesCS3D01G534500 chr2B 55695664 55696191 527 True 436.0 436 82.6010 3085 3599 1 chr2B.!!$R4 514
20 TraesCS3D01G534500 chr5D 374139816 374140614 798 False 665.0 665 82.1920 2820 3599 1 chr5D.!!$F1 779
21 TraesCS3D01G534500 chr5D 557521913 557522648 735 True 394.0 394 77.5190 2973 3707 1 chr5D.!!$R2 734
22 TraesCS3D01G534500 chrUn 34348981 34349727 746 False 634.0 634 82.4200 2833 3599 1 chrUn.!!$F1 766
23 TraesCS3D01G534500 chr5B 598436690 598437482 792 True 555.0 555 80.3440 2833 3599 1 chr5B.!!$R1 766
24 TraesCS3D01G534500 chr7D 52470632 52471508 876 False 424.0 424 76.5840 2820 3709 1 chr7D.!!$F1 889

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
212 213 0.250234 ATCTGCGCTAGAGGCAAACA 59.750 50.0 9.73 0.0 40.39 2.83 F
426 428 0.320421 CGGGGGACGCCTATGTTATG 60.320 60.0 8.66 0.0 38.40 1.90 F
1976 2766 0.107165 GGACAATAGTGGCACCCTCC 60.107 60.0 15.27 7.4 32.51 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1069 1078 0.754957 AGTGCGAGGAGGATGAGGAG 60.755 60.0 0.00 0.0 0.0 3.69 R
2372 3216 0.032678 CATAGATCCGCGTCTTGGCT 59.967 55.0 4.92 0.0 0.0 4.75 R
3015 3909 2.418976 GGTCCTTTGTTCGATGCCTAAC 59.581 50.0 0.00 0.0 0.0 2.34 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 4.445452 TCGATCGGTATACTTAATGGCC 57.555 45.455 16.41 0.00 0.00 5.36
22 23 3.827876 TCGATCGGTATACTTAATGGCCA 59.172 43.478 16.41 8.56 0.00 5.36
23 24 3.924686 CGATCGGTATACTTAATGGCCAC 59.075 47.826 8.16 0.00 0.00 5.01
24 25 3.756933 TCGGTATACTTAATGGCCACC 57.243 47.619 8.16 0.00 0.00 4.61
25 26 3.311091 TCGGTATACTTAATGGCCACCT 58.689 45.455 8.16 0.00 0.00 4.00
26 27 3.070446 TCGGTATACTTAATGGCCACCTG 59.930 47.826 8.16 0.70 0.00 4.00
27 28 3.146847 GGTATACTTAATGGCCACCTGC 58.853 50.000 8.16 0.00 40.16 4.85
28 29 3.434453 GGTATACTTAATGGCCACCTGCA 60.434 47.826 8.16 0.00 43.89 4.41
29 30 2.418368 TACTTAATGGCCACCTGCAG 57.582 50.000 8.16 6.78 43.89 4.41
30 31 0.967380 ACTTAATGGCCACCTGCAGC 60.967 55.000 8.16 0.00 43.89 5.25
31 32 0.966875 CTTAATGGCCACCTGCAGCA 60.967 55.000 8.16 0.00 43.89 4.41
32 33 0.541530 TTAATGGCCACCTGCAGCAA 60.542 50.000 8.16 0.00 43.89 3.91
51 52 4.218417 AGCAACAGTGATGTATTGGTTTCC 59.782 41.667 0.00 0.00 28.78 3.13
144 145 5.799936 CCTGAACAAATACTTACCAATTGCG 59.200 40.000 0.00 0.00 0.00 4.85
148 149 5.938322 ACAAATACTTACCAATTGCGACAG 58.062 37.500 0.00 0.00 0.00 3.51
151 152 2.151202 ACTTACCAATTGCGACAGTGG 58.849 47.619 0.00 0.00 37.17 4.00
153 154 0.250510 TACCAATTGCGACAGTGGCA 60.251 50.000 6.07 6.07 38.93 4.92
157 158 0.523072 AATTGCGACAGTGGCATGTC 59.477 50.000 11.45 15.60 45.01 3.06
164 165 2.223595 CGACAGTGGCATGTCTACCTAG 60.224 54.545 20.16 7.02 46.04 3.02
171 172 2.291741 GGCATGTCTACCTAGCAATTGC 59.708 50.000 23.05 23.05 42.49 3.56
187 188 6.119144 GCAATTGCGGTATAGAAGAAAGAA 57.881 37.500 15.87 0.00 0.00 2.52
189 190 7.196331 GCAATTGCGGTATAGAAGAAAGAAAT 58.804 34.615 15.87 0.00 0.00 2.17
190 191 7.702348 GCAATTGCGGTATAGAAGAAAGAAATT 59.298 33.333 15.87 0.00 0.00 1.82
201 202 7.150783 AGAAGAAAGAAATTTTATCTGCGCT 57.849 32.000 9.73 0.00 0.00 5.92
205 206 7.914465 AGAAAGAAATTTTATCTGCGCTAGAG 58.086 34.615 9.73 0.00 39.20 2.43
206 207 6.610741 AAGAAATTTTATCTGCGCTAGAGG 57.389 37.500 9.73 0.00 39.20 3.69
212 213 0.250234 ATCTGCGCTAGAGGCAAACA 59.750 50.000 9.73 0.00 40.39 2.83
219 220 3.561725 GCGCTAGAGGCAAACATTTATCT 59.438 43.478 0.00 0.00 41.91 1.98
223 224 5.277731 GCTAGAGGCAAACATTTATCTGAGC 60.278 44.000 0.00 0.00 41.35 4.26
246 247 6.486657 AGCTTCTTACAAACACACACATACAT 59.513 34.615 0.00 0.00 0.00 2.29
279 280 9.447157 AAAATTACATTTAAACACATGGGGATG 57.553 29.630 0.00 0.00 0.00 3.51
280 281 7.732222 ATTACATTTAAACACATGGGGATGT 57.268 32.000 0.00 4.37 34.64 3.06
281 282 5.659440 ACATTTAAACACATGGGGATGTC 57.341 39.130 0.00 0.00 31.37 3.06
282 283 4.157656 ACATTTAAACACATGGGGATGTCG 59.842 41.667 0.00 0.00 31.37 4.35
284 285 2.577606 AAACACATGGGGATGTCGAA 57.422 45.000 0.00 0.00 31.37 3.71
285 286 2.113860 AACACATGGGGATGTCGAAG 57.886 50.000 0.00 0.00 31.37 3.79
286 287 0.984230 ACACATGGGGATGTCGAAGT 59.016 50.000 0.00 0.00 31.37 3.01
287 288 1.066143 ACACATGGGGATGTCGAAGTC 60.066 52.381 0.00 0.00 31.37 3.01
289 290 1.909302 ACATGGGGATGTCGAAGTCTT 59.091 47.619 0.00 0.00 0.00 3.01
291 292 2.762535 TGGGGATGTCGAAGTCTTTC 57.237 50.000 0.00 0.00 0.00 2.62
292 293 2.257207 TGGGGATGTCGAAGTCTTTCT 58.743 47.619 0.00 0.00 0.00 2.52
293 294 2.637872 TGGGGATGTCGAAGTCTTTCTT 59.362 45.455 0.00 0.00 39.32 2.52
294 295 3.263261 GGGGATGTCGAAGTCTTTCTTC 58.737 50.000 0.00 0.00 46.39 2.87
295 296 3.263261 GGGATGTCGAAGTCTTTCTTCC 58.737 50.000 0.00 0.00 46.97 3.46
296 297 3.055747 GGGATGTCGAAGTCTTTCTTCCT 60.056 47.826 0.00 0.00 46.97 3.36
297 298 3.929610 GGATGTCGAAGTCTTTCTTCCTG 59.070 47.826 0.00 0.00 46.97 3.86
298 299 2.755650 TGTCGAAGTCTTTCTTCCTGC 58.244 47.619 0.00 0.00 46.97 4.85
299 300 2.102420 TGTCGAAGTCTTTCTTCCTGCA 59.898 45.455 0.00 0.00 46.97 4.41
300 301 3.244215 TGTCGAAGTCTTTCTTCCTGCAT 60.244 43.478 0.00 0.00 46.97 3.96
301 302 3.369451 GTCGAAGTCTTTCTTCCTGCATC 59.631 47.826 0.00 0.00 46.97 3.91
302 303 3.259374 TCGAAGTCTTTCTTCCTGCATCT 59.741 43.478 0.00 0.00 46.97 2.90
327 329 2.780595 GGCACACCGTGAGCATAAT 58.219 52.632 20.46 0.00 35.63 1.28
333 335 3.182372 CACACCGTGAGCATAATACGATG 59.818 47.826 5.28 0.00 35.23 3.84
342 344 1.995484 CATAATACGATGCCGCCTCTG 59.005 52.381 0.00 0.00 39.95 3.35
344 346 1.686325 AATACGATGCCGCCTCTGGT 61.686 55.000 0.00 0.00 39.95 4.00
347 349 3.474570 GATGCCGCCTCTGGTCCT 61.475 66.667 0.00 0.00 0.00 3.85
348 350 3.011517 ATGCCGCCTCTGGTCCTT 61.012 61.111 0.00 0.00 0.00 3.36
349 351 1.686325 GATGCCGCCTCTGGTCCTTA 61.686 60.000 0.00 0.00 0.00 2.69
350 352 1.690219 ATGCCGCCTCTGGTCCTTAG 61.690 60.000 0.00 0.00 0.00 2.18
351 353 2.058595 GCCGCCTCTGGTCCTTAGA 61.059 63.158 0.00 0.00 0.00 2.10
352 354 1.817209 CCGCCTCTGGTCCTTAGAC 59.183 63.158 0.00 0.00 42.73 2.59
354 356 0.741915 CGCCTCTGGTCCTTAGACTC 59.258 60.000 0.00 0.00 43.05 3.36
355 357 1.853963 GCCTCTGGTCCTTAGACTCA 58.146 55.000 0.00 0.00 43.05 3.41
356 358 1.754226 GCCTCTGGTCCTTAGACTCAG 59.246 57.143 0.00 0.00 43.05 3.35
357 359 2.886391 GCCTCTGGTCCTTAGACTCAGT 60.886 54.545 9.81 0.00 43.05 3.41
358 360 3.436243 CCTCTGGTCCTTAGACTCAGTT 58.564 50.000 9.81 0.00 43.05 3.16
359 361 3.194542 CCTCTGGTCCTTAGACTCAGTTG 59.805 52.174 9.81 6.27 43.05 3.16
363 365 2.563179 GGTCCTTAGACTCAGTTGAGCA 59.437 50.000 8.99 0.00 45.79 4.26
364 366 3.367910 GGTCCTTAGACTCAGTTGAGCAG 60.368 52.174 8.99 1.23 45.79 4.24
365 367 2.828520 TCCTTAGACTCAGTTGAGCAGG 59.171 50.000 8.99 9.25 45.79 4.85
366 368 2.828520 CCTTAGACTCAGTTGAGCAGGA 59.171 50.000 8.99 0.00 45.79 3.86
367 369 3.119173 CCTTAGACTCAGTTGAGCAGGAG 60.119 52.174 8.99 3.39 45.79 3.69
368 370 0.607620 AGACTCAGTTGAGCAGGAGC 59.392 55.000 8.99 0.00 45.79 4.70
383 385 3.020274 CAGGAGCTTGTAGAGAGCAGTA 58.980 50.000 0.00 0.00 42.56 2.74
385 387 2.223711 GGAGCTTGTAGAGAGCAGTAGC 60.224 54.545 0.00 0.00 42.56 3.58
406 408 3.002862 GCTGAGAAGTCGTCGATGTAGAT 59.997 47.826 4.21 0.00 0.00 1.98
417 419 2.156051 GATGTAGATCGGGGGACGCC 62.156 65.000 0.00 0.00 43.86 5.68
419 421 1.228367 GTAGATCGGGGGACGCCTA 60.228 63.158 8.66 0.00 43.86 3.93
421 423 0.611062 TAGATCGGGGGACGCCTATG 60.611 60.000 8.66 0.00 43.86 2.23
424 426 0.470456 ATCGGGGGACGCCTATGTTA 60.470 55.000 8.66 0.00 43.86 2.41
425 427 0.470456 TCGGGGGACGCCTATGTTAT 60.470 55.000 8.66 0.00 43.86 1.89
426 428 0.320421 CGGGGGACGCCTATGTTATG 60.320 60.000 8.66 0.00 38.40 1.90
427 429 0.763035 GGGGGACGCCTATGTTATGT 59.237 55.000 8.66 0.00 34.11 2.29
428 430 1.972795 GGGGGACGCCTATGTTATGTA 59.027 52.381 8.66 0.00 34.11 2.29
429 431 2.289257 GGGGGACGCCTATGTTATGTAC 60.289 54.545 8.66 0.00 34.11 2.90
430 432 2.631545 GGGGACGCCTATGTTATGTACT 59.368 50.000 0.24 0.00 0.00 2.73
431 433 3.554337 GGGGACGCCTATGTTATGTACTG 60.554 52.174 0.24 0.00 0.00 2.74
432 434 3.057734 GGACGCCTATGTTATGTACTGC 58.942 50.000 0.00 0.00 0.00 4.40
433 435 3.491964 GGACGCCTATGTTATGTACTGCA 60.492 47.826 0.00 0.00 0.00 4.41
434 436 3.454375 ACGCCTATGTTATGTACTGCAC 58.546 45.455 0.00 0.00 0.00 4.57
435 437 3.132289 ACGCCTATGTTATGTACTGCACT 59.868 43.478 0.00 0.00 0.00 4.40
436 438 4.119862 CGCCTATGTTATGTACTGCACTT 58.880 43.478 0.00 0.00 0.00 3.16
437 439 4.025730 CGCCTATGTTATGTACTGCACTTG 60.026 45.833 0.00 0.00 0.00 3.16
438 440 4.876107 GCCTATGTTATGTACTGCACTTGT 59.124 41.667 0.00 0.00 0.00 3.16
439 441 5.354234 GCCTATGTTATGTACTGCACTTGTT 59.646 40.000 0.00 0.00 0.00 2.83
440 442 6.675486 GCCTATGTTATGTACTGCACTTGTTG 60.675 42.308 0.00 0.00 0.00 3.33
441 443 6.371548 CCTATGTTATGTACTGCACTTGTTGT 59.628 38.462 0.00 0.00 0.00 3.32
442 444 6.633500 ATGTTATGTACTGCACTTGTTGTT 57.367 33.333 0.00 0.00 0.00 2.83
443 445 6.443934 TGTTATGTACTGCACTTGTTGTTT 57.556 33.333 0.00 0.00 0.00 2.83
444 446 6.857956 TGTTATGTACTGCACTTGTTGTTTT 58.142 32.000 0.00 0.00 0.00 2.43
445 447 7.316640 TGTTATGTACTGCACTTGTTGTTTTT 58.683 30.769 0.00 0.00 0.00 1.94
472 474 3.832527 AGGGAAATGTACTGCACTTGTT 58.167 40.909 0.00 0.00 0.00 2.83
480 482 4.450976 TGTACTGCACTTGTTGATGACTT 58.549 39.130 0.00 0.00 0.00 3.01
492 494 0.804989 GATGACTTTGGCCTCGTTGG 59.195 55.000 3.32 0.00 39.35 3.77
502 504 2.256391 CCTCGTTGGCTTGCATCAA 58.744 52.632 0.00 0.00 0.00 2.57
536 538 7.047891 AGATGGTTGTGTGTATCGTATTGATT 58.952 34.615 0.00 0.00 38.57 2.57
537 539 8.201464 AGATGGTTGTGTGTATCGTATTGATTA 58.799 33.333 0.00 0.00 38.57 1.75
538 540 7.528481 TGGTTGTGTGTATCGTATTGATTAC 57.472 36.000 0.00 0.00 38.57 1.89
539 541 7.097834 TGGTTGTGTGTATCGTATTGATTACA 58.902 34.615 0.00 0.00 38.57 2.41
540 542 7.276878 TGGTTGTGTGTATCGTATTGATTACAG 59.723 37.037 0.00 0.00 38.57 2.74
541 543 6.822073 TGTGTGTATCGTATTGATTACAGC 57.178 37.500 0.00 0.00 38.57 4.40
542 544 5.751509 TGTGTGTATCGTATTGATTACAGCC 59.248 40.000 0.00 0.00 38.57 4.85
543 545 5.983720 GTGTGTATCGTATTGATTACAGCCT 59.016 40.000 0.00 0.00 38.57 4.58
544 546 6.144080 GTGTGTATCGTATTGATTACAGCCTC 59.856 42.308 0.00 0.00 38.57 4.70
545 547 6.040504 TGTGTATCGTATTGATTACAGCCTCT 59.959 38.462 0.00 0.00 38.57 3.69
546 548 6.924060 GTGTATCGTATTGATTACAGCCTCTT 59.076 38.462 0.00 0.00 38.57 2.85
547 549 7.438459 GTGTATCGTATTGATTACAGCCTCTTT 59.562 37.037 0.00 0.00 38.57 2.52
548 550 7.985184 TGTATCGTATTGATTACAGCCTCTTTT 59.015 33.333 0.00 0.00 38.57 2.27
549 551 7.865706 ATCGTATTGATTACAGCCTCTTTTT 57.134 32.000 0.00 0.00 31.57 1.94
579 581 9.893305 AACAATAAAAAGAAAACTGATAGACCG 57.107 29.630 0.00 0.00 0.00 4.79
581 583 5.959618 AAAAAGAAAACTGATAGACCGGG 57.040 39.130 6.32 0.00 0.00 5.73
583 585 3.889520 AGAAAACTGATAGACCGGGAC 57.110 47.619 6.32 0.00 0.00 4.46
596 598 0.981943 CCGGGACTACAACCTCCTTT 59.018 55.000 0.00 0.00 0.00 3.11
597 599 1.350019 CCGGGACTACAACCTCCTTTT 59.650 52.381 0.00 0.00 0.00 2.27
598 600 2.224695 CCGGGACTACAACCTCCTTTTT 60.225 50.000 0.00 0.00 0.00 1.94
599 601 2.812011 CGGGACTACAACCTCCTTTTTG 59.188 50.000 0.00 0.00 0.00 2.44
619 626 7.905031 TTTTGCAACAACAAAAAGAAAACAG 57.095 28.000 0.00 0.00 44.32 3.16
626 633 6.887368 ACAACAAAAAGAAAACAGAACTTGC 58.113 32.000 0.00 0.00 0.00 4.01
691 698 2.034532 CTGCATGCACAGGGTGGA 59.965 61.111 18.46 0.00 38.41 4.02
736 743 3.461061 TGGCGCTAAATGAGAGATTCTG 58.539 45.455 7.64 0.00 0.00 3.02
741 748 5.962423 GCGCTAAATGAGAGATTCTGTTTTC 59.038 40.000 0.00 0.00 0.00 2.29
757 764 6.272318 TCTGTTTTCCACTTTGTGCATAAAG 58.728 36.000 28.18 28.18 42.09 1.85
770 777 3.673746 GCATAAAGCAATCGCAGTGTA 57.326 42.857 0.00 0.00 44.79 2.90
771 778 4.214980 GCATAAAGCAATCGCAGTGTAT 57.785 40.909 0.00 0.00 44.79 2.29
772 779 5.342806 GCATAAAGCAATCGCAGTGTATA 57.657 39.130 0.00 0.00 44.79 1.47
773 780 5.931532 GCATAAAGCAATCGCAGTGTATAT 58.068 37.500 0.00 0.00 44.79 0.86
820 827 1.638388 CGGCAGCTCAATCGCTTTCA 61.638 55.000 0.00 0.00 38.41 2.69
821 828 0.737219 GGCAGCTCAATCGCTTTCAT 59.263 50.000 0.00 0.00 38.41 2.57
822 829 1.268437 GGCAGCTCAATCGCTTTCATC 60.268 52.381 0.00 0.00 38.41 2.92
824 831 2.097142 GCAGCTCAATCGCTTTCATCTT 59.903 45.455 0.00 0.00 38.41 2.40
825 832 3.310774 GCAGCTCAATCGCTTTCATCTTA 59.689 43.478 0.00 0.00 38.41 2.10
826 833 4.024218 GCAGCTCAATCGCTTTCATCTTAT 60.024 41.667 0.00 0.00 38.41 1.73
921 930 3.685435 CCCGATATGGCAATGGGC 58.315 61.111 0.00 0.00 43.74 5.36
978 987 1.226746 AAAAGGAAACTCTGCGTCCG 58.773 50.000 0.00 0.00 42.68 4.79
1015 1024 1.938577 CTCAAATGGCCATCTCACTCG 59.061 52.381 21.08 2.75 0.00 4.18
1054 1063 2.628696 CCGCAACAATGGCAGCTCA 61.629 57.895 0.00 0.00 0.00 4.26
1069 1078 1.152139 CTCATCCTCCTCCCCCTCC 60.152 68.421 0.00 0.00 0.00 4.30
1075 1084 2.204624 TCCTCCCCCTCCTCCTCA 60.205 66.667 0.00 0.00 0.00 3.86
1090 1099 1.039785 CCTCATCCTCCTCGCACTCA 61.040 60.000 0.00 0.00 0.00 3.41
1109 1124 2.420372 TCATCTTCTTGACGAGGAGACG 59.580 50.000 2.48 0.00 42.90 4.18
1208 1223 2.124695 GCACCGGAGCTTAAGGGG 60.125 66.667 17.33 4.77 0.00 4.79
1434 1449 2.308039 GCGCAAGTTCCTCGTCGTT 61.308 57.895 0.30 0.00 41.68 3.85
1448 1463 0.384353 GTCGTTGAACTCTTTGGCGC 60.384 55.000 0.00 0.00 0.00 6.53
1541 1945 0.735471 TGACTGCTCGATCGAGGAAG 59.265 55.000 38.18 30.19 41.86 3.46
1602 2390 1.281287 ACTGATGAGCACCTTGAGCAT 59.719 47.619 0.00 0.00 0.00 3.79
1648 2436 0.990374 AGGAGCACATCTTCAGCCTT 59.010 50.000 0.00 0.00 0.00 4.35
1771 2559 4.093291 CAGGCCAGCTTCTCCGCT 62.093 66.667 5.01 0.00 41.90 5.52
1896 2686 2.949644 TCATCATTGAGCAGCATCTTGG 59.050 45.455 0.00 0.00 0.00 3.61
1942 2732 3.745803 GACCTCGTCGACCGCCTT 61.746 66.667 10.58 0.00 36.19 4.35
1976 2766 0.107165 GGACAATAGTGGCACCCTCC 60.107 60.000 15.27 7.40 32.51 4.30
2020 2810 6.318648 TCAAGGGCATCATCTTTGTATGTTAC 59.681 38.462 0.00 0.00 0.00 2.50
2025 2815 8.796475 GGGCATCATCTTTGTATGTTACATTAT 58.204 33.333 2.23 0.00 38.68 1.28
2052 2882 4.371855 TCTACATCGTGTCCTGATCAAC 57.628 45.455 0.00 0.00 0.00 3.18
2076 2908 6.144080 ACGAAGAAAAGATCAACTAACTGACG 59.856 38.462 0.00 0.00 0.00 4.35
2095 2939 1.480545 CGTCACTCACCACCATGGATA 59.519 52.381 21.47 0.00 40.96 2.59
2240 3084 2.031516 CAGCAACGAGAGGGTGCAG 61.032 63.158 6.50 0.00 45.36 4.41
2264 3108 4.748144 GACCTGGCCAAGCTGGGG 62.748 72.222 9.87 5.79 38.19 4.96
2363 3207 0.179045 ACATCCAGATTGGCGGCTAC 60.179 55.000 11.43 1.32 37.47 3.58
2466 3310 2.037772 GAGTTCAAGCCAGAGAGGTTCA 59.962 50.000 0.00 0.00 40.61 3.18
2492 3336 2.303311 GAGCAAGGTAGACTTCAAGGGT 59.697 50.000 0.00 0.00 37.29 4.34
2682 3526 2.915659 TCAAGACCCCGCTCGTGT 60.916 61.111 0.00 0.00 0.00 4.49
2850 3695 4.039973 TCCGATACAACCTCTTTGAACACT 59.960 41.667 0.00 0.00 38.73 3.55
2867 3712 4.955811 ACACTTCAATGGGCGAGATATA 57.044 40.909 0.00 0.00 0.00 0.86
2869 3714 5.869579 ACACTTCAATGGGCGAGATATATT 58.130 37.500 0.00 0.00 0.00 1.28
3030 3924 2.225491 GCACTTGTTAGGCATCGAACAA 59.775 45.455 0.00 0.11 43.00 2.83
3067 3961 4.040936 TGGGAAAAAGCTAATAGCCACA 57.959 40.909 8.88 0.00 43.77 4.17
3078 3972 4.884164 GCTAATAGCCACAAGAACCATCTT 59.116 41.667 0.00 0.00 39.93 2.40
3179 4100 5.886960 AGCAGATCAAAATTGGTACTGTC 57.113 39.130 0.00 0.00 0.00 3.51
3194 4115 4.717313 GTCCAACTGGGCCGGACC 62.717 72.222 23.70 23.70 42.87 4.46
3640 4626 8.783999 TGTCGCAATTATTTTCGTTTTTCTTA 57.216 26.923 0.00 0.00 0.00 2.10
3641 4627 8.683774 TGTCGCAATTATTTTCGTTTTTCTTAC 58.316 29.630 0.00 0.00 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.827876 TGGCCATTAAGTATACCGATCGA 59.172 43.478 18.66 0.00 0.00 3.59
1 2 3.924686 GTGGCCATTAAGTATACCGATCG 59.075 47.826 9.72 8.51 0.00 3.69
2 3 4.020485 AGGTGGCCATTAAGTATACCGATC 60.020 45.833 9.72 0.00 0.00 3.69
3 4 3.908103 AGGTGGCCATTAAGTATACCGAT 59.092 43.478 9.72 0.00 0.00 4.18
4 5 3.070446 CAGGTGGCCATTAAGTATACCGA 59.930 47.826 9.72 0.00 0.00 4.69
5 6 3.399330 CAGGTGGCCATTAAGTATACCG 58.601 50.000 9.72 0.00 0.00 4.02
6 7 3.146847 GCAGGTGGCCATTAAGTATACC 58.853 50.000 9.72 0.93 36.11 2.73
7 8 3.815401 CTGCAGGTGGCCATTAAGTATAC 59.185 47.826 9.72 0.00 43.89 1.47
8 9 3.747388 GCTGCAGGTGGCCATTAAGTATA 60.747 47.826 17.12 0.00 43.89 1.47
9 10 2.936202 CTGCAGGTGGCCATTAAGTAT 58.064 47.619 9.72 0.00 43.89 2.12
10 11 1.681780 GCTGCAGGTGGCCATTAAGTA 60.682 52.381 17.12 0.00 43.89 2.24
11 12 0.967380 GCTGCAGGTGGCCATTAAGT 60.967 55.000 17.12 0.00 43.89 2.24
12 13 0.966875 TGCTGCAGGTGGCCATTAAG 60.967 55.000 17.12 4.01 43.89 1.85
13 14 0.541530 TTGCTGCAGGTGGCCATTAA 60.542 50.000 17.12 0.00 43.89 1.40
14 15 1.076370 TTGCTGCAGGTGGCCATTA 59.924 52.632 17.12 0.00 43.89 1.90
15 16 2.203669 TTGCTGCAGGTGGCCATT 60.204 55.556 17.12 0.00 43.89 3.16
16 17 2.993264 GTTGCTGCAGGTGGCCAT 60.993 61.111 17.12 0.00 43.89 4.40
17 18 4.519612 TGTTGCTGCAGGTGGCCA 62.520 61.111 17.12 0.00 43.89 5.36
18 19 3.677648 CTGTTGCTGCAGGTGGCC 61.678 66.667 17.12 0.00 43.89 5.36
19 20 2.908940 ACTGTTGCTGCAGGTGGC 60.909 61.111 17.12 1.59 40.59 5.01
20 21 0.892358 ATCACTGTTGCTGCAGGTGG 60.892 55.000 17.12 10.70 40.59 4.61
21 22 0.240145 CATCACTGTTGCTGCAGGTG 59.760 55.000 17.12 14.30 40.59 4.00
22 23 0.179009 ACATCACTGTTGCTGCAGGT 60.179 50.000 17.12 0.62 40.59 4.00
23 24 1.812235 TACATCACTGTTGCTGCAGG 58.188 50.000 17.12 0.00 40.59 4.85
24 25 3.427098 CCAATACATCACTGTTGCTGCAG 60.427 47.826 10.11 10.11 41.92 4.41
25 26 2.488937 CCAATACATCACTGTTGCTGCA 59.511 45.455 0.00 0.00 36.79 4.41
26 27 2.489329 ACCAATACATCACTGTTGCTGC 59.511 45.455 0.00 0.00 36.79 5.25
27 28 4.771590 AACCAATACATCACTGTTGCTG 57.228 40.909 0.00 0.00 36.79 4.41
28 29 4.218417 GGAAACCAATACATCACTGTTGCT 59.782 41.667 0.00 0.00 36.79 3.91
29 30 4.022416 TGGAAACCAATACATCACTGTTGC 60.022 41.667 0.00 0.00 36.79 4.17
30 31 5.241506 AGTGGAAACCAATACATCACTGTTG 59.758 40.000 0.00 0.00 34.16 3.33
31 32 5.385198 AGTGGAAACCAATACATCACTGTT 58.615 37.500 0.00 0.00 34.16 3.16
32 33 4.985538 AGTGGAAACCAATACATCACTGT 58.014 39.130 0.00 0.00 35.73 3.55
51 52 8.579863 GGGATTTCTCCATATTTTCCATTAGTG 58.420 37.037 0.00 0.00 44.08 2.74
63 64 6.391055 TCTTCCAGAAAGGGATTTCTCCATAT 59.609 38.462 0.35 0.00 44.08 1.78
66 67 3.916349 TCTTCCAGAAAGGGATTTCTCCA 59.084 43.478 0.35 0.00 44.08 3.86
94 95 5.474825 TCACCGTTGCTTCTTTTTCTTTTT 58.525 33.333 0.00 0.00 0.00 1.94
95 96 5.066968 TCACCGTTGCTTCTTTTTCTTTT 57.933 34.783 0.00 0.00 0.00 2.27
96 97 4.712122 TCACCGTTGCTTCTTTTTCTTT 57.288 36.364 0.00 0.00 0.00 2.52
97 98 4.918810 ATCACCGTTGCTTCTTTTTCTT 57.081 36.364 0.00 0.00 0.00 2.52
98 99 4.215613 GGTATCACCGTTGCTTCTTTTTCT 59.784 41.667 0.00 0.00 0.00 2.52
99 100 4.215613 AGGTATCACCGTTGCTTCTTTTTC 59.784 41.667 0.00 0.00 44.90 2.29
113 114 7.107542 TGGTAAGTATTTGTTCAGGTATCACC 58.892 38.462 0.00 0.00 38.99 4.02
144 145 2.482142 GCTAGGTAGACATGCCACTGTC 60.482 54.545 0.00 3.64 44.78 3.51
148 149 2.691409 TTGCTAGGTAGACATGCCAC 57.309 50.000 0.00 0.00 32.66 5.01
151 152 2.032549 CGCAATTGCTAGGTAGACATGC 60.033 50.000 26.86 0.00 39.32 4.06
153 154 2.170607 ACCGCAATTGCTAGGTAGACAT 59.829 45.455 26.86 3.32 39.32 3.06
157 158 5.386958 TCTATACCGCAATTGCTAGGTAG 57.613 43.478 29.18 22.59 39.31 3.18
164 165 5.734855 TCTTTCTTCTATACCGCAATTGC 57.265 39.130 20.76 20.76 37.78 3.56
200 201 6.054295 AGCTCAGATAAATGTTTGCCTCTAG 58.946 40.000 0.00 0.00 0.00 2.43
201 202 5.994250 AGCTCAGATAAATGTTTGCCTCTA 58.006 37.500 0.00 0.00 0.00 2.43
205 206 5.573337 AGAAGCTCAGATAAATGTTTGCC 57.427 39.130 0.00 0.00 0.00 4.52
206 207 7.530010 TGTAAGAAGCTCAGATAAATGTTTGC 58.470 34.615 0.00 0.00 0.00 3.68
212 213 8.507249 GTGTGTTTGTAAGAAGCTCAGATAAAT 58.493 33.333 0.00 0.00 0.00 1.40
219 220 4.257731 TGTGTGTGTTTGTAAGAAGCTCA 58.742 39.130 0.00 0.00 0.00 4.26
264 265 3.008594 ACTTCGACATCCCCATGTGTTTA 59.991 43.478 0.00 0.00 43.79 2.01
266 267 1.351017 ACTTCGACATCCCCATGTGTT 59.649 47.619 0.00 0.00 43.79 3.32
268 269 1.208052 AGACTTCGACATCCCCATGTG 59.792 52.381 0.00 0.00 43.79 3.21
269 270 1.573108 AGACTTCGACATCCCCATGT 58.427 50.000 0.00 0.00 46.64 3.21
271 272 2.840651 AGAAAGACTTCGACATCCCCAT 59.159 45.455 0.00 0.00 36.61 4.00
284 285 3.118956 CGGTAGATGCAGGAAGAAAGACT 60.119 47.826 0.00 0.00 0.00 3.24
285 286 3.190874 CGGTAGATGCAGGAAGAAAGAC 58.809 50.000 0.00 0.00 0.00 3.01
286 287 2.168521 CCGGTAGATGCAGGAAGAAAGA 59.831 50.000 0.00 0.00 0.00 2.52
287 288 2.555199 CCGGTAGATGCAGGAAGAAAG 58.445 52.381 0.00 0.00 0.00 2.62
289 290 0.178068 GCCGGTAGATGCAGGAAGAA 59.822 55.000 1.90 0.00 0.00 2.52
291 292 1.592669 CGCCGGTAGATGCAGGAAG 60.593 63.158 1.90 0.00 0.00 3.46
292 293 2.499205 CGCCGGTAGATGCAGGAA 59.501 61.111 1.90 0.00 0.00 3.36
293 294 3.536917 CCGCCGGTAGATGCAGGA 61.537 66.667 1.90 0.00 0.00 3.86
295 296 4.529219 TGCCGCCGGTAGATGCAG 62.529 66.667 4.45 0.00 0.00 4.41
296 297 4.830765 GTGCCGCCGGTAGATGCA 62.831 66.667 4.45 2.09 0.00 3.96
297 298 4.830765 TGTGCCGCCGGTAGATGC 62.831 66.667 4.45 0.00 0.00 3.91
298 299 2.890474 GTGTGCCGCCGGTAGATG 60.890 66.667 4.45 0.00 0.00 2.90
299 300 4.157120 GGTGTGCCGCCGGTAGAT 62.157 66.667 4.45 0.00 0.00 1.98
327 329 2.758327 ACCAGAGGCGGCATCGTA 60.758 61.111 13.08 0.00 38.89 3.43
333 335 2.058595 TCTAAGGACCAGAGGCGGC 61.059 63.158 0.00 0.00 0.00 6.53
342 344 2.563179 TGCTCAACTGAGTCTAAGGACC 59.437 50.000 8.46 0.00 43.85 4.46
344 346 2.828520 CCTGCTCAACTGAGTCTAAGGA 59.171 50.000 8.46 0.00 43.85 3.36
347 349 2.232452 GCTCCTGCTCAACTGAGTCTAA 59.768 50.000 8.46 0.00 43.85 2.10
348 350 1.821753 GCTCCTGCTCAACTGAGTCTA 59.178 52.381 8.46 0.00 43.85 2.59
349 351 0.607620 GCTCCTGCTCAACTGAGTCT 59.392 55.000 8.46 0.00 43.85 3.24
350 352 3.135942 GCTCCTGCTCAACTGAGTC 57.864 57.895 8.46 2.16 43.85 3.36
361 363 0.534412 TGCTCTCTACAAGCTCCTGC 59.466 55.000 0.00 0.00 40.50 4.85
363 365 2.230130 ACTGCTCTCTACAAGCTCCT 57.770 50.000 0.00 0.00 40.50 3.69
364 366 2.223711 GCTACTGCTCTCTACAAGCTCC 60.224 54.545 0.00 0.00 40.50 4.70
365 367 3.078594 GCTACTGCTCTCTACAAGCTC 57.921 52.381 0.00 0.00 40.50 4.09
383 385 1.169577 ACATCGACGACTTCTCAGCT 58.830 50.000 0.00 0.00 0.00 4.24
385 387 4.768145 GATCTACATCGACGACTTCTCAG 58.232 47.826 0.00 0.00 0.00 3.35
406 408 0.470456 ATAACATAGGCGTCCCCCGA 60.470 55.000 0.00 0.00 39.56 5.14
408 410 0.763035 ACATAACATAGGCGTCCCCC 59.237 55.000 0.00 0.00 0.00 5.40
411 413 3.057734 GCAGTACATAACATAGGCGTCC 58.942 50.000 0.00 0.00 0.00 4.79
414 416 3.717707 AGTGCAGTACATAACATAGGCG 58.282 45.455 0.00 0.00 0.00 5.52
417 419 7.364522 ACAACAAGTGCAGTACATAACATAG 57.635 36.000 0.00 0.00 0.00 2.23
419 421 6.633500 AACAACAAGTGCAGTACATAACAT 57.367 33.333 0.00 0.00 0.00 2.71
421 423 7.749539 AAAAACAACAAGTGCAGTACATAAC 57.250 32.000 0.00 0.00 0.00 1.89
446 448 6.322712 ACAAGTGCAGTACATTTCCCTAAAAA 59.677 34.615 0.00 0.00 0.00 1.94
447 449 5.830991 ACAAGTGCAGTACATTTCCCTAAAA 59.169 36.000 0.00 0.00 0.00 1.52
448 450 5.381757 ACAAGTGCAGTACATTTCCCTAAA 58.618 37.500 0.00 0.00 0.00 1.85
449 451 4.980573 ACAAGTGCAGTACATTTCCCTAA 58.019 39.130 0.00 0.00 0.00 2.69
450 452 4.634012 ACAAGTGCAGTACATTTCCCTA 57.366 40.909 0.00 0.00 0.00 3.53
451 453 3.508845 ACAAGTGCAGTACATTTCCCT 57.491 42.857 0.00 0.00 0.00 4.20
452 454 3.568007 TCAACAAGTGCAGTACATTTCCC 59.432 43.478 0.00 0.00 0.00 3.97
453 455 4.829064 TCAACAAGTGCAGTACATTTCC 57.171 40.909 0.00 0.00 0.00 3.13
454 456 5.853282 GTCATCAACAAGTGCAGTACATTTC 59.147 40.000 0.00 0.00 0.00 2.17
455 457 5.532406 AGTCATCAACAAGTGCAGTACATTT 59.468 36.000 0.00 0.00 0.00 2.32
456 458 5.065914 AGTCATCAACAAGTGCAGTACATT 58.934 37.500 0.00 0.00 0.00 2.71
465 467 2.624838 AGGCCAAAGTCATCAACAAGTG 59.375 45.455 5.01 0.00 0.00 3.16
472 474 1.522668 CAACGAGGCCAAAGTCATCA 58.477 50.000 5.01 0.00 0.00 3.07
492 494 8.652810 ACCATCTTTATTAAATTGATGCAAGC 57.347 30.769 10.65 0.00 34.79 4.01
494 496 9.941325 ACAACCATCTTTATTAAATTGATGCAA 57.059 25.926 10.65 0.00 34.79 4.08
496 498 9.369904 ACACAACCATCTTTATTAAATTGATGC 57.630 29.630 10.65 0.00 34.79 3.91
553 555 9.893305 CGGTCTATCAGTTTTCTTTTTATTGTT 57.107 29.630 0.00 0.00 0.00 2.83
554 556 8.512138 CCGGTCTATCAGTTTTCTTTTTATTGT 58.488 33.333 0.00 0.00 0.00 2.71
555 557 7.968405 CCCGGTCTATCAGTTTTCTTTTTATTG 59.032 37.037 0.00 0.00 0.00 1.90
556 558 7.886446 TCCCGGTCTATCAGTTTTCTTTTTATT 59.114 33.333 0.00 0.00 0.00 1.40
557 559 7.336176 GTCCCGGTCTATCAGTTTTCTTTTTAT 59.664 37.037 0.00 0.00 0.00 1.40
558 560 6.652062 GTCCCGGTCTATCAGTTTTCTTTTTA 59.348 38.462 0.00 0.00 0.00 1.52
559 561 5.472478 GTCCCGGTCTATCAGTTTTCTTTTT 59.528 40.000 0.00 0.00 0.00 1.94
560 562 5.001874 GTCCCGGTCTATCAGTTTTCTTTT 58.998 41.667 0.00 0.00 0.00 2.27
561 563 4.286291 AGTCCCGGTCTATCAGTTTTCTTT 59.714 41.667 0.00 0.00 0.00 2.52
562 564 3.838903 AGTCCCGGTCTATCAGTTTTCTT 59.161 43.478 0.00 0.00 0.00 2.52
563 565 3.442076 AGTCCCGGTCTATCAGTTTTCT 58.558 45.455 0.00 0.00 0.00 2.52
564 566 3.889520 AGTCCCGGTCTATCAGTTTTC 57.110 47.619 0.00 0.00 0.00 2.29
565 567 4.091549 TGTAGTCCCGGTCTATCAGTTTT 58.908 43.478 0.00 0.00 0.00 2.43
566 568 3.705051 TGTAGTCCCGGTCTATCAGTTT 58.295 45.455 0.00 0.00 0.00 2.66
567 569 3.377253 TGTAGTCCCGGTCTATCAGTT 57.623 47.619 0.00 0.00 0.00 3.16
568 570 3.022406 GTTGTAGTCCCGGTCTATCAGT 58.978 50.000 0.00 0.00 0.00 3.41
569 571 2.361438 GGTTGTAGTCCCGGTCTATCAG 59.639 54.545 0.00 0.00 0.00 2.90
570 572 2.024655 AGGTTGTAGTCCCGGTCTATCA 60.025 50.000 0.00 2.11 0.00 2.15
571 573 2.622470 GAGGTTGTAGTCCCGGTCTATC 59.378 54.545 0.00 0.00 0.00 2.08
579 581 2.557056 GCAAAAAGGAGGTTGTAGTCCC 59.443 50.000 0.00 0.00 32.70 4.46
581 583 4.097286 TGTTGCAAAAAGGAGGTTGTAGTC 59.903 41.667 0.00 0.00 0.00 2.59
583 585 4.647424 TGTTGCAAAAAGGAGGTTGTAG 57.353 40.909 0.00 0.00 0.00 2.74
596 598 7.251704 TCTGTTTTCTTTTTGTTGTTGCAAA 57.748 28.000 0.00 0.00 36.67 3.68
597 599 6.851222 TCTGTTTTCTTTTTGTTGTTGCAA 57.149 29.167 0.00 0.00 0.00 4.08
598 600 6.481644 AGTTCTGTTTTCTTTTTGTTGTTGCA 59.518 30.769 0.00 0.00 0.00 4.08
599 601 6.887368 AGTTCTGTTTTCTTTTTGTTGTTGC 58.113 32.000 0.00 0.00 0.00 4.17
691 698 3.853307 GCTTGCAACACGTTATGCTTTCT 60.853 43.478 19.64 0.00 42.97 2.52
721 728 8.924511 AAGTGGAAAACAGAATCTCTCATTTA 57.075 30.769 0.00 0.00 0.00 1.40
736 743 5.328886 GCTTTATGCACAAAGTGGAAAAC 57.671 39.130 18.21 0.00 37.44 2.43
757 764 5.178252 ACAGAATCATATACACTGCGATTGC 59.822 40.000 0.00 0.00 43.20 3.56
765 772 5.590259 GGGCAAACACAGAATCATATACACT 59.410 40.000 0.00 0.00 0.00 3.55
766 773 5.356751 TGGGCAAACACAGAATCATATACAC 59.643 40.000 0.00 0.00 0.00 2.90
767 774 5.356751 GTGGGCAAACACAGAATCATATACA 59.643 40.000 1.18 0.00 40.99 2.29
768 775 5.504010 CGTGGGCAAACACAGAATCATATAC 60.504 44.000 6.30 0.00 41.38 1.47
770 777 3.378112 CGTGGGCAAACACAGAATCATAT 59.622 43.478 6.30 0.00 41.38 1.78
771 778 2.746904 CGTGGGCAAACACAGAATCATA 59.253 45.455 6.30 0.00 41.38 2.15
772 779 1.541147 CGTGGGCAAACACAGAATCAT 59.459 47.619 6.30 0.00 41.38 2.45
773 780 0.950836 CGTGGGCAAACACAGAATCA 59.049 50.000 6.30 0.00 41.38 2.57
821 828 9.679661 TGGACTTTGCATCAGTTTAATATAAGA 57.320 29.630 0.81 0.00 0.00 2.10
822 829 9.722056 GTGGACTTTGCATCAGTTTAATATAAG 57.278 33.333 0.81 0.00 0.00 1.73
824 831 8.800370 TGTGGACTTTGCATCAGTTTAATATA 57.200 30.769 0.81 0.00 0.00 0.86
825 832 7.701539 TGTGGACTTTGCATCAGTTTAATAT 57.298 32.000 0.81 0.00 0.00 1.28
826 833 7.537715 CATGTGGACTTTGCATCAGTTTAATA 58.462 34.615 0.81 0.00 0.00 0.98
870 879 4.690748 CGACTTGCCATATTTGATCCGTAT 59.309 41.667 0.00 0.00 0.00 3.06
921 930 0.804989 GCCAAGTTTGATCCGTGGAG 59.195 55.000 6.61 0.00 0.00 3.86
978 987 3.963428 TGAGTTTCTTAGCTGGAGGAC 57.037 47.619 0.00 0.00 0.00 3.85
1054 1063 2.416923 GGAGGAGGGGGAGGAGGAT 61.417 68.421 0.00 0.00 0.00 3.24
1069 1078 0.754957 AGTGCGAGGAGGATGAGGAG 60.755 60.000 0.00 0.00 0.00 3.69
1075 1084 1.686052 GAAGATGAGTGCGAGGAGGAT 59.314 52.381 0.00 0.00 0.00 3.24
1090 1099 1.746220 CCGTCTCCTCGTCAAGAAGAT 59.254 52.381 0.00 0.00 0.00 2.40
1109 1124 1.077429 CTGAGCCCTTTGTAGCCCC 60.077 63.158 0.00 0.00 0.00 5.80
1266 1281 1.363807 CTCTGCTGACGACACCACA 59.636 57.895 0.00 0.00 0.00 4.17
1434 1449 3.711842 CGCGCGCCAAAGAGTTCA 61.712 61.111 27.72 0.00 0.00 3.18
1508 1523 5.348724 TCGAGCAGTCACATTCATTCTAAAC 59.651 40.000 0.00 0.00 0.00 2.01
1523 1544 1.018148 TCTTCCTCGATCGAGCAGTC 58.982 55.000 34.54 0.00 40.69 3.51
1918 2708 0.813184 GGTCGACGAGGTCACCATTA 59.187 55.000 9.92 0.00 35.45 1.90
1976 2766 1.869574 CGTGGTCTCTCGTGATGCG 60.870 63.158 0.00 0.00 43.01 4.73
2020 2810 7.904977 CAGGACACGATGTAGAAACAAATAATG 59.095 37.037 0.00 0.00 39.58 1.90
2025 2815 4.951254 TCAGGACACGATGTAGAAACAAA 58.049 39.130 0.00 0.00 39.58 2.83
2030 2852 4.674362 CGTTGATCAGGACACGATGTAGAA 60.674 45.833 11.35 0.00 0.00 2.10
2039 2863 4.750098 TCTTTTCTTCGTTGATCAGGACAC 59.250 41.667 0.00 0.00 0.00 3.67
2052 2882 6.144080 ACGTCAGTTAGTTGATCTTTTCTTCG 59.856 38.462 0.00 0.00 0.00 3.79
2076 2908 2.236146 TGTATCCATGGTGGTGAGTGAC 59.764 50.000 12.58 0.00 39.03 3.67
2264 3108 3.600388 CTTCACCACCATCTTGAGGTAC 58.400 50.000 0.00 0.00 37.23 3.34
2363 3207 3.414700 GTCTTGGCTGGCACGTCG 61.415 66.667 2.29 0.00 0.00 5.12
2372 3216 0.032678 CATAGATCCGCGTCTTGGCT 59.967 55.000 4.92 0.00 0.00 4.75
2466 3310 3.511477 TGAAGTCTACCTTGCTCTCCTT 58.489 45.455 0.00 0.00 32.03 3.36
2492 3336 1.068610 GGCGTTAGCTCAAAATGTGCA 60.069 47.619 0.00 0.00 44.37 4.57
2628 3472 0.469070 CCTTCCTCCTCCATGCTCAG 59.531 60.000 0.00 0.00 0.00 3.35
2700 3544 2.503331 CCACTGTGCTTACATGTTCCA 58.497 47.619 2.30 0.00 0.00 3.53
2828 3673 4.315803 AGTGTTCAAAGAGGTTGTATCGG 58.684 43.478 0.00 0.00 38.47 4.18
2850 3695 7.047891 GGTATGAATATATCTCGCCCATTGAA 58.952 38.462 0.00 0.00 0.00 2.69
2869 3714 8.217799 CCAACCCTTTATTATGAAGAGGTATGA 58.782 37.037 9.15 0.00 31.65 2.15
2893 3738 6.942976 ACGTATTTTCTAGAAAGACCATCCA 58.057 36.000 17.05 1.54 0.00 3.41
3011 3904 3.502211 CCTTTGTTCGATGCCTAACAAGT 59.498 43.478 0.00 0.00 44.05 3.16
3015 3909 2.418976 GGTCCTTTGTTCGATGCCTAAC 59.581 50.000 0.00 0.00 0.00 2.34
3030 3924 3.922366 CAACCCCTGGAGGTCCTT 58.078 61.111 7.23 0.00 40.05 3.36
3054 3948 4.164988 AGATGGTTCTTGTGGCTATTAGCT 59.835 41.667 15.02 0.00 41.99 3.32
3078 3972 7.334858 TGCACTACATAAGTATCACCAAATCA 58.665 34.615 0.00 0.00 35.76 2.57
3147 4049 7.014615 ACCAATTTTGATCTGCTAGAGTGTTTT 59.985 33.333 0.00 0.00 0.00 2.43
3513 4460 9.107367 CAATTTGAAAAAGTGTTTGCGTTTTAA 57.893 25.926 0.00 0.00 32.05 1.52
3580 4536 6.365520 AGGCCCTAGTATATTTGGAAAAGTG 58.634 40.000 0.00 0.00 0.00 3.16
3582 4538 7.175119 GCTTAGGCCCTAGTATATTTGGAAAAG 59.825 40.741 0.00 0.00 0.00 2.27
3616 4602 8.151533 GGTAAGAAAAACGAAAATAATTGCGAC 58.848 33.333 0.00 0.00 40.19 5.19
3618 4604 8.222984 AGGTAAGAAAAACGAAAATAATTGCG 57.777 30.769 0.00 0.00 43.58 4.85
3682 4668 7.821359 TCAAATTTTGAACATGTTTCACAAGGA 59.179 29.630 13.36 5.96 36.59 3.36


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

AutoCloner maintained by Alex Coulton.