Multiple sequence alignment - TraesCS6B01G430900

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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 TraesCS6B01G430900 chr6B 100.000 5958 0 0 1 5958 698986216 698992173 0.000000e+00 11003.0
1 TraesCS6B01G430900 chr6B 88.301 2248 200 29 2978 5211 698976252 698978450 0.000000e+00 2636.0
2 TraesCS6B01G430900 chr6B 88.033 2156 218 21 350 2488 698974077 698976209 0.000000e+00 2516.0
3 TraesCS6B01G430900 chr6B 87.069 2119 213 25 2519 4622 698104004 698106076 0.000000e+00 2338.0
4 TraesCS6B01G430900 chr6B 87.054 1823 183 19 635 2450 698102228 698104004 0.000000e+00 2010.0
5 TraesCS6B01G430900 chr6B 86.331 556 67 7 4647 5198 698106292 698106842 1.110000e-166 597.0
6 TraesCS6B01G430900 chr6B 83.838 99 12 2 661 758 698089605 698089700 2.290000e-14 91.6
7 TraesCS6B01G430900 chr6D 87.517 4446 449 52 796 5211 459244191 459248560 0.000000e+00 5038.0
8 TraesCS6B01G430900 chr6D 96.525 2475 59 8 2679 5130 459263216 459265686 0.000000e+00 4069.0
9 TraesCS6B01G430900 chr6D 95.991 1846 66 4 28 1869 459251815 459253656 0.000000e+00 2992.0
10 TraesCS6B01G430900 chr6D 89.147 2285 189 36 2904 5176 458975447 458977684 0.000000e+00 2791.0
11 TraesCS6B01G430900 chr6D 84.681 2794 339 52 153 2905 459048779 459051524 0.000000e+00 2706.0
12 TraesCS6B01G430900 chr6D 84.406 2796 344 53 153 2905 458972619 458975365 0.000000e+00 2663.0
13 TraesCS6B01G430900 chr6D 85.980 2418 257 48 11 2403 459045814 459048174 0.000000e+00 2512.0
14 TraesCS6B01G430900 chr6D 88.054 1783 181 16 635 2403 458970683 458972447 0.000000e+00 2084.0
15 TraesCS6B01G430900 chr6D 89.769 1427 116 23 2904 4321 459051601 459053006 0.000000e+00 1799.0
16 TraesCS6B01G430900 chr6D 86.075 912 83 24 4317 5212 459058146 459059029 0.000000e+00 941.0
17 TraesCS6B01G430900 chr6D 95.871 557 17 5 5122 5675 459265860 459266413 0.000000e+00 896.0
18 TraesCS6B01G430900 chr6D 88.372 172 14 4 5741 5910 459266578 459266745 1.010000e-47 202.0
19 TraesCS6B01G430900 chr6D 78.963 328 37 18 5374 5695 459059026 459059327 1.690000e-45 195.0
20 TraesCS6B01G430900 chr6A 93.528 2472 103 32 187 2631 605366280 605368721 0.000000e+00 3626.0
21 TraesCS6B01G430900 chr6A 95.180 2199 69 6 3221 5387 605368718 605370911 0.000000e+00 3439.0
22 TraesCS6B01G430900 chr6A 86.472 2846 303 44 219 3032 605358217 605361012 0.000000e+00 3048.0
23 TraesCS6B01G430900 chr6A 88.643 2307 202 38 2904 5200 605337432 605339688 0.000000e+00 2754.0
24 TraesCS6B01G430900 chr6A 88.559 2089 180 27 3100 5179 605361583 605363621 0.000000e+00 2479.0
25 TraesCS6B01G430900 chr6A 89.591 269 15 9 5450 5712 605371528 605371789 4.450000e-86 329.0
26 TraesCS6B01G430900 chr6A 80.938 320 33 14 326 631 605324287 605324592 1.670000e-55 228.0
27 TraesCS6B01G430900 chr6A 81.570 293 35 11 11 301 605324017 605324292 2.160000e-54 224.0
28 TraesCS6B01G430900 chr6A 85.135 74 4 2 5382 5449 605371434 605371506 1.070000e-07 69.4
29 TraesCS6B01G430900 chr6A 89.583 48 4 1 5912 5958 605371950 605371997 6.450000e-05 60.2
30 TraesCS6B01G430900 chr2B 76.765 439 85 13 4104 4530 758899129 758899562 4.640000e-56 230.0
31 TraesCS6B01G430900 chr2B 75.737 441 87 16 4104 4530 706790026 706789592 2.820000e-48 204.0


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 TraesCS6B01G430900 chr6B 698986216 698992173 5957 False 11003.000000 11003 100.000000 1 5958 1 chr6B.!!$F2 5957
1 TraesCS6B01G430900 chr6B 698974077 698978450 4373 False 2576.000000 2636 88.167000 350 5211 2 chr6B.!!$F4 4861
2 TraesCS6B01G430900 chr6B 698102228 698106842 4614 False 1648.333333 2338 86.818000 635 5198 3 chr6B.!!$F3 4563
3 TraesCS6B01G430900 chr6D 459244191 459253656 9465 False 4015.000000 5038 91.754000 28 5211 2 chr6D.!!$F4 5183
4 TraesCS6B01G430900 chr6D 458970683 458977684 7001 False 2512.666667 2791 87.202333 153 5176 3 chr6D.!!$F1 5023
5 TraesCS6B01G430900 chr6D 459045814 459053006 7192 False 2339.000000 2706 86.810000 11 4321 3 chr6D.!!$F2 4310
6 TraesCS6B01G430900 chr6D 459263216 459266745 3529 False 1722.333333 4069 93.589333 2679 5910 3 chr6D.!!$F5 3231
7 TraesCS6B01G430900 chr6D 459058146 459059327 1181 False 568.000000 941 82.519000 4317 5695 2 chr6D.!!$F3 1378
8 TraesCS6B01G430900 chr6A 605337432 605339688 2256 False 2754.000000 2754 88.643000 2904 5200 1 chr6A.!!$F1 2296
9 TraesCS6B01G430900 chr6A 605358217 605371997 13780 False 1864.371429 3626 89.721143 187 5958 7 chr6A.!!$F3 5771
10 TraesCS6B01G430900 chr6A 605324017 605324592 575 False 226.000000 228 81.254000 11 631 2 chr6A.!!$F2 620

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
25 26 0.108424 CAGAGCTTTCACCTCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63 F
1315 3806 0.395724 AAACGGATCCAATCTGGCCC 60.396 55.000 13.41 0.00 40.02 5.80 F
2755 8101 0.319405 GAAACATTTGGCCAGCAGCT 59.681 50.000 5.11 0.00 43.05 4.24 F
3415 9365 2.684943 TGGGAGGTAGAACACAGTTCA 58.315 47.619 11.92 0.00 0.00 3.18 F
3416 9366 3.248024 TGGGAGGTAGAACACAGTTCAT 58.752 45.455 11.92 1.12 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 4169 0.107897 TCGACGTACCGCCCTACTAA 60.108 55.000 0.00 0.0 0.00 2.24 R
2811 8167 0.322975 CGCCCATATGAGCTAGGCTT 59.677 55.000 15.27 0.0 39.88 4.35 R
3916 9872 1.210538 TCTCCATGGATGCAGAAGCT 58.789 50.000 16.63 0.0 42.74 3.74 R
4408 10394 2.031157 ACATGTAACCGCTGTTTGAAGC 60.031 45.455 0.00 0.0 39.94 3.86 R
4973 18229 2.082140 ACCCACGGCATATACAGAGA 57.918 50.000 0.00 0.0 0.00 3.10 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
25 26 0.108424 CAGAGCTTTCACCTCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
27 28 1.536662 AGCTTTCACCTCCTCCGGT 60.537 57.895 0.00 0.00 37.93 5.28
62 64 6.435430 TTTCCGAGTCATACATTTTGATGG 57.565 37.500 0.00 0.00 0.00 3.51
99 101 8.449251 TGTGAGCATCTGCAATAACATAAATA 57.551 30.769 4.79 0.00 45.16 1.40
103 105 9.552114 GAGCATCTGCAATAACATAAATACATC 57.448 33.333 4.79 0.00 45.16 3.06
104 106 9.070179 AGCATCTGCAATAACATAAATACATCA 57.930 29.630 4.79 0.00 45.16 3.07
138 140 8.801882 AAAATATCCTTTTTCAGGTGATACGA 57.198 30.769 0.00 0.00 44.37 3.43
148 150 5.011090 TCAGGTGATACGATCTTTTCAGG 57.989 43.478 0.00 0.00 0.00 3.86
176 178 4.021104 TGAGGAGACACTAAACAGGTGATG 60.021 45.833 0.00 0.00 38.01 3.07
178 180 3.557054 GGAGACACTAAACAGGTGATGCA 60.557 47.826 0.00 0.00 38.01 3.96
193 195 4.382470 GGTGATGCACTCTATTCAGACAGT 60.382 45.833 0.00 0.00 34.40 3.55
195 197 5.063186 GTGATGCACTCTATTCAGACAGTTG 59.937 44.000 0.00 0.00 0.00 3.16
196 198 3.329386 TGCACTCTATTCAGACAGTTGC 58.671 45.455 0.00 0.00 0.00 4.17
197 199 3.244181 TGCACTCTATTCAGACAGTTGCA 60.244 43.478 0.00 0.00 0.00 4.08
198 200 3.124297 GCACTCTATTCAGACAGTTGCAC 59.876 47.826 0.00 0.00 0.00 4.57
199 201 4.309933 CACTCTATTCAGACAGTTGCACA 58.690 43.478 0.00 0.00 0.00 4.57
200 202 4.751600 CACTCTATTCAGACAGTTGCACAA 59.248 41.667 0.00 0.00 0.00 3.33
201 203 4.993584 ACTCTATTCAGACAGTTGCACAAG 59.006 41.667 0.00 0.00 0.00 3.16
202 204 5.213891 TCTATTCAGACAGTTGCACAAGA 57.786 39.130 0.00 0.00 0.00 3.02
203 205 4.991056 TCTATTCAGACAGTTGCACAAGAC 59.009 41.667 0.00 0.00 0.00 3.01
204 206 2.689553 TCAGACAGTTGCACAAGACA 57.310 45.000 0.00 0.00 0.00 3.41
205 207 2.554142 TCAGACAGTTGCACAAGACAG 58.446 47.619 0.00 0.00 0.00 3.51
206 208 1.003116 CAGACAGTTGCACAAGACAGC 60.003 52.381 0.00 0.00 0.00 4.40
207 209 1.016627 GACAGTTGCACAAGACAGCA 58.983 50.000 0.00 0.00 39.32 4.41
208 210 1.003116 GACAGTTGCACAAGACAGCAG 60.003 52.381 0.00 0.00 42.39 4.24
209 211 1.302366 CAGTTGCACAAGACAGCAGA 58.698 50.000 0.00 0.00 42.39 4.26
271 273 1.265095 CAAGACTGCACGCTCAAATGT 59.735 47.619 0.00 0.00 0.00 2.71
287 289 4.099266 TCAAATGTGTAGCTGGCAAACTTT 59.901 37.500 0.00 0.00 0.00 2.66
288 290 5.300539 TCAAATGTGTAGCTGGCAAACTTTA 59.699 36.000 0.00 0.00 0.00 1.85
289 291 5.982890 AATGTGTAGCTGGCAAACTTTAT 57.017 34.783 0.00 0.00 0.00 1.40
290 292 7.175816 TCAAATGTGTAGCTGGCAAACTTTATA 59.824 33.333 0.00 0.00 0.00 0.98
292 294 7.645058 ATGTGTAGCTGGCAAACTTTATAAT 57.355 32.000 0.00 0.00 0.00 1.28
294 296 7.312154 TGTGTAGCTGGCAAACTTTATAATTG 58.688 34.615 0.00 0.00 0.00 2.32
295 297 6.253512 GTGTAGCTGGCAAACTTTATAATTGC 59.746 38.462 12.02 12.02 46.60 3.56
303 305 7.650834 GCAAACTTTATAATTGCAAAGACCA 57.349 32.000 14.52 0.00 46.57 4.02
304 306 7.732664 GCAAACTTTATAATTGCAAAGACCAG 58.267 34.615 14.52 0.00 46.57 4.00
305 307 7.598493 GCAAACTTTATAATTGCAAAGACCAGA 59.402 33.333 14.52 0.00 46.57 3.86
306 308 9.474920 CAAACTTTATAATTGCAAAGACCAGAA 57.525 29.630 1.71 0.00 35.70 3.02
308 310 9.643693 AACTTTATAATTGCAAAGACCAGAATG 57.356 29.630 1.71 0.00 35.70 2.67
309 311 9.023962 ACTTTATAATTGCAAAGACCAGAATGA 57.976 29.630 1.71 0.00 35.12 2.57
310 312 9.859427 CTTTATAATTGCAAAGACCAGAATGAA 57.141 29.630 1.71 0.00 34.06 2.57
312 314 9.806203 TTATAATTGCAAAGACCAGAATGAATG 57.194 29.630 1.71 0.00 39.69 2.67
313 315 5.733620 ATTGCAAAGACCAGAATGAATGT 57.266 34.783 1.71 0.00 39.69 2.71
314 316 4.508461 TGCAAAGACCAGAATGAATGTG 57.492 40.909 0.00 0.00 39.69 3.21
315 317 3.248266 GCAAAGACCAGAATGAATGTGC 58.752 45.455 0.00 0.00 39.69 4.57
316 318 3.495193 CAAAGACCAGAATGAATGTGCG 58.505 45.455 0.00 0.00 39.69 5.34
317 319 2.768253 AGACCAGAATGAATGTGCGA 57.232 45.000 0.00 0.00 39.69 5.10
318 320 2.625737 AGACCAGAATGAATGTGCGAG 58.374 47.619 0.00 0.00 39.69 5.03
319 321 2.027745 AGACCAGAATGAATGTGCGAGT 60.028 45.455 0.00 0.00 39.69 4.18
320 322 2.744202 GACCAGAATGAATGTGCGAGTT 59.256 45.455 0.00 0.00 39.69 3.01
321 323 2.744202 ACCAGAATGAATGTGCGAGTTC 59.256 45.455 0.00 0.00 39.69 3.01
322 324 2.743664 CCAGAATGAATGTGCGAGTTCA 59.256 45.455 0.00 0.83 39.69 3.18
323 325 3.425359 CCAGAATGAATGTGCGAGTTCAC 60.425 47.826 0.00 0.00 39.69 3.18
324 326 2.744202 AGAATGAATGTGCGAGTTCACC 59.256 45.455 0.00 0.00 37.19 4.02
340 372 2.684943 TCACCCACAGAGTTTGACCTA 58.315 47.619 0.00 0.00 0.00 3.08
359 397 8.865590 TGACCTAACATTTTTAAGAAACAAGC 57.134 30.769 0.00 0.00 0.00 4.01
360 398 7.646130 TGACCTAACATTTTTAAGAAACAAGCG 59.354 33.333 0.00 0.00 0.00 4.68
416 454 5.772825 TGATGTTCTTCTGAAACCCAAAG 57.227 39.130 0.00 0.00 33.52 2.77
422 460 5.592104 TCTTCTGAAACCCAAAGGAAAAC 57.408 39.130 0.00 0.00 36.73 2.43
456 497 4.313277 TCTTAATGAGCTGATCTGTCCG 57.687 45.455 0.00 0.00 0.00 4.79
511 552 5.638657 TGGTCAAACAATAAATGATGCAAGC 59.361 36.000 0.00 0.00 0.00 4.01
516 557 5.163281 ACAATAAATGATGCAAGCCCAAA 57.837 34.783 0.00 0.00 0.00 3.28
532 573 2.888212 CCAAAGGGAAGACCATGGAAA 58.112 47.619 21.47 0.00 46.18 3.13
550 591 4.989334 GGAAATTCCTGCACCACTGATGG 61.989 52.174 4.46 0.00 42.13 3.51
567 609 3.505680 TGATGGTCACATTTACCTGCAAC 59.494 43.478 0.00 0.00 37.47 4.17
570 612 3.073209 TGGTCACATTTACCTGCAACCTA 59.927 43.478 0.00 0.00 37.91 3.08
571 613 4.263727 TGGTCACATTTACCTGCAACCTAT 60.264 41.667 0.00 0.00 37.91 2.57
572 614 5.045505 TGGTCACATTTACCTGCAACCTATA 60.046 40.000 0.00 0.00 37.91 1.31
573 615 5.296035 GGTCACATTTACCTGCAACCTATAC 59.704 44.000 0.00 0.00 33.97 1.47
574 616 5.006358 GTCACATTTACCTGCAACCTATACG 59.994 44.000 0.00 0.00 0.00 3.06
575 617 3.875134 ACATTTACCTGCAACCTATACGC 59.125 43.478 0.00 0.00 0.00 4.42
576 618 3.613494 TTTACCTGCAACCTATACGCA 57.387 42.857 0.00 0.00 0.00 5.24
577 619 2.589798 TACCTGCAACCTATACGCAC 57.410 50.000 0.00 0.00 0.00 5.34
657 725 7.277760 GGGGTTTGTTCTGTTCATAAAATATGC 59.722 37.037 0.00 0.00 0.00 3.14
682 750 4.720046 TCCAACTAACATTGTACCAGCAA 58.280 39.130 0.00 0.00 0.00 3.91
728 796 3.251004 CCAGCAGTCACACCTAAAAGAAC 59.749 47.826 0.00 0.00 0.00 3.01
731 799 3.877508 GCAGTCACACCTAAAAGAACAGT 59.122 43.478 0.00 0.00 0.00 3.55
732 800 5.054477 GCAGTCACACCTAAAAGAACAGTA 58.946 41.667 0.00 0.00 0.00 2.74
735 803 7.255139 GCAGTCACACCTAAAAGAACAGTAAAT 60.255 37.037 0.00 0.00 0.00 1.40
855 926 3.462205 ACTACTTCCAAGGTTCCCACTTT 59.538 43.478 0.00 0.00 0.00 2.66
860 931 1.620822 CAAGGTTCCCACTTTCCCAG 58.379 55.000 0.00 0.00 0.00 4.45
872 943 4.065789 CACTTTCCCAGTAACTTCCTGTC 58.934 47.826 0.00 0.00 32.76 3.51
892 964 3.194755 GTCGGAAAAGGGCCACAAATAAT 59.805 43.478 6.18 0.00 0.00 1.28
894 966 5.017490 TCGGAAAAGGGCCACAAATAATAA 58.983 37.500 6.18 0.00 0.00 1.40
945 1017 4.524316 TCTGATTTGCATTGTCCAAAGG 57.476 40.909 0.00 0.00 35.84 3.11
1005 3496 1.726853 AGTTCGCTACAGCAATGGAC 58.273 50.000 1.61 0.00 42.21 4.02
1009 3500 1.609783 GCTACAGCAATGGACCCCT 59.390 57.895 0.00 0.00 41.59 4.79
1022 3513 1.356398 GGACCCCTTTCCCATACACAA 59.644 52.381 0.00 0.00 0.00 3.33
1200 3691 3.922240 GCAGAAAACATTACTACGTCGGA 59.078 43.478 0.00 0.00 0.00 4.55
1230 3721 6.433093 GGTACAAGAACATACCCAAAGACAAT 59.567 38.462 0.00 0.00 35.71 2.71
1248 3739 1.422531 ATGTTGTGTGGGTTGCCAAT 58.577 45.000 0.00 0.00 0.00 3.16
1263 3754 1.229428 CCAATCGTGCTATGCCGATT 58.771 50.000 16.61 16.61 45.21 3.34
1280 3771 3.529533 CGATTGCTGATCCTTCTTCTGT 58.470 45.455 0.00 0.00 0.00 3.41
1287 3778 4.629200 GCTGATCCTTCTTCTGTAACACTG 59.371 45.833 0.00 0.00 0.00 3.66
1311 3802 3.127548 CCTTCACAAACGGATCCAATCTG 59.872 47.826 13.41 5.60 41.49 2.90
1315 3806 0.395724 AAACGGATCCAATCTGGCCC 60.396 55.000 13.41 0.00 40.02 5.80
1362 3853 1.001293 TGGATGACAGATATCAGCGCC 59.999 52.381 2.29 0.00 35.80 6.53
1443 3934 6.238484 GGAATTTTATCCTTCGGTCATCACAG 60.238 42.308 0.00 0.00 36.50 3.66
1473 3964 6.712095 TCATCTTATGGCAAAGCTTCGATTAT 59.288 34.615 0.00 0.00 0.00 1.28
1529 4020 0.677731 ATCACCCACAAGACGCATGG 60.678 55.000 0.00 0.00 0.00 3.66
1543 4034 1.421410 GCATGGACTACAACGGCTCG 61.421 60.000 0.00 0.00 0.00 5.03
1558 4049 1.000955 GGCTCGTCTCTTGGAGAAACA 59.999 52.381 0.00 0.00 40.59 2.83
1597 4088 2.098117 GGCAACTTCTCATATGGTGCAC 59.902 50.000 8.80 8.80 45.47 4.57
1616 4107 1.081892 CACCCTGATGAGTTTCTGCG 58.918 55.000 0.00 0.00 0.00 5.18
1624 4115 0.736053 TGAGTTTCTGCGGCGTTTTT 59.264 45.000 9.37 0.00 0.00 1.94
1635 4126 1.067915 CGGCGTTTTTCATGGAATGGT 60.068 47.619 0.00 0.00 46.73 3.55
1638 4129 2.661195 GCGTTTTTCATGGAATGGTTCG 59.339 45.455 0.00 0.00 46.73 3.95
1678 4169 4.839121 TCCAGCGTGGAATAACTATTTGT 58.161 39.130 4.51 0.00 45.00 2.83
1688 4179 6.987992 TGGAATAACTATTTGTTAGTAGGGCG 59.012 38.462 0.00 0.00 43.46 6.13
1692 4183 5.268118 ACTATTTGTTAGTAGGGCGGTAC 57.732 43.478 0.00 0.00 39.44 3.34
1717 4208 3.430218 CGAGAGTGTCAAGTCCACAATTC 59.570 47.826 0.00 0.00 35.24 2.17
1722 4213 4.576463 AGTGTCAAGTCCACAATTCACTTC 59.424 41.667 0.00 0.00 35.24 3.01
1729 4220 3.876914 GTCCACAATTCACTTCACACTGA 59.123 43.478 0.00 0.00 0.00 3.41
1749 4240 7.930325 ACACTGAATACTATTGATGATGAGGTG 59.070 37.037 0.00 0.00 0.00 4.00
1795 4289 3.258622 ACCAAGTGTCTCCTTAGTGCTAC 59.741 47.826 0.00 0.00 0.00 3.58
1815 4309 4.323569 ACTGAAGATGGACTACTCAGGA 57.676 45.455 0.00 0.00 37.63 3.86
1825 4319 5.087323 TGGACTACTCAGGAAAGATGAAGT 58.913 41.667 0.00 0.00 0.00 3.01
1858 4352 4.441913 GGAATAGCAACATGTCCAAATGGG 60.442 45.833 0.00 0.00 35.41 4.00
1869 4363 1.675310 CAAATGGGCTGACCTGCGA 60.675 57.895 0.00 0.00 41.11 5.10
1881 4375 2.565391 TGACCTGCGATCAGAACCTAAA 59.435 45.455 0.00 0.00 42.95 1.85
2000 7339 0.535102 AACAAGCAAGACTGGACGGG 60.535 55.000 0.00 0.00 0.00 5.28
2001 7340 1.672356 CAAGCAAGACTGGACGGGG 60.672 63.158 0.00 0.00 0.00 5.73
2003 7342 4.329545 GCAAGACTGGACGGGGCA 62.330 66.667 0.00 0.00 0.00 5.36
2053 7392 3.437049 GGAAGCACTAAGATGTGGTCAAC 59.563 47.826 0.00 0.00 46.25 3.18
2059 7398 4.028131 ACTAAGATGTGGTCAACGGGATA 58.972 43.478 0.00 0.00 0.00 2.59
2071 7410 5.589050 GGTCAACGGGATAGCTTCTTAAATT 59.411 40.000 0.00 0.00 0.00 1.82
2074 7413 5.500645 ACGGGATAGCTTCTTAAATTTGC 57.499 39.130 0.00 0.00 0.00 3.68
2078 7417 6.276091 GGGATAGCTTCTTAAATTTGCCAAG 58.724 40.000 0.00 0.00 0.00 3.61
2092 7431 1.607801 GCCAAGCATGAAGGTTCCCC 61.608 60.000 0.00 0.00 35.33 4.81
2095 7434 0.609131 AAGCATGAAGGTTCCCCACG 60.609 55.000 0.00 0.00 30.75 4.94
2099 7438 0.613777 ATGAAGGTTCCCCACGAGTC 59.386 55.000 0.00 0.00 0.00 3.36
2104 7443 1.671379 GTTCCCCACGAGTCCTTGC 60.671 63.158 0.00 0.00 0.00 4.01
2177 7516 2.398554 CCTGCACGGCGTATGCTTT 61.399 57.895 20.77 0.00 43.77 3.51
2186 7525 2.018717 GCGTATGCTTTCGCCAATAC 57.981 50.000 11.75 0.00 45.54 1.89
2198 7537 0.392461 GCCAATACGAGCACCAAGGA 60.392 55.000 0.00 0.00 0.00 3.36
2234 7573 6.569127 TGAAACTAGGTGCCTATTATGGAA 57.431 37.500 0.00 0.00 0.00 3.53
2253 7592 3.751175 GGAACGGAGATTTGATTGACACA 59.249 43.478 0.00 0.00 0.00 3.72
2275 7614 0.813821 GAAGCTCATTGGACAAGGGC 59.186 55.000 0.00 0.37 0.00 5.19
2345 7684 3.059884 TCTGTTTCTCTGCTTGCGTTAG 58.940 45.455 0.00 0.00 0.00 2.34
2402 7741 7.104974 AGCTCCAGTAATATCTCCCTTAGTA 57.895 40.000 0.00 0.00 0.00 1.82
2403 7742 7.714500 AGCTCCAGTAATATCTCCCTTAGTAT 58.286 38.462 0.00 0.00 0.00 2.12
2470 7809 6.059484 CGGGCAAATATTAGAGGGTAAAGAA 58.941 40.000 0.00 0.00 0.00 2.52
2474 7813 8.360390 GGCAAATATTAGAGGGTAAAGAATTGG 58.640 37.037 0.00 0.00 0.00 3.16
2503 7845 3.431055 TGGAACAGTTTGGCGCAG 58.569 55.556 10.83 0.00 0.00 5.18
2755 8101 0.319405 GAAACATTTGGCCAGCAGCT 59.681 50.000 5.11 0.00 43.05 4.24
2809 8165 8.089625 TCCAATCTCAGTCAATGTATAGGAAA 57.910 34.615 0.00 0.00 0.00 3.13
3071 8819 3.420893 GAATGACAACCACTCCATCCAA 58.579 45.455 0.00 0.00 0.00 3.53
3127 9072 8.594881 TTTTAAGTGTCAAGCAAAAGTTTTGA 57.405 26.923 28.36 7.97 0.00 2.69
3258 9208 9.515226 TGGCTTGTGAAACTAACTATTTAGAAT 57.485 29.630 6.84 0.00 37.49 2.40
3415 9365 2.684943 TGGGAGGTAGAACACAGTTCA 58.315 47.619 11.92 0.00 0.00 3.18
3416 9366 3.248024 TGGGAGGTAGAACACAGTTCAT 58.752 45.455 11.92 1.12 0.00 2.57
3417 9367 4.422057 TGGGAGGTAGAACACAGTTCATA 58.578 43.478 11.92 0.30 0.00 2.15
3418 9368 4.222145 TGGGAGGTAGAACACAGTTCATAC 59.778 45.833 11.92 10.30 0.00 2.39
3426 9377 7.873505 GGTAGAACACAGTTCATACTTTTCTCT 59.126 37.037 11.92 0.00 30.26 3.10
3916 9872 7.719633 AGCATAAAAACTTGGTTAGACTTCTCA 59.280 33.333 0.00 0.00 0.00 3.27
3918 9874 6.378710 AAAAACTTGGTTAGACTTCTCAGC 57.621 37.500 0.00 0.00 0.00 4.26
4074 10051 3.369242 TGTCATCCCTCAATTGATGCA 57.631 42.857 8.96 4.54 38.57 3.96
4281 10258 6.260700 TGGTATAGCAAGGATATTTGGTGT 57.739 37.500 1.19 0.00 39.01 4.16
4408 10394 1.278985 TGTGCTCCTAACTGGGACATG 59.721 52.381 0.00 0.00 38.20 3.21
4635 10621 9.866655 AAATATATGCATCTTTGAAGGGTTAGA 57.133 29.630 0.19 0.00 0.00 2.10
4807 10996 1.453155 GGCCACTCGTGTCATCAATT 58.547 50.000 0.00 0.00 0.00 2.32
4979 18235 8.671384 CTAGTACTTAGCAGTCTAATCTCTGT 57.329 38.462 0.00 0.00 34.54 3.41
4980 18236 9.767228 CTAGTACTTAGCAGTCTAATCTCTGTA 57.233 37.037 0.00 0.00 34.54 2.74
5126 18599 7.210174 TGGGAGAGATCTAAATGTTCGTATTG 58.790 38.462 0.00 0.00 0.00 1.90
5294 18773 2.367567 TCCCGGTCTGCCATACTATTTC 59.632 50.000 0.00 0.00 34.09 2.17
5350 18831 4.398044 TCCAAGCCGATTGTTTCTTAATCC 59.602 41.667 0.00 0.00 37.17 3.01
5358 18839 4.864704 TTGTTTCTTAATCCAGGCCAAC 57.135 40.909 5.01 0.00 0.00 3.77
5619 19656 6.699895 TGAAAGTGCGTAAAGTATACTGTG 57.300 37.500 6.06 0.00 0.00 3.66
5675 19717 8.100791 TGACCAGCAATAAGAAACTTATGTAGT 58.899 33.333 5.04 0.84 39.32 2.73
5676 19718 8.268850 ACCAGCAATAAGAAACTTATGTAGTG 57.731 34.615 5.04 2.09 37.12 2.74
5677 19719 7.883311 ACCAGCAATAAGAAACTTATGTAGTGT 59.117 33.333 5.04 0.01 37.12 3.55
5678 19720 9.378551 CCAGCAATAAGAAACTTATGTAGTGTA 57.621 33.333 5.04 0.00 37.12 2.90
5697 19739 3.515502 TGTAGGAGAATGTGAACCCTGAG 59.484 47.826 0.00 0.00 0.00 3.35
5700 19742 2.354259 GAGAATGTGAACCCTGAGCAG 58.646 52.381 0.00 0.00 0.00 4.24
5712 19754 3.118592 ACCCTGAGCAGCACTAAGATTAC 60.119 47.826 0.00 0.00 0.00 1.89
5713 19755 3.118629 CCCTGAGCAGCACTAAGATTACA 60.119 47.826 0.00 0.00 0.00 2.41
5717 19855 4.116238 GAGCAGCACTAAGATTACACTCC 58.884 47.826 0.00 0.00 0.00 3.85
5719 19857 3.798202 CAGCACTAAGATTACACTCCCC 58.202 50.000 0.00 0.00 0.00 4.81
5725 19863 5.897824 CACTAAGATTACACTCCCCCTCTTA 59.102 44.000 0.00 0.00 0.00 2.10
5787 19959 2.287644 GGCATTTTCACAAACACCTTGC 59.712 45.455 0.00 0.00 38.75 4.01
5819 19995 3.044305 GCTGCTCACGGTCACCAC 61.044 66.667 0.00 0.00 0.00 4.16
5823 19999 1.741770 GCTCACGGTCACCACCATC 60.742 63.158 0.00 0.00 44.02 3.51
5830 20008 2.040544 GTCACCACCATCCAAGGCG 61.041 63.158 0.00 0.00 0.00 5.52
5868 20046 2.204237 GCAGCAAAGTTCCAACCAAAG 58.796 47.619 0.00 0.00 0.00 2.77
5875 20053 2.525368 AGTTCCAACCAAAGGGCATAC 58.475 47.619 0.00 0.00 37.90 2.39
5893 20071 1.881252 CGGGTTCCGCTAATCCACG 60.881 63.158 0.00 0.00 41.17 4.94
5903 20081 1.269621 GCTAATCCACGTCGCATAGGT 60.270 52.381 0.00 0.00 0.00 3.08
5910 20088 2.665777 CGTCGCATAGGTTGTGAGG 58.334 57.895 0.00 0.00 45.22 3.86
5928 20106 1.706443 GGAACAACTAGGTCCGTTCG 58.294 55.000 5.24 0.00 46.05 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 7.864108 TCAAAATGTATGACTCGGAAATGAT 57.136 32.000 0.00 0.00 0.00 2.45
43 44 6.908870 TCTTCCATCAAAATGTATGACTCG 57.091 37.500 0.00 0.00 0.00 4.18
48 49 7.762615 AGTGCATTTCTTCCATCAAAATGTATG 59.237 33.333 0.00 0.00 40.71 2.39
49 50 7.762615 CAGTGCATTTCTTCCATCAAAATGTAT 59.237 33.333 0.00 0.00 40.71 2.29
53 54 5.929992 CACAGTGCATTTCTTCCATCAAAAT 59.070 36.000 0.00 0.00 0.00 1.82
122 124 7.094805 CCTGAAAAGATCGTATCACCTGAAAAA 60.095 37.037 0.00 0.00 0.00 1.94
137 139 7.065204 GTGTCTCCTCATTTACCTGAAAAGATC 59.935 40.741 0.00 0.00 0.00 2.75
138 140 6.881602 GTGTCTCCTCATTTACCTGAAAAGAT 59.118 38.462 0.00 0.00 0.00 2.40
148 150 6.369065 CACCTGTTTAGTGTCTCCTCATTTAC 59.631 42.308 0.00 0.00 0.00 2.01
176 178 3.124297 GTGCAACTGTCTGAATAGAGTGC 59.876 47.826 0.00 12.27 32.48 4.40
178 180 4.607293 TGTGCAACTGTCTGAATAGAGT 57.393 40.909 0.00 0.00 38.04 3.24
193 195 3.865011 TTTTTCTGCTGTCTTGTGCAA 57.135 38.095 0.00 0.00 38.81 4.08
218 220 2.037121 GCCCCTAGCTTTGCAAGAAAAA 59.963 45.455 0.00 0.00 38.99 1.94
253 255 0.870393 CACATTTGAGCGTGCAGTCT 59.130 50.000 0.00 0.00 0.00 3.24
271 273 6.071672 TGCAATTATAAAGTTTGCCAGCTACA 60.072 34.615 16.02 0.00 43.91 2.74
287 289 8.970020 ACATTCATTCTGGTCTTTGCAATTATA 58.030 29.630 0.00 0.00 0.00 0.98
288 290 7.762615 CACATTCATTCTGGTCTTTGCAATTAT 59.237 33.333 0.00 0.00 0.00 1.28
289 291 7.092079 CACATTCATTCTGGTCTTTGCAATTA 58.908 34.615 0.00 0.00 0.00 1.40
290 292 5.929992 CACATTCATTCTGGTCTTTGCAATT 59.070 36.000 0.00 0.00 0.00 2.32
292 294 4.796946 GCACATTCATTCTGGTCTTTGCAA 60.797 41.667 0.00 0.00 0.00 4.08
294 296 3.248266 GCACATTCATTCTGGTCTTTGC 58.752 45.455 0.00 0.00 0.00 3.68
295 297 3.189080 TCGCACATTCATTCTGGTCTTTG 59.811 43.478 0.00 0.00 0.00 2.77
296 298 3.411446 TCGCACATTCATTCTGGTCTTT 58.589 40.909 0.00 0.00 0.00 2.52
297 299 3.005554 CTCGCACATTCATTCTGGTCTT 58.994 45.455 0.00 0.00 0.00 3.01
298 300 2.027745 ACTCGCACATTCATTCTGGTCT 60.028 45.455 0.00 0.00 0.00 3.85
299 301 2.350522 ACTCGCACATTCATTCTGGTC 58.649 47.619 0.00 0.00 0.00 4.02
300 302 2.479566 ACTCGCACATTCATTCTGGT 57.520 45.000 0.00 0.00 0.00 4.00
301 303 2.743664 TGAACTCGCACATTCATTCTGG 59.256 45.455 0.00 0.00 29.89 3.86
302 304 3.425359 GGTGAACTCGCACATTCATTCTG 60.425 47.826 0.00 0.00 40.52 3.02
303 305 2.744202 GGTGAACTCGCACATTCATTCT 59.256 45.455 0.00 0.00 40.52 2.40
304 306 2.159517 GGGTGAACTCGCACATTCATTC 60.160 50.000 0.00 0.00 40.52 2.67
305 307 1.812571 GGGTGAACTCGCACATTCATT 59.187 47.619 0.00 0.00 40.52 2.57
306 308 1.271325 TGGGTGAACTCGCACATTCAT 60.271 47.619 0.00 0.00 40.52 2.57
307 309 0.107643 TGGGTGAACTCGCACATTCA 59.892 50.000 0.00 0.00 40.52 2.57
308 310 0.517316 GTGGGTGAACTCGCACATTC 59.483 55.000 15.39 0.00 45.98 2.67
309 311 2.629002 GTGGGTGAACTCGCACATT 58.371 52.632 15.39 0.00 45.98 2.71
310 312 4.379174 GTGGGTGAACTCGCACAT 57.621 55.556 15.39 0.00 45.98 3.21
312 314 0.946221 CTCTGTGGGTGAACTCGCAC 60.946 60.000 14.06 14.06 46.57 5.34
313 315 1.367471 CTCTGTGGGTGAACTCGCA 59.633 57.895 0.00 0.00 0.00 5.10
314 316 0.249911 AACTCTGTGGGTGAACTCGC 60.250 55.000 0.00 0.00 0.00 5.03
315 317 1.867233 CAAACTCTGTGGGTGAACTCG 59.133 52.381 0.00 0.00 0.00 4.18
316 318 2.872858 GTCAAACTCTGTGGGTGAACTC 59.127 50.000 0.00 0.00 0.00 3.01
317 319 2.421529 GGTCAAACTCTGTGGGTGAACT 60.422 50.000 0.00 0.00 0.00 3.01
318 320 1.947456 GGTCAAACTCTGTGGGTGAAC 59.053 52.381 0.00 0.00 0.00 3.18
319 321 1.843851 AGGTCAAACTCTGTGGGTGAA 59.156 47.619 0.00 0.00 0.00 3.18
320 322 1.507140 AGGTCAAACTCTGTGGGTGA 58.493 50.000 0.00 0.00 0.00 4.02
321 323 3.139077 GTTAGGTCAAACTCTGTGGGTG 58.861 50.000 0.00 0.00 0.00 4.61
322 324 2.775384 TGTTAGGTCAAACTCTGTGGGT 59.225 45.455 0.00 0.00 0.00 4.51
323 325 3.485463 TGTTAGGTCAAACTCTGTGGG 57.515 47.619 0.00 0.00 0.00 4.61
324 326 6.391227 AAAATGTTAGGTCAAACTCTGTGG 57.609 37.500 0.00 0.00 0.00 4.17
340 372 6.238076 CCTTGCGCTTGTTTCTTAAAAATGTT 60.238 34.615 9.73 0.00 0.00 2.71
355 393 1.286880 CAAAGGGACCTTGCGCTTG 59.713 57.895 9.73 0.33 40.40 4.01
356 394 0.109723 TACAAAGGGACCTTGCGCTT 59.890 50.000 9.73 0.00 42.04 4.68
357 395 0.605589 GTACAAAGGGACCTTGCGCT 60.606 55.000 9.73 0.00 36.26 5.92
358 396 0.887387 TGTACAAAGGGACCTTGCGC 60.887 55.000 4.03 0.00 36.26 6.09
359 397 1.737793 GATGTACAAAGGGACCTTGCG 59.262 52.381 4.03 2.01 36.26 4.85
360 398 2.092323 GGATGTACAAAGGGACCTTGC 58.908 52.381 4.03 0.00 36.26 4.01
416 454 8.764287 CATTAAGAAGGACACAATTTGTTTTCC 58.236 33.333 15.12 15.12 39.17 3.13
422 460 6.805271 CAGCTCATTAAGAAGGACACAATTTG 59.195 38.462 0.00 0.00 0.00 2.32
500 541 0.906775 CCCTTTGGGCTTGCATCATT 59.093 50.000 0.00 0.00 35.35 2.57
501 542 0.041535 TCCCTTTGGGCTTGCATCAT 59.958 50.000 0.00 0.00 43.94 2.45
511 552 0.704076 TCCATGGTCTTCCCTTTGGG 59.296 55.000 12.58 0.00 46.11 4.12
516 557 2.929043 AGGAATTTCCATGGTCTTCCCT 59.071 45.455 25.68 18.90 39.61 4.20
532 573 3.583054 CCATCAGTGGTGCAGGAAT 57.417 52.632 0.00 0.00 40.83 3.01
550 591 5.006358 CGTATAGGTTGCAGGTAAATGTGAC 59.994 44.000 0.00 0.00 0.00 3.67
567 609 4.680110 CGAACCTATCTTTGTGCGTATAGG 59.320 45.833 0.00 0.00 44.37 2.57
570 612 4.119442 ACGAACCTATCTTTGTGCGTAT 57.881 40.909 0.00 0.00 44.62 3.06
571 613 3.581024 ACGAACCTATCTTTGTGCGTA 57.419 42.857 0.00 0.00 44.62 4.42
572 614 2.450609 ACGAACCTATCTTTGTGCGT 57.549 45.000 0.00 0.00 41.78 5.24
573 615 3.806316 AAACGAACCTATCTTTGTGCG 57.194 42.857 0.00 0.00 39.46 5.34
574 616 7.917720 TTTTTAAACGAACCTATCTTTGTGC 57.082 32.000 0.00 0.00 0.00 4.57
604 657 8.259049 TGTTCCGGTTTTAGTATGTTATCTTG 57.741 34.615 0.00 0.00 0.00 3.02
605 658 8.851541 TTGTTCCGGTTTTAGTATGTTATCTT 57.148 30.769 0.00 0.00 0.00 2.40
606 659 7.551617 CCTTGTTCCGGTTTTAGTATGTTATCT 59.448 37.037 0.00 0.00 0.00 1.98
607 660 7.201670 CCCTTGTTCCGGTTTTAGTATGTTATC 60.202 40.741 0.00 0.00 0.00 1.75
609 662 5.939296 CCCTTGTTCCGGTTTTAGTATGTTA 59.061 40.000 0.00 0.00 0.00 2.41
610 663 4.763279 CCCTTGTTCCGGTTTTAGTATGTT 59.237 41.667 0.00 0.00 0.00 2.71
617 673 2.694109 CAAACCCCTTGTTCCGGTTTTA 59.306 45.455 0.00 0.00 45.41 1.52
657 725 5.182950 TGCTGGTACAATGTTAGTTGGATTG 59.817 40.000 0.00 0.00 38.70 2.67
669 737 1.068333 GTGCTGGTTGCTGGTACAATG 60.068 52.381 0.00 0.00 43.37 2.82
682 750 4.734398 TTTCTTGTTTGAATGTGCTGGT 57.266 36.364 0.00 0.00 0.00 4.00
728 796 9.049523 TCTCAGCAAATAGAATAGCATTTACTG 57.950 33.333 0.00 0.00 37.07 2.74
732 800 8.411683 CCTTTCTCAGCAAATAGAATAGCATTT 58.588 33.333 0.00 0.00 32.05 2.32
735 803 5.297776 GCCTTTCTCAGCAAATAGAATAGCA 59.702 40.000 0.00 0.00 33.57 3.49
855 926 1.203087 TCCGACAGGAAGTTACTGGGA 60.203 52.381 19.43 13.64 45.12 4.37
872 943 3.885724 ATTATTTGTGGCCCTTTTCCG 57.114 42.857 0.00 0.00 0.00 4.30
881 952 6.030228 GTCAGTCAAGCTTATTATTTGTGGC 58.970 40.000 0.00 0.00 0.00 5.01
892 964 2.232452 GAGGCAGAGTCAGTCAAGCTTA 59.768 50.000 0.00 0.00 0.00 3.09
894 966 0.607620 GAGGCAGAGTCAGTCAAGCT 59.392 55.000 0.00 0.00 0.00 3.74
945 1017 1.668047 GCAAAGCAGTGGATGAGTTGC 60.668 52.381 0.00 0.00 40.65 4.17
1005 3496 4.093011 TGATTTTGTGTATGGGAAAGGGG 58.907 43.478 0.00 0.00 0.00 4.79
1009 3500 5.105392 GGCAGATGATTTTGTGTATGGGAAA 60.105 40.000 0.00 0.00 0.00 3.13
1022 3513 4.101430 ACCAACAAACAAGGCAGATGATTT 59.899 37.500 0.00 0.00 0.00 2.17
1146 3637 1.147153 GGAGAAGAATCCCAGGGCG 59.853 63.158 0.00 0.00 32.79 6.13
1200 3691 8.333235 TCTTTGGGTATGTTCTTGTACCATATT 58.667 33.333 4.20 0.00 41.71 1.28
1222 3713 3.678529 GCAACCCACACAACATTGTCTTT 60.679 43.478 0.00 0.00 39.91 2.52
1230 3721 0.749649 GATTGGCAACCCACACAACA 59.250 50.000 0.00 0.00 41.97 3.33
1248 3739 3.717899 GCAATCGGCATAGCACGA 58.282 55.556 0.00 5.36 43.97 4.35
1263 3754 4.284490 AGTGTTACAGAAGAAGGATCAGCA 59.716 41.667 0.00 0.00 0.00 4.41
1280 3771 1.944024 CGTTTGTGAAGGCCAGTGTTA 59.056 47.619 5.01 0.00 0.00 2.41
1287 3778 0.608035 TGGATCCGTTTGTGAAGGCC 60.608 55.000 7.39 0.00 0.00 5.19
1311 3802 0.962356 CATTGGTGTCTGACAGGGCC 60.962 60.000 11.41 9.73 0.00 5.80
1315 3806 0.250858 TGGCCATTGGTGTCTGACAG 60.251 55.000 11.41 0.00 0.00 3.51
1351 3842 2.715532 TTCCCTGCGGCGCTGATATC 62.716 60.000 35.29 1.86 0.00 1.63
1353 3844 2.324014 AATTCCCTGCGGCGCTGATA 62.324 55.000 35.29 21.45 0.00 2.15
1362 3853 0.933097 CTGACGATGAATTCCCTGCG 59.067 55.000 2.27 4.11 0.00 5.18
1404 3895 9.492730 AGGATAAAATTCCCATTGTTATCAAGT 57.507 29.630 0.00 0.00 36.35 3.16
1443 3934 2.288640 GCTTTGCCATAAGATGATGCCC 60.289 50.000 0.00 0.00 0.00 5.36
1473 3964 0.959372 GAAGGAGAGTGTCGGTCGGA 60.959 60.000 0.00 0.00 0.00 4.55
1529 4020 0.803740 AGAGACGAGCCGTTGTAGTC 59.196 55.000 1.80 0.00 41.37 2.59
1543 4034 2.551071 CCTGGGTGTTTCTCCAAGAGAC 60.551 54.545 0.00 0.00 38.51 3.36
1597 4088 1.081892 CGCAGAAACTCATCAGGGTG 58.918 55.000 0.00 0.00 0.00 4.61
1616 4107 2.741759 ACCATTCCATGAAAAACGCC 57.258 45.000 0.00 0.00 0.00 5.68
1648 4139 4.680237 CCACGCTGGACTTCGCCA 62.680 66.667 0.00 0.00 40.96 5.69
1661 4152 7.042254 GCCCTACTAACAAATAGTTATTCCACG 60.042 40.741 0.00 0.00 42.31 4.94
1662 4153 7.042254 CGCCCTACTAACAAATAGTTATTCCAC 60.042 40.741 0.00 0.00 42.31 4.02
1678 4169 0.107897 TCGACGTACCGCCCTACTAA 60.108 55.000 0.00 0.00 0.00 2.24
1688 4179 1.534595 ACTTGACACTCTCGACGTACC 59.465 52.381 0.00 0.00 0.00 3.34
1692 4183 0.591659 TGGACTTGACACTCTCGACG 59.408 55.000 0.00 0.00 0.00 5.12
1702 4193 4.335315 TGTGAAGTGAATTGTGGACTTGAC 59.665 41.667 0.00 0.00 35.25 3.18
1717 4208 8.707938 TCATCAATAGTATTCAGTGTGAAGTG 57.292 34.615 0.00 0.00 40.05 3.16
1722 4213 7.930325 ACCTCATCATCAATAGTATTCAGTGTG 59.070 37.037 0.00 0.00 0.00 3.82
1749 4240 5.801380 TCTGGTAGTCCAAAGGAAATGTAC 58.199 41.667 0.00 0.00 43.81 2.90
1772 4263 2.706190 AGCACTAAGGAGACACTTGGTT 59.294 45.455 0.00 0.00 39.71 3.67
1795 4289 5.420421 TCTTTCCTGAGTAGTCCATCTTCAG 59.580 44.000 0.00 0.00 33.29 3.02
1815 4309 5.223449 TCCAGGTTCGTAACTTCATCTTT 57.777 39.130 0.00 0.00 0.00 2.52
1825 4319 4.274602 TGTTGCTATTCCAGGTTCGTAA 57.725 40.909 0.00 0.00 0.00 3.18
1858 4352 1.086634 GGTTCTGATCGCAGGTCAGC 61.087 60.000 12.23 2.36 42.17 4.26
1869 4363 4.922206 TGCATTCCTGTTTAGGTTCTGAT 58.078 39.130 0.00 0.00 44.88 2.90
1881 4375 4.420522 ACCAAATTTGTTGCATTCCTGT 57.579 36.364 16.73 1.01 0.00 4.00
1986 7325 4.329545 TGCCCCGTCCAGTCTTGC 62.330 66.667 0.00 0.00 0.00 4.01
2000 7339 2.644992 CCTGCGAAAACCTGTGCC 59.355 61.111 0.00 0.00 0.00 5.01
2001 7340 1.244019 ATCCCTGCGAAAACCTGTGC 61.244 55.000 0.00 0.00 0.00 4.57
2003 7342 1.244019 GCATCCCTGCGAAAACCTGT 61.244 55.000 0.00 0.00 38.92 4.00
2053 7392 4.338118 TGGCAAATTTAAGAAGCTATCCCG 59.662 41.667 0.00 0.00 0.00 5.14
2059 7398 4.605640 TGCTTGGCAAATTTAAGAAGCT 57.394 36.364 19.76 0.00 37.34 3.74
2071 7410 0.968405 GGAACCTTCATGCTTGGCAA 59.032 50.000 0.00 0.00 43.62 4.52
2092 7431 1.511850 TTGACATGCAAGGACTCGTG 58.488 50.000 0.00 0.00 31.55 4.35
2117 7456 6.762333 TCTGCTATGCATTCATCTAAGCTTA 58.238 36.000 3.54 5.94 38.13 3.09
2177 7516 0.739462 CTTGGTGCTCGTATTGGCGA 60.739 55.000 0.00 0.00 39.22 5.54
2186 7525 2.810274 CCATTGATATCCTTGGTGCTCG 59.190 50.000 11.24 0.00 0.00 5.03
2198 7537 6.546484 CACCTAGTTTCATCCCCATTGATAT 58.454 40.000 0.00 0.00 0.00 1.63
2234 7573 4.021104 TCTCTGTGTCAATCAAATCTCCGT 60.021 41.667 0.00 0.00 0.00 4.69
2253 7592 2.026449 CCCTTGTCCAATGAGCTTCTCT 60.026 50.000 0.00 0.00 0.00 3.10
2275 7614 6.430000 CCATTAACCCGGATATAGAGGTTTTG 59.570 42.308 0.73 6.86 42.50 2.44
2323 7662 1.506493 ACGCAAGCAGAGAAACAGAG 58.494 50.000 0.00 0.00 45.62 3.35
2365 7704 0.920763 TGGAGCTCCATTGGACCCAT 60.921 55.000 32.00 0.00 42.01 4.00
2374 7713 4.100373 GGGAGATATTACTGGAGCTCCAT 58.900 47.826 35.11 25.15 46.46 3.41
2407 7746 8.967664 AAACCTTACTTGTACTGACATTGTAA 57.032 30.769 0.00 0.00 34.86 2.41
2474 7813 4.989279 AACTGTTCCATCATGGCATTAC 57.011 40.909 0.00 0.00 37.47 1.89
2539 7881 8.500753 TGGATAAGCTGTTATGTTTTCGTATT 57.499 30.769 0.00 0.00 0.00 1.89
2554 7897 2.954318 CACCCTCCAATTGGATAAGCTG 59.046 50.000 27.20 14.16 44.46 4.24
2588 7931 7.649533 TCATATTTTCATTCTGCATCCAGTT 57.350 32.000 0.00 0.00 40.09 3.16
2649 7994 9.874215 GGAAGTGTTTTACATACTAACAACTTC 57.126 33.333 1.28 1.28 38.07 3.01
2809 8165 2.169352 CGCCCATATGAGCTAGGCTTAT 59.831 50.000 15.27 2.63 39.88 1.73
2811 8167 0.322975 CGCCCATATGAGCTAGGCTT 59.677 55.000 15.27 0.00 39.88 4.35
3118 9062 8.611757 GCTAACATTTTGGACATTCAAAACTTT 58.388 29.630 0.07 0.67 45.58 2.66
3127 9072 6.374333 ACGAGTATGCTAACATTTTGGACATT 59.626 34.615 0.00 0.00 37.74 2.71
3415 9365 7.918076 TGAGGGAAATACACAGAGAAAAGTAT 58.082 34.615 0.00 0.00 0.00 2.12
3416 9366 7.311092 TGAGGGAAATACACAGAGAAAAGTA 57.689 36.000 0.00 0.00 0.00 2.24
3417 9367 6.187727 TGAGGGAAATACACAGAGAAAAGT 57.812 37.500 0.00 0.00 0.00 2.66
3418 9368 6.348868 GCTTGAGGGAAATACACAGAGAAAAG 60.349 42.308 0.00 0.00 0.00 2.27
3426 9377 4.299586 TCATGCTTGAGGGAAATACACA 57.700 40.909 0.00 0.00 0.00 3.72
3626 9580 7.518731 TGTTGCAAGTACAATTTCTTTGAAC 57.481 32.000 0.00 0.00 38.76 3.18
3725 9679 8.609176 GGAAATACAGTTATGTTGCTCGATAAA 58.391 33.333 0.00 0.00 41.01 1.40
3916 9872 1.210538 TCTCCATGGATGCAGAAGCT 58.789 50.000 16.63 0.00 42.74 3.74
3918 9874 3.071167 TCTCATCTCCATGGATGCAGAAG 59.929 47.826 16.63 6.26 41.83 2.85
4281 10258 3.623060 GGTATTTTCTTGCTGCTGATCGA 59.377 43.478 0.00 0.00 0.00 3.59
4408 10394 2.031157 ACATGTAACCGCTGTTTGAAGC 60.031 45.455 0.00 0.00 39.94 3.86
4634 10620 5.374071 TGCCTGCATCCATCATATCATATC 58.626 41.667 0.00 0.00 0.00 1.63
4635 10621 5.382664 TGCCTGCATCCATCATATCATAT 57.617 39.130 0.00 0.00 0.00 1.78
4636 10622 4.847990 TGCCTGCATCCATCATATCATA 57.152 40.909 0.00 0.00 0.00 2.15
4637 10623 3.732048 TGCCTGCATCCATCATATCAT 57.268 42.857 0.00 0.00 0.00 2.45
4638 10624 3.352648 CATGCCTGCATCCATCATATCA 58.647 45.455 0.70 0.00 33.90 2.15
4807 10996 2.978978 TCCATTCTCCAGAAAGGACACA 59.021 45.455 8.86 0.00 44.20 3.72
4968 18224 4.462834 CCCACGGCATATACAGAGATTAGA 59.537 45.833 0.00 0.00 0.00 2.10
4969 18225 4.220821 ACCCACGGCATATACAGAGATTAG 59.779 45.833 0.00 0.00 0.00 1.73
4970 18226 4.157246 ACCCACGGCATATACAGAGATTA 58.843 43.478 0.00 0.00 0.00 1.75
4971 18227 2.972713 ACCCACGGCATATACAGAGATT 59.027 45.455 0.00 0.00 0.00 2.40
4972 18228 2.609747 ACCCACGGCATATACAGAGAT 58.390 47.619 0.00 0.00 0.00 2.75
4973 18229 2.082140 ACCCACGGCATATACAGAGA 57.918 50.000 0.00 0.00 0.00 3.10
4974 18230 2.891580 AGTACCCACGGCATATACAGAG 59.108 50.000 0.00 0.00 0.00 3.35
4975 18231 2.953453 AGTACCCACGGCATATACAGA 58.047 47.619 0.00 0.00 0.00 3.41
4976 18232 3.746045 AAGTACCCACGGCATATACAG 57.254 47.619 0.00 0.00 0.00 2.74
4977 18233 4.490899 AAAAGTACCCACGGCATATACA 57.509 40.909 0.00 0.00 0.00 2.29
4978 18234 5.816777 TGTAAAAAGTACCCACGGCATATAC 59.183 40.000 0.00 0.00 0.00 1.47
4979 18235 5.987098 TGTAAAAAGTACCCACGGCATATA 58.013 37.500 0.00 0.00 0.00 0.86
4980 18236 4.846040 TGTAAAAAGTACCCACGGCATAT 58.154 39.130 0.00 0.00 0.00 1.78
4981 18237 4.283363 TGTAAAAAGTACCCACGGCATA 57.717 40.909 0.00 0.00 0.00 3.14
4982 18238 3.143211 TGTAAAAAGTACCCACGGCAT 57.857 42.857 0.00 0.00 0.00 4.40
5126 18599 3.771577 TTCTTGGTGAGAAGGGTCTTC 57.228 47.619 0.00 0.00 39.44 2.87
5358 18839 7.531280 ACATTCTACTCAATCGAAATGACAG 57.469 36.000 8.71 5.92 0.00 3.51
5387 19395 8.537223 CAGACATATTGCATGCAAAATTAAGAC 58.463 33.333 34.84 19.37 39.55 3.01
5619 19656 9.486497 GGCACTAGTTTAGTTAAGGGTTATATC 57.514 37.037 0.00 0.00 36.76 1.63
5675 19717 3.515502 CTCAGGGTTCACATTCTCCTACA 59.484 47.826 0.00 0.00 0.00 2.74
5676 19718 3.680196 GCTCAGGGTTCACATTCTCCTAC 60.680 52.174 0.00 0.00 0.00 3.18
5677 19719 2.501723 GCTCAGGGTTCACATTCTCCTA 59.498 50.000 0.00 0.00 0.00 2.94
5678 19720 1.280421 GCTCAGGGTTCACATTCTCCT 59.720 52.381 0.00 0.00 0.00 3.69
5679 19721 1.003580 TGCTCAGGGTTCACATTCTCC 59.996 52.381 0.00 0.00 0.00 3.71
5697 19739 3.198872 GGGAGTGTAATCTTAGTGCTGC 58.801 50.000 0.00 0.00 0.00 5.25
5700 19742 2.772515 AGGGGGAGTGTAATCTTAGTGC 59.227 50.000 0.00 0.00 0.00 4.40
5712 19754 3.372025 CCCTTGAAATAAGAGGGGGAGTG 60.372 52.174 0.00 0.00 45.27 3.51
5713 19755 2.853077 CCCTTGAAATAAGAGGGGGAGT 59.147 50.000 0.00 0.00 45.27 3.85
5719 19857 5.136105 CCTCCAATCCCTTGAAATAAGAGG 58.864 45.833 0.00 0.00 34.04 3.69
5725 19863 3.879321 GCTGACCTCCAATCCCTTGAAAT 60.879 47.826 0.00 0.00 34.04 2.17
5739 19877 0.036022 AGAAACCAGCTGCTGACCTC 59.964 55.000 30.10 20.44 32.44 3.85
5819 19995 4.161295 TCGAGGCGCCTTGGATGG 62.161 66.667 37.57 19.77 0.00 3.51
5845 20023 1.007387 GTTGGAACTTTGCTGCGGG 60.007 57.895 0.00 0.00 0.00 6.13
5846 20024 1.007387 GGTTGGAACTTTGCTGCGG 60.007 57.895 0.00 0.00 0.00 5.69
5849 20027 2.483538 CCCTTTGGTTGGAACTTTGCTG 60.484 50.000 0.00 0.00 0.00 4.41
5893 20071 2.000447 GTTCCTCACAACCTATGCGAC 59.000 52.381 0.00 0.00 0.00 5.19
5903 20081 2.036733 CGGACCTAGTTGTTCCTCACAA 59.963 50.000 0.00 0.00 43.55 3.33
5910 20088 1.066136 GCGAACGGACCTAGTTGTTC 58.934 55.000 0.00 0.00 37.84 3.18
5924 20102 0.442310 TGCGTGCTCTAATTGCGAAC 59.558 50.000 0.00 0.00 0.00 3.95
5928 20106 0.375106 GAGGTGCGTGCTCTAATTGC 59.625 55.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.