Multiple sequence alignment - TraesCS3A01G381100

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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 TraesCS3A01G381100 chr3A 100.000 5963 0 0 1 5963 631574737 631580699 0.000000e+00 11012.0
1 TraesCS3A01G381100 chr3D 94.671 3265 110 28 292 3504 487806616 487809868 0.000000e+00 5007.0
2 TraesCS3A01G381100 chr3D 93.463 1438 56 23 3867 5278 487810145 487811570 0.000000e+00 2100.0
3 TraesCS3A01G381100 chr3D 90.179 224 21 1 5741 5963 487812024 487812247 2.100000e-74 291.0
4 TraesCS3A01G381100 chr3D 89.326 178 17 1 5286 5461 487811654 487811831 7.780000e-54 222.0
5 TraesCS3A01G381100 chr3D 89.655 87 4 3 189 275 487806550 487806631 8.170000e-19 106.0
6 TraesCS3A01G381100 chr3D 86.667 90 7 2 3504 3592 487809902 487809987 1.770000e-15 95.3
7 TraesCS3A01G381100 chr3B 91.912 3425 115 55 1 3324 650796263 650799626 0.000000e+00 4641.0
8 TraesCS3A01G381100 chr3B 94.857 1711 59 10 3589 5282 650800075 650801773 0.000000e+00 2645.0
9 TraesCS3A01G381100 chr3B 89.560 182 13 5 3323 3504 650799686 650799861 6.010000e-55 226.0
10 TraesCS3A01G381100 chr4A 84.516 620 61 18 5355 5958 621443347 621443947 1.110000e-161 580.0
11 TraesCS3A01G381100 chr4A 84.160 625 62 20 5355 5961 618041020 618040415 6.700000e-159 571.0
12 TraesCS3A01G381100 chr4A 87.500 112 12 2 5176 5287 618041294 618041185 1.740000e-25 128.0
13 TraesCS3A01G381100 chr4A 87.500 112 12 2 5176 5287 621443073 621443182 1.740000e-25 128.0
14 TraesCS3A01G381100 chr4A 92.593 81 6 0 1259 1339 544198796 544198876 3.780000e-22 117.0
15 TraesCS3A01G381100 chr2B 85.780 436 26 12 5055 5477 460323032 460323444 4.270000e-116 429.0
16 TraesCS3A01G381100 chr2B 88.608 79 9 0 1261 1339 801162567 801162645 4.920000e-16 97.1
17 TraesCS3A01G381100 chrUn 87.465 359 32 8 5355 5701 472852046 472852403 9.310000e-108 401.0
18 TraesCS3A01G381100 chrUn 89.062 192 17 2 5774 5961 345814814 345814623 9.990000e-58 235.0
19 TraesCS3A01G381100 chr1B 90.099 101 10 0 2284 2384 489251925 489251825 1.350000e-26 132.0
20 TraesCS3A01G381100 chr1A 90.099 101 10 0 2284 2384 464839370 464839270 1.350000e-26 132.0
21 TraesCS3A01G381100 chr1D 89.109 101 11 0 2284 2384 365730150 365730050 6.270000e-25 126.0
22 TraesCS3A01G381100 chr4B 92.683 82 6 0 1258 1339 76818905 76818824 1.050000e-22 119.0
23 TraesCS3A01G381100 chr4D 91.358 81 7 0 1259 1339 52472717 52472637 1.760000e-20 111.0
24 TraesCS3A01G381100 chr5A 85.714 98 12 2 1252 1349 78157969 78158064 1.060000e-17 102.0
25 TraesCS3A01G381100 chr5B 88.889 81 9 0 1259 1339 90507723 90507803 3.800000e-17 100.0
26 TraesCS3A01G381100 chr2D 88.608 79 9 0 1261 1339 640298895 640298817 4.920000e-16 97.1


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 TraesCS3A01G381100 chr3A 631574737 631580699 5962 False 11012.00 11012 100.000000 1 5963 1 chr3A.!!$F1 5962
1 TraesCS3A01G381100 chr3D 487806550 487812247 5697 False 1303.55 5007 90.660167 189 5963 6 chr3D.!!$F1 5774
2 TraesCS3A01G381100 chr3B 650796263 650801773 5510 False 2504.00 4641 92.109667 1 5282 3 chr3B.!!$F1 5281
3 TraesCS3A01G381100 chr4A 621443073 621443947 874 False 354.00 580 86.008000 5176 5958 2 chr4A.!!$F2 782
4 TraesCS3A01G381100 chr4A 618040415 618041294 879 True 349.50 571 85.830000 5176 5961 2 chr4A.!!$R1 785

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
160 164 0.251916 TCCATGATCCAACGACCCAC 59.748 55.000 0.0 0.00 0.00 4.61 F
498 563 0.373716 GTAGCGAGCCATTTTGGACG 59.626 55.000 0.0 3.78 40.96 4.79 F
1235 1354 1.621814 CGGCGGGAGGAGGATTAATTA 59.378 52.381 0.0 0.00 0.00 1.40 F
2124 2264 0.323178 ATCAGCAGCCCACTTTCCTG 60.323 55.000 0.0 0.00 0.00 3.86 F
2127 2267 0.407139 AGCAGCCCACTTTCCTGAAT 59.593 50.000 0.0 0.00 0.00 2.57 F
2397 2537 0.991355 AGGTTGTCCCTGAACCCACA 60.991 55.000 0.0 0.00 44.08 4.17 F
3699 4057 0.036388 TTGGTGCTTCCCTGATCGAC 60.036 55.000 0.0 0.00 34.77 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 2233 0.323178 CAGGAAAGTGGGCTGCTGAT 60.323 55.000 0.00 0.0 33.16 2.90 R
2108 2236 0.407139 ATTCAGGAAAGTGGGCTGCT 59.593 50.000 0.00 0.0 0.00 4.24 R
2767 2934 0.612732 CCAATCAGGAAGGCTTGGCA 60.613 55.000 3.46 0.0 41.22 4.92 R
3379 3608 0.460459 GGCCGAGCTGGACTTACTTC 60.460 60.000 0.00 0.0 45.46 3.01 R
3405 3634 1.150827 GGCTGCAGAAAATTTGCCAC 58.849 50.000 20.43 0.0 40.81 5.01 R
4377 4779 1.922447 AGTGGCCATAATGAGGGTCAA 59.078 47.619 9.72 0.0 44.13 3.18 R
5697 6281 0.038744 ATTCTGTGAAGGCCCCTGTG 59.961 55.000 0.00 0.0 0.00 3.66 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
28 29 5.165911 CATGTAATGCCTCACTTGATGTC 57.834 43.478 0.00 0.00 37.62 3.06
32 33 4.978083 AATGCCTCACTTGATGTCATTC 57.022 40.909 0.00 0.00 0.00 2.67
44 45 8.446273 CACTTGATGTCATTCTTTAGTGGTTAG 58.554 37.037 0.00 0.00 0.00 2.34
48 49 7.665559 TGATGTCATTCTTTAGTGGTTAGCTTT 59.334 33.333 0.00 0.00 0.00 3.51
54 55 7.492352 TTCTTTAGTGGTTAGCTTTGAAGTC 57.508 36.000 0.00 0.00 0.00 3.01
64 65 3.481453 AGCTTTGAAGTCTTTGGACCTC 58.519 45.455 0.00 0.00 43.05 3.85
69 70 0.472471 AAGTCTTTGGACCTCGGCAA 59.528 50.000 0.00 0.00 43.05 4.52
76 77 2.570415 TGGACCTCGGCAAAATTACA 57.430 45.000 0.00 0.00 0.00 2.41
77 78 2.156098 TGGACCTCGGCAAAATTACAC 58.844 47.619 0.00 0.00 0.00 2.90
78 79 2.156098 GGACCTCGGCAAAATTACACA 58.844 47.619 0.00 0.00 0.00 3.72
79 80 2.554893 GGACCTCGGCAAAATTACACAA 59.445 45.455 0.00 0.00 0.00 3.33
80 81 3.004944 GGACCTCGGCAAAATTACACAAA 59.995 43.478 0.00 0.00 0.00 2.83
81 82 4.500035 GGACCTCGGCAAAATTACACAAAA 60.500 41.667 0.00 0.00 0.00 2.44
82 83 4.364860 ACCTCGGCAAAATTACACAAAAC 58.635 39.130 0.00 0.00 0.00 2.43
83 84 4.098807 ACCTCGGCAAAATTACACAAAACT 59.901 37.500 0.00 0.00 0.00 2.66
84 85 5.299782 ACCTCGGCAAAATTACACAAAACTA 59.700 36.000 0.00 0.00 0.00 2.24
85 86 5.627780 CCTCGGCAAAATTACACAAAACTAC 59.372 40.000 0.00 0.00 0.00 2.73
95 96 4.772886 ACACAAAACTACAGGACTCCTT 57.227 40.909 0.00 0.00 0.00 3.36
110 111 3.508845 CTCCTTGAGGGGTTTTCTTGA 57.491 47.619 0.00 0.00 35.41 3.02
120 121 4.968719 AGGGGTTTTCTTGAAAGTTTGGAT 59.031 37.500 0.00 0.00 0.00 3.41
126 127 5.695851 TTCTTGAAAGTTTGGATGAGCTC 57.304 39.130 6.82 6.82 0.00 4.09
160 164 0.251916 TCCATGATCCAACGACCCAC 59.748 55.000 0.00 0.00 0.00 4.61
195 218 3.201487 TGGAAGCACATGATCATCCTCTT 59.799 43.478 4.86 8.68 0.00 2.85
207 234 1.490910 CATCCTCTTCCCCCTACAACC 59.509 57.143 0.00 0.00 0.00 3.77
219 246 5.131475 TCCCCCTACAACCACAATATTACTC 59.869 44.000 0.00 0.00 0.00 2.59
221 248 5.104277 CCCCTACAACCACAATATTACTCCA 60.104 44.000 0.00 0.00 0.00 3.86
223 250 6.352737 CCCTACAACCACAATATTACTCCACT 60.353 42.308 0.00 0.00 0.00 4.00
224 251 7.147620 CCCTACAACCACAATATTACTCCACTA 60.148 40.741 0.00 0.00 0.00 2.74
225 252 7.709613 CCTACAACCACAATATTACTCCACTAC 59.290 40.741 0.00 0.00 0.00 2.73
227 254 6.214819 ACAACCACAATATTACTCCACTACCT 59.785 38.462 0.00 0.00 0.00 3.08
268 296 5.975344 CGGCTAAGATAACACAAAGATACGA 59.025 40.000 0.00 0.00 0.00 3.43
269 297 6.074994 CGGCTAAGATAACACAAAGATACGAC 60.075 42.308 0.00 0.00 0.00 4.34
270 298 6.755141 GGCTAAGATAACACAAAGATACGACA 59.245 38.462 0.00 0.00 0.00 4.35
271 299 7.277098 GGCTAAGATAACACAAAGATACGACAA 59.723 37.037 0.00 0.00 0.00 3.18
272 300 8.653338 GCTAAGATAACACAAAGATACGACAAA 58.347 33.333 0.00 0.00 0.00 2.83
274 302 8.603242 AAGATAACACAAAGATACGACAAAGT 57.397 30.769 0.00 0.00 0.00 2.66
275 303 8.018677 AGATAACACAAAGATACGACAAAGTG 57.981 34.615 0.00 0.00 0.00 3.16
276 304 7.870954 AGATAACACAAAGATACGACAAAGTGA 59.129 33.333 0.00 0.00 0.00 3.41
277 305 6.671614 AACACAAAGATACGACAAAGTGAA 57.328 33.333 0.00 0.00 0.00 3.18
278 306 6.861065 ACACAAAGATACGACAAAGTGAAT 57.139 33.333 0.00 0.00 0.00 2.57
279 307 7.259290 ACACAAAGATACGACAAAGTGAATT 57.741 32.000 0.00 0.00 0.00 2.17
280 308 7.703328 ACACAAAGATACGACAAAGTGAATTT 58.297 30.769 0.00 0.00 0.00 1.82
281 309 7.855904 ACACAAAGATACGACAAAGTGAATTTC 59.144 33.333 0.00 0.00 0.00 2.17
282 310 7.855409 CACAAAGATACGACAAAGTGAATTTCA 59.145 33.333 0.00 0.00 0.00 2.69
283 311 8.402472 ACAAAGATACGACAAAGTGAATTTCAA 58.598 29.630 0.00 0.00 0.00 2.69
284 312 9.232082 CAAAGATACGACAAAGTGAATTTCAAA 57.768 29.630 0.00 0.00 0.00 2.69
285 313 9.796120 AAAGATACGACAAAGTGAATTTCAAAA 57.204 25.926 0.00 0.00 0.00 2.44
286 314 9.796120 AAGATACGACAAAGTGAATTTCAAAAA 57.204 25.926 0.00 0.00 0.00 1.94
430 495 5.049749 CCAAATGGATGTTTTCCCGTTTTTC 60.050 40.000 0.00 0.00 44.77 2.29
469 534 1.081509 GCCGATCAAACAGCGCAAA 60.082 52.632 11.47 0.00 0.00 3.68
480 545 3.360340 GCGCAAAGCTCCAGCAGT 61.360 61.111 0.30 0.00 45.16 4.40
483 548 1.799383 GCAAAGCTCCAGCAGTAGC 59.201 57.895 0.48 0.00 45.16 3.58
498 563 0.373716 GTAGCGAGCCATTTTGGACG 59.626 55.000 0.00 3.78 40.96 4.79
618 704 3.330720 CCACTCCACCTCCCCACC 61.331 72.222 0.00 0.00 0.00 4.61
1171 1278 7.480542 CGTCCTCTCCGTTTATTTATTTTTGTG 59.519 37.037 0.00 0.00 0.00 3.33
1235 1354 1.621814 CGGCGGGAGGAGGATTAATTA 59.378 52.381 0.00 0.00 0.00 1.40
1360 1479 1.778591 CGTGCAAAAATTCGTCCACAC 59.221 47.619 0.00 0.00 0.00 3.82
1406 1525 7.934222 TTTAAAACAAAATTTTCGCGTTTCC 57.066 28.000 14.61 0.00 0.00 3.13
1449 1568 4.929707 GGGTAGGAATGGCGCGGG 62.930 72.222 8.83 0.00 0.00 6.13
1596 1718 3.191581 TGTATATTTGTGTGGTTTGGGCG 59.808 43.478 0.00 0.00 0.00 6.13
1693 1815 4.269363 GGCATATCTTTCTGTTTGCATTGC 59.731 41.667 0.46 0.46 0.00 3.56
1808 1933 7.475137 TGATTTTAATTAGTTGTTCTGGGGG 57.525 36.000 0.00 0.00 0.00 5.40
2124 2264 0.323178 ATCAGCAGCCCACTTTCCTG 60.323 55.000 0.00 0.00 0.00 3.86
2127 2267 0.407139 AGCAGCCCACTTTCCTGAAT 59.593 50.000 0.00 0.00 0.00 2.57
2201 2341 2.552315 CACGGCTGGTTTCACTGTTAAT 59.448 45.455 0.00 0.00 0.00 1.40
2319 2459 5.526846 CCATAGAGATTTGAAGCTGGAGAAC 59.473 44.000 0.00 0.00 0.00 3.01
2397 2537 0.991355 AGGTTGTCCCTGAACCCACA 60.991 55.000 0.00 0.00 44.08 4.17
2766 2933 6.791303 TGAAATTACGAGTATTTGGGCATTC 58.209 36.000 0.00 0.00 0.00 2.67
2767 2934 6.601613 TGAAATTACGAGTATTTGGGCATTCT 59.398 34.615 0.00 0.00 0.00 2.40
2902 3069 4.224818 TGGCCCCTCAATTTAATCAAAAGG 59.775 41.667 0.00 0.00 0.00 3.11
2977 3144 6.866480 TGCATTATCTAAAAGCAGGGAAAAG 58.134 36.000 0.00 0.00 0.00 2.27
3026 3193 9.829507 TGGCTTTATTTATTAAATTGTGATGGG 57.170 29.630 6.95 0.00 32.38 4.00
3178 3346 5.873164 GGTTTGTCGAGGTAAGATGTACAAT 59.127 40.000 0.00 0.00 0.00 2.71
3334 3563 9.452065 GAGTTTTTGGATTCTAGTTTCTTGTTC 57.548 33.333 0.00 0.00 0.00 3.18
3393 3622 3.901844 TGGTAACAGAAGTAAGTCCAGCT 59.098 43.478 0.00 0.00 46.17 4.24
3405 3634 3.996124 CCAGCTCGGCCCCTATCG 61.996 72.222 0.00 0.00 0.00 2.92
3523 3786 3.887716 GCATGCAAGGATGTCTAATTCCT 59.112 43.478 14.21 0.00 44.35 3.36
3575 3838 4.439289 GGCTTCCTTGATACAAAGATGCAC 60.439 45.833 16.64 7.73 0.00 4.57
3696 4054 1.747355 CATGTTGGTGCTTCCCTGATC 59.253 52.381 0.00 0.00 34.77 2.92
3699 4057 0.036388 TTGGTGCTTCCCTGATCGAC 60.036 55.000 0.00 0.00 34.77 4.20
3796 4154 7.023575 GCTTTAATCATTATTCATGGCTACCG 58.976 38.462 0.00 0.00 33.07 4.02
3797 4155 7.447374 TTTAATCATTATTCATGGCTACCGG 57.553 36.000 0.00 0.00 33.07 5.28
3841 4199 1.097232 TTTGCTGATCAAGGCGATGG 58.903 50.000 0.00 0.00 35.84 3.51
3892 4272 3.312421 TGCTAGCACACTGAAACTTCAAC 59.688 43.478 14.93 0.00 36.64 3.18
4043 4441 5.638234 GCGGTTACTGAATCTGAAGTTTAGT 59.362 40.000 0.00 0.00 0.00 2.24
4061 4461 7.611213 GTTTAGTATCACAGTAAACCATGCT 57.389 36.000 4.18 0.00 43.14 3.79
4110 4512 4.223032 AGATGTCGGTCCTGAACTTTGTAT 59.777 41.667 0.00 0.00 0.00 2.29
4152 4554 8.610248 TTAGCTAGTATCTAGTGACATGAGAC 57.390 38.462 0.00 0.00 0.00 3.36
4164 4566 5.421693 AGTGACATGAGACTATTCTTCAGCT 59.578 40.000 0.00 0.00 29.47 4.24
4165 4567 6.605194 AGTGACATGAGACTATTCTTCAGCTA 59.395 38.462 0.00 0.00 29.47 3.32
4377 4779 4.614993 CGGTATTTCCTTTTGCACGTCAAT 60.615 41.667 0.00 0.00 34.12 2.57
4496 4898 5.240844 GCTTATGGCCCGTATCTTTGTTAAT 59.759 40.000 0.00 0.00 34.27 1.40
4533 4935 8.371770 GGTAATGACCTCAATCTGTATCTTTC 57.628 38.462 0.00 0.00 43.16 2.62
4556 4958 4.143094 CGCCTTCTTCTTTTTAGGAAGTCG 60.143 45.833 0.00 0.00 40.50 4.18
4860 5262 3.981212 AGAGAAGGAAGAGGAAGAGAGG 58.019 50.000 0.00 0.00 0.00 3.69
5179 5589 4.816385 CGTATGCTTGTATTCCCTGTGATT 59.184 41.667 0.00 0.00 0.00 2.57
5192 5602 1.402968 CTGTGATTGGGAGAAATGGCG 59.597 52.381 0.00 0.00 0.00 5.69
5194 5604 0.034186 TGATTGGGAGAAATGGCGCT 60.034 50.000 7.64 0.00 0.00 5.92
5227 5637 2.095059 CCAGCGCTTCATGTTTAAAGCT 60.095 45.455 7.50 6.38 44.49 3.74
5228 5638 3.568538 CAGCGCTTCATGTTTAAAGCTT 58.431 40.909 7.50 0.00 44.49 3.74
5229 5639 3.362831 CAGCGCTTCATGTTTAAAGCTTG 59.637 43.478 7.50 8.67 44.49 4.01
5230 5640 3.253188 AGCGCTTCATGTTTAAAGCTTGA 59.747 39.130 2.64 0.00 44.49 3.02
5231 5641 3.980775 GCGCTTCATGTTTAAAGCTTGAA 59.019 39.130 13.20 0.00 44.49 2.69
5232 5642 4.089065 GCGCTTCATGTTTAAAGCTTGAAG 59.911 41.667 23.64 23.64 44.49 3.02
5233 5643 5.215160 CGCTTCATGTTTAAAGCTTGAAGT 58.785 37.500 25.62 0.00 44.49 3.01
5234 5644 6.370593 CGCTTCATGTTTAAAGCTTGAAGTA 58.629 36.000 25.62 4.62 44.49 2.24
5235 5645 7.023575 CGCTTCATGTTTAAAGCTTGAAGTAT 58.976 34.615 25.62 6.42 44.49 2.12
5244 5662 1.076332 GCTTGAAGTATTGCCGACGT 58.924 50.000 0.00 0.00 0.00 4.34
5294 5827 2.254546 TGTGCTACAAGTGGGAGTTG 57.745 50.000 0.00 0.00 34.77 3.16
5295 5828 1.488812 TGTGCTACAAGTGGGAGTTGT 59.511 47.619 0.00 0.00 43.55 3.32
5303 5836 0.401738 AGTGGGAGTTGTGGTGGATG 59.598 55.000 0.00 0.00 0.00 3.51
5340 5873 1.294068 TCCCTGGGCTACTTCTGGTAT 59.706 52.381 8.22 0.00 0.00 2.73
5342 5875 3.051650 TCCCTGGGCTACTTCTGGTATAA 60.052 47.826 8.22 0.00 0.00 0.98
5350 5883 5.984323 GGCTACTTCTGGTATAACAGTTAGC 59.016 44.000 25.10 25.10 39.23 3.09
5351 5884 6.406624 GGCTACTTCTGGTATAACAGTTAGCA 60.407 42.308 29.33 16.55 40.30 3.49
5371 5906 1.074072 CACCAACCCATCCAACCGA 59.926 57.895 0.00 0.00 0.00 4.69
5381 5916 3.818773 CCCATCCAACCGATACCAAATAC 59.181 47.826 0.00 0.00 0.00 1.89
5410 5948 2.821366 GGTGCAGCCATCTCCACG 60.821 66.667 4.03 0.00 37.17 4.94
5446 5987 0.898320 AGCACCACCTACAGCTACAG 59.102 55.000 0.00 0.00 35.19 2.74
5467 6008 3.924144 GCTCCTAAGCTGGTATCATGAG 58.076 50.000 0.09 0.00 45.55 2.90
5468 6009 3.306641 GCTCCTAAGCTGGTATCATGAGG 60.307 52.174 0.09 0.00 45.55 3.86
5469 6010 2.634940 TCCTAAGCTGGTATCATGAGGC 59.365 50.000 0.09 0.71 0.00 4.70
5470 6011 2.369860 CCTAAGCTGGTATCATGAGGCA 59.630 50.000 0.09 0.00 0.00 4.75
5471 6012 2.338577 AAGCTGGTATCATGAGGCAC 57.661 50.000 0.09 0.00 0.00 5.01
5473 6014 1.842562 AGCTGGTATCATGAGGCACTT 59.157 47.619 0.09 0.00 41.55 3.16
5474 6015 1.945394 GCTGGTATCATGAGGCACTTG 59.055 52.381 0.09 0.00 41.55 3.16
5475 6016 2.681976 GCTGGTATCATGAGGCACTTGT 60.682 50.000 0.09 0.00 41.55 3.16
5476 6017 3.201290 CTGGTATCATGAGGCACTTGTC 58.799 50.000 0.09 0.00 41.55 3.18
5477 6018 2.840038 TGGTATCATGAGGCACTTGTCT 59.160 45.455 0.09 0.00 41.55 3.41
5478 6019 3.264193 TGGTATCATGAGGCACTTGTCTT 59.736 43.478 0.09 0.00 41.55 3.01
5479 6020 4.263462 TGGTATCATGAGGCACTTGTCTTT 60.263 41.667 0.09 0.00 41.55 2.52
5480 6021 4.333926 GGTATCATGAGGCACTTGTCTTTC 59.666 45.833 0.09 0.00 41.55 2.62
5481 6022 3.777106 TCATGAGGCACTTGTCTTTCT 57.223 42.857 0.00 0.00 41.55 2.52
5482 6023 4.090761 TCATGAGGCACTTGTCTTTCTT 57.909 40.909 0.00 0.00 41.55 2.52
5483 6024 4.464008 TCATGAGGCACTTGTCTTTCTTT 58.536 39.130 0.00 0.00 41.55 2.52
5484 6025 4.516698 TCATGAGGCACTTGTCTTTCTTTC 59.483 41.667 0.00 0.00 41.55 2.62
5485 6026 4.156455 TGAGGCACTTGTCTTTCTTTCT 57.844 40.909 0.00 0.00 41.55 2.52
5486 6027 4.130118 TGAGGCACTTGTCTTTCTTTCTC 58.870 43.478 0.00 0.00 41.55 2.87
5487 6028 4.130118 GAGGCACTTGTCTTTCTTTCTCA 58.870 43.478 0.00 0.00 41.55 3.27
5488 6029 4.526970 AGGCACTTGTCTTTCTTTCTCAA 58.473 39.130 0.00 0.00 27.25 3.02
5489 6030 4.336713 AGGCACTTGTCTTTCTTTCTCAAC 59.663 41.667 0.00 0.00 27.25 3.18
5490 6031 4.336713 GGCACTTGTCTTTCTTTCTCAACT 59.663 41.667 0.00 0.00 0.00 3.16
5491 6032 5.163612 GGCACTTGTCTTTCTTTCTCAACTT 60.164 40.000 0.00 0.00 0.00 2.66
5492 6033 6.325596 GCACTTGTCTTTCTTTCTCAACTTT 58.674 36.000 0.00 0.00 0.00 2.66
5493 6034 6.252228 GCACTTGTCTTTCTTTCTCAACTTTG 59.748 38.462 0.00 0.00 0.00 2.77
5494 6035 6.252228 CACTTGTCTTTCTTTCTCAACTTTGC 59.748 38.462 0.00 0.00 0.00 3.68
5495 6036 5.895636 TGTCTTTCTTTCTCAACTTTGCA 57.104 34.783 0.00 0.00 0.00 4.08
5496 6037 5.883661 TGTCTTTCTTTCTCAACTTTGCAG 58.116 37.500 0.00 0.00 0.00 4.41
5499 6079 5.297776 TCTTTCTTTCTCAACTTTGCAGAGG 59.702 40.000 9.34 0.00 0.00 3.69
5523 6103 4.380843 TGCCAGGATTCAAACCTTCTTA 57.619 40.909 0.00 0.00 35.35 2.10
5525 6105 5.332743 TGCCAGGATTCAAACCTTCTTAAT 58.667 37.500 0.00 0.00 35.35 1.40
5532 6112 7.944554 AGGATTCAAACCTTCTTAATTGTCTCA 59.055 33.333 0.00 0.00 33.55 3.27
5554 6134 0.898320 AGTCAACGAGCTAGCACCAT 59.102 50.000 18.83 0.00 0.00 3.55
5603 6183 1.135083 ACGGAGGTGCTCTATTTCACG 60.135 52.381 0.00 0.00 34.20 4.35
5666 6250 6.360370 AAGTAGAAGAACCAAGATGCACTA 57.640 37.500 0.00 0.00 0.00 2.74
5702 6286 5.174395 GCTATGGTTAGATAGCATCACAGG 58.826 45.833 7.50 0.00 46.91 4.00
5704 6288 2.705658 TGGTTAGATAGCATCACAGGGG 59.294 50.000 0.00 0.00 0.00 4.79
5705 6289 2.551071 GGTTAGATAGCATCACAGGGGC 60.551 54.545 0.00 0.00 0.00 5.80
5706 6290 1.352083 TAGATAGCATCACAGGGGCC 58.648 55.000 0.00 0.00 0.00 5.80
5708 6292 0.475906 GATAGCATCACAGGGGCCTT 59.524 55.000 0.84 0.00 0.00 4.35
5710 6294 0.913934 TAGCATCACAGGGGCCTTCA 60.914 55.000 0.84 0.00 0.00 3.02
5711 6295 2.048603 GCATCACAGGGGCCTTCAC 61.049 63.158 0.84 0.00 0.00 3.18
5712 6296 1.379916 CATCACAGGGGCCTTCACA 59.620 57.895 0.84 0.00 0.00 3.58
5713 6297 0.679002 CATCACAGGGGCCTTCACAG 60.679 60.000 0.84 0.00 0.00 3.66
5714 6298 0.842030 ATCACAGGGGCCTTCACAGA 60.842 55.000 0.84 0.00 0.00 3.41
5715 6299 1.059584 TCACAGGGGCCTTCACAGAA 61.060 55.000 0.84 0.00 0.00 3.02
5716 6300 0.038744 CACAGGGGCCTTCACAGAAT 59.961 55.000 0.84 0.00 0.00 2.40
5717 6301 0.329596 ACAGGGGCCTTCACAGAATC 59.670 55.000 0.84 0.00 0.00 2.52
5718 6302 0.329261 CAGGGGCCTTCACAGAATCA 59.671 55.000 0.84 0.00 0.00 2.57
5719 6303 0.329596 AGGGGCCTTCACAGAATCAC 59.670 55.000 0.84 0.00 0.00 3.06
5720 6304 0.038166 GGGGCCTTCACAGAATCACA 59.962 55.000 0.84 0.00 0.00 3.58
5721 6305 1.457346 GGGCCTTCACAGAATCACAG 58.543 55.000 0.84 0.00 0.00 3.66
5722 6306 1.457346 GGCCTTCACAGAATCACAGG 58.543 55.000 0.00 0.00 0.00 4.00
5723 6307 0.807496 GCCTTCACAGAATCACAGGC 59.193 55.000 0.00 0.00 40.13 4.85
5724 6308 1.612726 GCCTTCACAGAATCACAGGCT 60.613 52.381 0.58 0.00 43.06 4.58
5725 6309 2.355108 GCCTTCACAGAATCACAGGCTA 60.355 50.000 0.58 0.00 43.06 3.93
5726 6310 3.265791 CCTTCACAGAATCACAGGCTAC 58.734 50.000 0.00 0.00 0.00 3.58
5727 6311 3.306989 CCTTCACAGAATCACAGGCTACA 60.307 47.826 0.00 0.00 0.00 2.74
5728 6312 3.319137 TCACAGAATCACAGGCTACAC 57.681 47.619 0.00 0.00 0.00 2.90
5729 6313 2.899900 TCACAGAATCACAGGCTACACT 59.100 45.455 0.00 0.00 0.00 3.55
5730 6314 2.998670 CACAGAATCACAGGCTACACTG 59.001 50.000 0.00 0.00 44.03 3.66
5731 6315 2.005451 CAGAATCACAGGCTACACTGC 58.995 52.381 0.00 0.00 42.21 4.40
5732 6316 1.625315 AGAATCACAGGCTACACTGCA 59.375 47.619 0.00 0.00 42.21 4.41
5733 6317 2.238144 AGAATCACAGGCTACACTGCAT 59.762 45.455 0.00 0.00 42.21 3.96
5757 6348 4.065088 TCCTCTTTCTTGGAACATCAACG 58.935 43.478 0.00 0.00 39.30 4.10
5758 6349 3.365364 CCTCTTTCTTGGAACATCAACGC 60.365 47.826 0.00 0.00 39.30 4.84
5777 6370 4.475944 ACGCAGCATAGCAAAAGTAAAAG 58.524 39.130 0.00 0.00 0.00 2.27
5781 6374 5.920273 GCAGCATAGCAAAAGTAAAAGAACA 59.080 36.000 0.00 0.00 0.00 3.18
5797 6390 2.358898 AGAACAAAGATGCACGCTGTTT 59.641 40.909 0.00 0.00 31.73 2.83
5816 6409 6.476053 GCTGTTTAGCTATGTCTAGGTACAAC 59.524 42.308 0.00 0.00 46.57 3.32
5826 6419 4.015084 GTCTAGGTACAACTACAGGAGCA 58.985 47.826 0.00 0.00 0.00 4.26
5830 6423 3.838317 AGGTACAACTACAGGAGCATTCA 59.162 43.478 0.00 0.00 0.00 2.57
5839 6432 4.833478 ACAGGAGCATTCACAGAATACT 57.167 40.909 0.00 0.00 0.00 2.12
5910 6508 7.826252 AGCATATCACGGATTCAATAATTAGCT 59.174 33.333 0.00 0.00 0.00 3.32
5935 6533 5.734498 GCGAGCTTACAAAATACAACATGAG 59.266 40.000 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.124457 ACATCAAGTGAGGCATTACATGTTC 59.876 40.000 2.30 0.00 0.00 3.18
5 6 4.592942 ACATCAAGTGAGGCATTACATGT 58.407 39.130 2.69 2.69 0.00 3.21
14 15 5.645497 ACTAAAGAATGACATCAAGTGAGGC 59.355 40.000 0.00 0.00 0.00 4.70
15 16 6.093219 CCACTAAAGAATGACATCAAGTGAGG 59.907 42.308 9.64 0.00 36.13 3.86
18 19 6.808008 ACCACTAAAGAATGACATCAAGTG 57.192 37.500 3.24 3.24 34.33 3.16
28 29 7.875971 ACTTCAAAGCTAACCACTAAAGAATG 58.124 34.615 0.00 0.00 0.00 2.67
32 33 7.497925 AAGACTTCAAAGCTAACCACTAAAG 57.502 36.000 0.00 0.00 0.00 1.85
44 45 2.224314 CGAGGTCCAAAGACTTCAAAGC 59.776 50.000 6.21 0.00 46.67 3.51
48 49 0.034896 GCCGAGGTCCAAAGACTTCA 59.965 55.000 6.21 0.00 46.67 3.02
54 55 3.254657 TGTAATTTTGCCGAGGTCCAAAG 59.745 43.478 0.00 0.00 33.07 2.77
64 65 5.401079 CCTGTAGTTTTGTGTAATTTTGCCG 59.599 40.000 0.00 0.00 0.00 5.69
69 70 7.287810 AGGAGTCCTGTAGTTTTGTGTAATTT 58.712 34.615 12.07 0.00 29.57 1.82
76 77 4.202367 CCTCAAGGAGTCCTGTAGTTTTGT 60.202 45.833 13.89 0.00 37.39 2.83
77 78 4.319177 CCTCAAGGAGTCCTGTAGTTTTG 58.681 47.826 13.89 5.38 37.39 2.44
78 79 3.328050 CCCTCAAGGAGTCCTGTAGTTTT 59.672 47.826 13.89 0.00 38.24 2.43
79 80 2.907042 CCCTCAAGGAGTCCTGTAGTTT 59.093 50.000 13.89 0.00 38.24 2.66
80 81 2.541466 CCCTCAAGGAGTCCTGTAGTT 58.459 52.381 13.89 0.00 38.24 2.24
81 82 1.273324 CCCCTCAAGGAGTCCTGTAGT 60.273 57.143 13.89 0.00 38.24 2.73
82 83 1.273324 ACCCCTCAAGGAGTCCTGTAG 60.273 57.143 13.89 12.90 38.24 2.74
83 84 0.790993 ACCCCTCAAGGAGTCCTGTA 59.209 55.000 13.89 2.76 38.24 2.74
84 85 0.104409 AACCCCTCAAGGAGTCCTGT 60.104 55.000 13.89 1.59 38.24 4.00
85 86 1.068121 AAACCCCTCAAGGAGTCCTG 58.932 55.000 13.89 7.36 38.24 3.86
95 96 4.161377 CCAAACTTTCAAGAAAACCCCTCA 59.839 41.667 0.00 0.00 0.00 3.86
102 103 6.322201 AGAGCTCATCCAAACTTTCAAGAAAA 59.678 34.615 17.77 0.00 0.00 2.29
110 111 4.379302 AGGAAGAGCTCATCCAAACTTT 57.621 40.909 33.29 13.89 36.26 2.66
120 121 0.895530 CCAACGGTAGGAAGAGCTCA 59.104 55.000 17.77 0.00 0.00 4.26
126 127 2.434336 TCATGGATCCAACGGTAGGAAG 59.566 50.000 20.67 0.00 38.93 3.46
195 218 5.041015 AGTAATATTGTGGTTGTAGGGGGA 58.959 41.667 0.00 0.00 0.00 4.81
207 234 8.692710 TGAACTAGGTAGTGGAGTAATATTGTG 58.307 37.037 0.00 0.00 36.50 3.33
219 246 5.122396 GCTGATTTTGTGAACTAGGTAGTGG 59.878 44.000 0.00 0.00 36.50 4.00
221 248 5.246307 GGCTGATTTTGTGAACTAGGTAGT 58.754 41.667 0.00 0.00 38.39 2.73
223 250 4.250464 CGGCTGATTTTGTGAACTAGGTA 58.750 43.478 0.00 0.00 0.00 3.08
224 251 3.074412 CGGCTGATTTTGTGAACTAGGT 58.926 45.455 0.00 0.00 0.00 3.08
225 252 2.420022 CCGGCTGATTTTGTGAACTAGG 59.580 50.000 0.00 0.00 0.00 3.02
227 254 1.810151 GCCGGCTGATTTTGTGAACTA 59.190 47.619 22.15 0.00 0.00 2.24
287 315 8.601476 CGGCTTTACTTTATCGTATCTTTTTCT 58.399 33.333 0.00 0.00 0.00 2.52
288 316 8.598075 TCGGCTTTACTTTATCGTATCTTTTTC 58.402 33.333 0.00 0.00 0.00 2.29
289 317 8.385858 GTCGGCTTTACTTTATCGTATCTTTTT 58.614 33.333 0.00 0.00 0.00 1.94
290 318 7.546667 TGTCGGCTTTACTTTATCGTATCTTTT 59.453 33.333 0.00 0.00 0.00 2.27
291 319 7.037438 TGTCGGCTTTACTTTATCGTATCTTT 58.963 34.615 0.00 0.00 0.00 2.52
292 320 6.567050 TGTCGGCTTTACTTTATCGTATCTT 58.433 36.000 0.00 0.00 0.00 2.40
293 321 6.140303 TGTCGGCTTTACTTTATCGTATCT 57.860 37.500 0.00 0.00 0.00 1.98
294 322 6.615839 GCATGTCGGCTTTACTTTATCGTATC 60.616 42.308 0.00 0.00 0.00 2.24
295 323 5.176958 GCATGTCGGCTTTACTTTATCGTAT 59.823 40.000 0.00 0.00 0.00 3.06
296 324 4.505191 GCATGTCGGCTTTACTTTATCGTA 59.495 41.667 0.00 0.00 0.00 3.43
297 325 3.308866 GCATGTCGGCTTTACTTTATCGT 59.691 43.478 0.00 0.00 0.00 3.73
298 326 3.601586 CGCATGTCGGCTTTACTTTATCG 60.602 47.826 0.00 0.00 33.78 2.92
299 327 3.554324 TCGCATGTCGGCTTTACTTTATC 59.446 43.478 9.16 0.00 39.05 1.75
469 534 3.074999 GCTCGCTACTGCTGGAGCT 62.075 63.158 23.63 0.00 44.05 4.09
480 545 2.762360 CGTCCAAAATGGCTCGCTA 58.238 52.632 0.00 0.00 37.47 4.26
483 548 0.248215 GATGCGTCCAAAATGGCTCG 60.248 55.000 0.00 8.59 37.47 5.03
486 551 0.170116 TTCGATGCGTCCAAAATGGC 59.830 50.000 0.00 0.00 37.47 4.40
498 563 0.028110 GGCTGGATTCGTTTCGATGC 59.972 55.000 0.00 0.00 35.23 3.91
758 844 1.673337 GTTGGGTCGGTAGGTTGGC 60.673 63.158 0.00 0.00 0.00 4.52
984 1082 3.462501 ATCCCCTCCCTCCCTCCC 61.463 72.222 0.00 0.00 0.00 4.30
1171 1278 5.992217 CCAATTACTCCTCCTTGTATGTAGC 59.008 44.000 0.00 0.00 0.00 3.58
1225 1344 5.195848 TCCCCAAAACGGTAATTAATCCT 57.804 39.130 0.00 0.00 0.00 3.24
1235 1354 0.893727 GCACAGATCCCCAAAACGGT 60.894 55.000 0.00 0.00 0.00 4.83
1360 1479 0.539051 ACAGAGAGAGAATTGGCCCG 59.461 55.000 0.00 0.00 0.00 6.13
1411 1530 1.778591 CGTGAACACCAAACGATTTGC 59.221 47.619 0.00 0.00 39.64 3.68
1428 1547 2.203015 CGCCATTCCTACCCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
1478 1598 2.768253 TCCTCACCACATGCAGTTAG 57.232 50.000 0.00 0.00 0.00 2.34
1596 1718 4.877823 TGCATCTGTAACATGAGAATCCAC 59.122 41.667 0.00 0.00 0.00 4.02
1632 1754 1.244019 AATTGCCACGGAGAAGGTGC 61.244 55.000 0.00 0.00 34.08 5.01
1693 1815 7.147312 TCTTCCATCAAAAGTTTGTGCTATTG 58.853 34.615 3.82 0.00 39.18 1.90
1808 1933 3.263425 TCAGTACCACCTGGAGAATTTCC 59.737 47.826 0.00 1.09 46.98 3.13
1809 1934 4.254492 GTCAGTACCACCTGGAGAATTTC 58.746 47.826 0.00 0.00 38.94 2.17
2101 2229 1.888512 GAAAGTGGGCTGCTGATTTGA 59.111 47.619 0.00 0.00 0.00 2.69
2102 2230 1.067354 GGAAAGTGGGCTGCTGATTTG 60.067 52.381 0.00 0.00 0.00 2.32
2103 2231 1.203100 AGGAAAGTGGGCTGCTGATTT 60.203 47.619 0.00 0.00 0.00 2.17
2104 2232 0.407139 AGGAAAGTGGGCTGCTGATT 59.593 50.000 0.00 0.00 0.00 2.57
2105 2233 0.323178 CAGGAAAGTGGGCTGCTGAT 60.323 55.000 0.00 0.00 33.16 2.90
2106 2234 1.073722 CAGGAAAGTGGGCTGCTGA 59.926 57.895 0.00 0.00 33.16 4.26
2107 2235 0.538057 TTCAGGAAAGTGGGCTGCTG 60.538 55.000 0.00 0.00 32.69 4.41
2108 2236 0.407139 ATTCAGGAAAGTGGGCTGCT 59.593 50.000 0.00 0.00 0.00 4.24
2109 2237 0.813821 GATTCAGGAAAGTGGGCTGC 59.186 55.000 0.00 0.00 0.00 5.25
2110 2238 1.815003 GTGATTCAGGAAAGTGGGCTG 59.185 52.381 0.00 0.00 0.00 4.85
2111 2239 1.425066 TGTGATTCAGGAAAGTGGGCT 59.575 47.619 0.00 0.00 0.00 5.19
2112 2240 1.909700 TGTGATTCAGGAAAGTGGGC 58.090 50.000 0.00 0.00 0.00 5.36
2124 2264 4.697352 AGGCACACTAGTCATTTGTGATTC 59.303 41.667 13.09 3.75 42.77 2.52
2127 2267 3.769739 AGGCACACTAGTCATTTGTGA 57.230 42.857 13.09 0.00 42.77 3.58
2201 2341 5.452496 GGCTCATACATAAGACTGCAGAAGA 60.452 44.000 23.35 2.54 0.00 2.87
2319 2459 1.081892 CACTGCCATCCAAGAGAACG 58.918 55.000 0.00 0.00 0.00 3.95
2397 2537 8.964476 ACATCGATAACTTGAAGGTTCAATAT 57.036 30.769 5.63 2.61 45.26 1.28
2538 2678 2.419990 CCTTTCCATCATACTCACGGCA 60.420 50.000 0.00 0.00 0.00 5.69
2594 2735 6.430000 GCAAAGGACTAACAGAAACCAGATAA 59.570 38.462 0.00 0.00 0.00 1.75
2766 2933 0.815734 CAATCAGGAAGGCTTGGCAG 59.184 55.000 3.46 0.00 0.00 4.85
2767 2934 0.612732 CCAATCAGGAAGGCTTGGCA 60.613 55.000 3.46 0.00 41.22 4.92
2778 2945 4.035208 GCACCGACTATTTAACCAATCAGG 59.965 45.833 0.00 0.00 45.67 3.86
2902 3069 3.810896 GCCCGTCATTCAACCGGC 61.811 66.667 0.00 0.00 40.38 6.13
2922 3089 2.197465 AGGTACTCCTTTAGCCTTGGG 58.803 52.381 0.00 0.00 42.12 4.12
2977 3144 9.914131 GCCAAATATCAGGTATTTCCTAAAATC 57.086 33.333 0.00 0.00 46.24 2.17
3334 3563 9.398170 CCTACCTATTTGCGATAAAATGATTTG 57.602 33.333 0.00 0.00 32.16 2.32
3345 3574 5.365619 CAAACCTACCTACCTATTTGCGAT 58.634 41.667 0.00 0.00 0.00 4.58
3379 3608 0.460459 GGCCGAGCTGGACTTACTTC 60.460 60.000 0.00 0.00 45.46 3.01
3405 3634 1.150827 GGCTGCAGAAAATTTGCCAC 58.849 50.000 20.43 0.00 40.81 5.01
3696 4054 4.742201 CCCACAGTCGCTGGGTCG 62.742 72.222 10.80 0.00 43.32 4.79
3796 4154 9.803507 AACCAACTTATAAATTATACTAGCCCC 57.196 33.333 0.00 0.00 0.00 5.80
3841 4199 7.708998 TGAACTTACAAATTAACCACAAGGAC 58.291 34.615 0.00 0.00 38.69 3.85
4043 4441 9.710900 CTATGATTAGCATGGTTTACTGTGATA 57.289 33.333 1.12 0.00 37.87 2.15
4377 4779 1.922447 AGTGGCCATAATGAGGGTCAA 59.078 47.619 9.72 0.00 44.13 3.18
4496 4898 2.169769 GGTCATTACCTTCGATGGGACA 59.830 50.000 20.44 5.25 43.28 4.02
4533 4935 5.284428 GACTTCCTAAAAAGAAGAAGGCG 57.716 43.478 7.47 0.00 42.80 5.52
4556 4958 3.191162 TGTCACTTGCTATGAAACATGGC 59.809 43.478 11.94 11.94 0.00 4.40
4597 4999 3.622163 GTGATTCTCTGGACAGCATTCAG 59.378 47.826 0.00 0.00 0.00 3.02
5098 5508 6.361481 CCAAATATTACAGCATTCATCAAGCG 59.639 38.462 0.00 0.00 0.00 4.68
5179 5589 2.272146 GGAGCGCCATTTCTCCCA 59.728 61.111 2.29 0.00 42.30 4.37
5189 5599 2.341911 GATAGCCTGAGGAGCGCC 59.658 66.667 0.65 0.00 34.64 6.53
5192 5602 1.370810 GCTGGATAGCCTGAGGAGC 59.629 63.158 0.65 0.00 44.33 4.70
5227 5637 4.565166 CAGAATACGTCGGCAATACTTCAA 59.435 41.667 0.00 0.00 0.00 2.69
5228 5638 4.109766 CAGAATACGTCGGCAATACTTCA 58.890 43.478 0.00 0.00 0.00 3.02
5229 5639 4.026804 CACAGAATACGTCGGCAATACTTC 60.027 45.833 0.00 0.00 0.00 3.01
5230 5640 3.863424 CACAGAATACGTCGGCAATACTT 59.137 43.478 0.00 0.00 0.00 2.24
5231 5641 3.444916 CACAGAATACGTCGGCAATACT 58.555 45.455 0.00 0.00 0.00 2.12
5232 5642 2.538449 CCACAGAATACGTCGGCAATAC 59.462 50.000 0.00 0.00 0.00 1.89
5233 5643 2.166870 ACCACAGAATACGTCGGCAATA 59.833 45.455 0.00 0.00 0.00 1.90
5234 5644 1.066430 ACCACAGAATACGTCGGCAAT 60.066 47.619 0.00 0.00 0.00 3.56
5235 5645 0.319083 ACCACAGAATACGTCGGCAA 59.681 50.000 0.00 0.00 0.00 4.52
5244 5662 3.985019 TTTAGGGCGAACCACAGAATA 57.015 42.857 0.00 0.00 43.89 1.75
5282 5700 0.182537 TCCACCACAACTCCCACTTG 59.817 55.000 0.00 0.00 0.00 3.16
5303 5836 1.680249 GGGACATTCTGAAGAGGGTGC 60.680 57.143 0.00 0.00 0.00 5.01
5340 5873 2.487625 GGGTTGGTGGTGCTAACTGTTA 60.488 50.000 0.00 0.00 38.44 2.41
5342 5875 0.179001 GGGTTGGTGGTGCTAACTGT 60.179 55.000 0.00 0.00 38.44 3.55
5350 5883 1.184970 GGTTGGATGGGTTGGTGGTG 61.185 60.000 0.00 0.00 0.00 4.17
5351 5884 1.155155 GGTTGGATGGGTTGGTGGT 59.845 57.895 0.00 0.00 0.00 4.16
5371 5906 6.248569 CCAACTGGTAGGAGTATTTGGTAT 57.751 41.667 0.00 0.00 0.00 2.73
5454 5995 1.945394 CAAGTGCCTCATGATACCAGC 59.055 52.381 0.00 0.00 0.00 4.85
5460 6001 4.298103 AGAAAGACAAGTGCCTCATGAT 57.702 40.909 0.00 0.00 0.00 2.45
5461 6002 3.777106 AGAAAGACAAGTGCCTCATGA 57.223 42.857 0.00 0.00 0.00 3.07
5462 6003 4.518211 AGAAAGAAAGACAAGTGCCTCATG 59.482 41.667 0.00 0.00 0.00 3.07
5463 6004 4.723309 AGAAAGAAAGACAAGTGCCTCAT 58.277 39.130 0.00 0.00 0.00 2.90
5464 6005 4.130118 GAGAAAGAAAGACAAGTGCCTCA 58.870 43.478 0.00 0.00 0.00 3.86
5465 6006 4.130118 TGAGAAAGAAAGACAAGTGCCTC 58.870 43.478 0.00 0.00 0.00 4.70
5466 6007 4.156455 TGAGAAAGAAAGACAAGTGCCT 57.844 40.909 0.00 0.00 0.00 4.75
5467 6008 4.336713 AGTTGAGAAAGAAAGACAAGTGCC 59.663 41.667 0.00 0.00 0.00 5.01
5468 6009 5.491635 AGTTGAGAAAGAAAGACAAGTGC 57.508 39.130 0.00 0.00 0.00 4.40
5469 6010 6.252228 GCAAAGTTGAGAAAGAAAGACAAGTG 59.748 38.462 0.00 0.00 0.00 3.16
5470 6011 6.071952 TGCAAAGTTGAGAAAGAAAGACAAGT 60.072 34.615 0.00 0.00 0.00 3.16
5471 6012 6.324819 TGCAAAGTTGAGAAAGAAAGACAAG 58.675 36.000 0.00 0.00 0.00 3.16
5472 6013 6.150976 TCTGCAAAGTTGAGAAAGAAAGACAA 59.849 34.615 0.00 0.00 0.00 3.18
5473 6014 5.647658 TCTGCAAAGTTGAGAAAGAAAGACA 59.352 36.000 0.00 0.00 0.00 3.41
5474 6015 6.124088 TCTGCAAAGTTGAGAAAGAAAGAC 57.876 37.500 0.00 0.00 0.00 3.01
5475 6016 5.297776 CCTCTGCAAAGTTGAGAAAGAAAGA 59.702 40.000 1.66 0.00 0.00 2.52
5476 6017 5.517904 CCTCTGCAAAGTTGAGAAAGAAAG 58.482 41.667 1.66 0.00 0.00 2.62
5477 6018 4.202050 GCCTCTGCAAAGTTGAGAAAGAAA 60.202 41.667 1.66 0.00 37.47 2.52
5478 6019 3.316308 GCCTCTGCAAAGTTGAGAAAGAA 59.684 43.478 1.66 0.00 37.47 2.52
5479 6020 2.880890 GCCTCTGCAAAGTTGAGAAAGA 59.119 45.455 1.66 0.00 37.47 2.52
5480 6021 2.620115 TGCCTCTGCAAAGTTGAGAAAG 59.380 45.455 1.66 0.00 46.66 2.62
5481 6022 2.653726 TGCCTCTGCAAAGTTGAGAAA 58.346 42.857 1.66 0.00 46.66 2.52
5482 6023 2.346766 TGCCTCTGCAAAGTTGAGAA 57.653 45.000 1.66 0.00 46.66 2.87
5493 6034 1.453762 GAATCCTGGCATGCCTCTGC 61.454 60.000 35.53 16.95 41.53 4.26
5494 6035 0.106868 TGAATCCTGGCATGCCTCTG 60.107 55.000 35.53 24.11 36.94 3.35
5495 6036 0.627451 TTGAATCCTGGCATGCCTCT 59.373 50.000 35.53 16.17 36.94 3.69
5496 6037 1.135721 GTTTGAATCCTGGCATGCCTC 59.864 52.381 35.53 24.49 36.94 4.70
5499 6079 1.188863 AGGTTTGAATCCTGGCATGC 58.811 50.000 9.90 9.90 33.62 4.06
5523 6103 3.248602 GCTCGTTGACTGTTGAGACAATT 59.751 43.478 0.00 0.00 36.48 2.32
5525 6105 2.159099 AGCTCGTTGACTGTTGAGACAA 60.159 45.455 5.02 0.00 34.85 3.18
5532 6112 1.605712 GGTGCTAGCTCGTTGACTGTT 60.606 52.381 17.23 0.00 0.00 3.16
5554 6134 3.766051 AGCATATCATCGGAGCTATGTGA 59.234 43.478 0.00 0.00 33.06 3.58
5589 6169 2.076863 AGCAACCGTGAAATAGAGCAC 58.923 47.619 0.00 0.00 0.00 4.40
5636 6220 7.360776 GCATCTTGGTTCTTCTACTTTCTCTTG 60.361 40.741 0.00 0.00 0.00 3.02
5648 6232 4.284378 GCATAGTGCATCTTGGTTCTTC 57.716 45.455 0.00 0.00 44.26 2.87
5666 6250 2.402564 ACCATAGCTGTACCTCTGCAT 58.597 47.619 0.00 0.00 42.26 3.96
5671 6255 5.956642 GCTATCTAACCATAGCTGTACCTC 58.043 45.833 0.00 0.00 45.46 3.85
5697 6281 0.038744 ATTCTGTGAAGGCCCCTGTG 59.961 55.000 0.00 0.00 0.00 3.66
5701 6285 0.038166 TGTGATTCTGTGAAGGCCCC 59.962 55.000 0.00 0.00 0.00 5.80
5702 6286 1.457346 CTGTGATTCTGTGAAGGCCC 58.543 55.000 0.00 0.00 0.00 5.80
5704 6288 0.807496 GCCTGTGATTCTGTGAAGGC 59.193 55.000 0.00 0.00 43.05 4.35
5705 6289 2.486472 AGCCTGTGATTCTGTGAAGG 57.514 50.000 0.00 0.00 0.00 3.46
5706 6290 3.681897 GTGTAGCCTGTGATTCTGTGAAG 59.318 47.826 0.00 0.00 0.00 3.02
5708 6292 2.899900 AGTGTAGCCTGTGATTCTGTGA 59.100 45.455 0.00 0.00 0.00 3.58
5710 6294 2.613977 GCAGTGTAGCCTGTGATTCTGT 60.614 50.000 0.00 0.00 34.84 3.41
5711 6295 2.005451 GCAGTGTAGCCTGTGATTCTG 58.995 52.381 0.00 0.00 34.84 3.02
5712 6296 1.625315 TGCAGTGTAGCCTGTGATTCT 59.375 47.619 0.00 0.00 34.84 2.40
5713 6297 2.099141 TGCAGTGTAGCCTGTGATTC 57.901 50.000 0.00 0.00 34.84 2.52
5714 6298 2.290514 ACATGCAGTGTAGCCTGTGATT 60.291 45.455 0.00 0.00 40.95 2.57
5715 6299 1.280133 ACATGCAGTGTAGCCTGTGAT 59.720 47.619 0.00 0.00 40.95 3.06
5716 6300 0.686789 ACATGCAGTGTAGCCTGTGA 59.313 50.000 0.00 0.00 40.95 3.58
5717 6301 1.081892 GACATGCAGTGTAGCCTGTG 58.918 55.000 1.73 0.00 42.22 3.66
5718 6302 0.036010 GGACATGCAGTGTAGCCTGT 60.036 55.000 0.00 0.00 44.30 4.00
5719 6303 0.251354 AGGACATGCAGTGTAGCCTG 59.749 55.000 0.00 0.00 42.36 4.85
5720 6304 0.539051 GAGGACATGCAGTGTAGCCT 59.461 55.000 0.00 1.16 42.36 4.58
5721 6305 0.539051 AGAGGACATGCAGTGTAGCC 59.461 55.000 0.00 0.00 42.36 3.93
5722 6306 2.393271 AAGAGGACATGCAGTGTAGC 57.607 50.000 0.00 0.00 42.36 3.58
5723 6307 4.199432 AGAAAGAGGACATGCAGTGTAG 57.801 45.455 0.00 0.00 42.36 2.74
5724 6308 4.318332 CAAGAAAGAGGACATGCAGTGTA 58.682 43.478 0.00 0.00 42.36 2.90
5725 6309 3.144506 CAAGAAAGAGGACATGCAGTGT 58.855 45.455 0.00 0.00 45.83 3.55
5726 6310 2.486982 CCAAGAAAGAGGACATGCAGTG 59.513 50.000 0.00 0.00 0.00 3.66
5727 6311 2.373169 TCCAAGAAAGAGGACATGCAGT 59.627 45.455 0.00 0.00 0.00 4.40
5728 6312 3.063510 TCCAAGAAAGAGGACATGCAG 57.936 47.619 0.00 0.00 0.00 4.41
5729 6313 3.149196 GTTCCAAGAAAGAGGACATGCA 58.851 45.455 0.00 0.00 32.62 3.96
5730 6314 3.149196 TGTTCCAAGAAAGAGGACATGC 58.851 45.455 0.00 0.00 32.62 4.06
5731 6315 5.005740 TGATGTTCCAAGAAAGAGGACATG 58.994 41.667 0.00 0.00 32.62 3.21
5732 6316 5.246981 TGATGTTCCAAGAAAGAGGACAT 57.753 39.130 0.00 0.00 32.62 3.06
5733 6317 4.705110 TGATGTTCCAAGAAAGAGGACA 57.295 40.909 0.00 0.00 32.62 4.02
5734 6318 4.083802 CGTTGATGTTCCAAGAAAGAGGAC 60.084 45.833 0.00 0.00 32.62 3.85
5757 6348 5.920273 TGTTCTTTTACTTTTGCTATGCTGC 59.080 36.000 0.00 0.00 0.00 5.25
5758 6349 7.928908 TTGTTCTTTTACTTTTGCTATGCTG 57.071 32.000 0.00 0.00 0.00 4.41
5777 6370 2.405892 AACAGCGTGCATCTTTGTTC 57.594 45.000 0.00 0.00 0.00 3.18
5781 6374 2.154462 AGCTAAACAGCGTGCATCTTT 58.846 42.857 0.00 0.00 40.27 2.52
5797 6390 6.996879 CCTGTAGTTGTACCTAGACATAGCTA 59.003 42.308 0.00 0.00 0.00 3.32
5806 6399 5.127194 TGAATGCTCCTGTAGTTGTACCTAG 59.873 44.000 0.00 0.00 0.00 3.02
5810 6403 4.566004 TGTGAATGCTCCTGTAGTTGTAC 58.434 43.478 0.00 0.00 0.00 2.90
5813 6406 3.930336 TCTGTGAATGCTCCTGTAGTTG 58.070 45.455 0.00 0.00 0.00 3.16
5816 6409 5.911752 AGTATTCTGTGAATGCTCCTGTAG 58.088 41.667 5.33 0.00 0.00 2.74
5839 6432 3.072915 TCAAAGGAAAGAGGACATGCAGA 59.927 43.478 0.00 0.00 0.00 4.26
5893 6491 4.667668 GCTCGCAGCTAATTATTGAATCCG 60.668 45.833 0.00 0.00 38.45 4.18
5910 6508 5.180304 TCATGTTGTATTTTGTAAGCTCGCA 59.820 36.000 0.00 0.00 0.00 5.10
5935 6533 3.861840 TGCAGTAGGAATAGCTTGTGAC 58.138 45.455 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.