Multiple sequence alignment - TraesCS5B01G398100

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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 TraesCS5B01G398100 chr5B 100.000 4644 0 0 1 4644 575783480 575778837 0.000000e+00 8576.0
1 TraesCS5B01G398100 chr5B 80.745 322 41 13 4313 4623 635465134 635465445 1.000000e-56 231.0
2 TraesCS5B01G398100 chr5B 77.261 387 53 19 1907 2267 697244965 697244588 1.320000e-45 195.0
3 TraesCS5B01G398100 chr5B 82.412 199 24 6 2080 2267 697568124 697567926 3.720000e-36 163.0
4 TraesCS5B01G398100 chr5B 86.290 124 14 3 2104 2226 697186619 697186498 1.050000e-26 132.0
5 TraesCS5B01G398100 chr5B 82.500 120 11 5 2153 2262 697610158 697610039 3.820000e-16 97.1
6 TraesCS5B01G398100 chr5A 89.622 3305 194 65 1439 4644 589221964 589218710 0.000000e+00 4065.0
7 TraesCS5B01G398100 chr5A 87.328 1089 78 24 403 1443 589223062 589221986 0.000000e+00 1192.0
8 TraesCS5B01G398100 chr5A 86.389 360 22 8 1 360 589223716 589223384 7.340000e-98 368.0
9 TraesCS5B01G398100 chr5A 80.251 319 42 11 4315 4619 603528445 603528134 2.180000e-53 220.0
10 TraesCS5B01G398100 chr5A 80.159 252 34 12 4370 4616 143851113 143851353 1.720000e-39 174.0
11 TraesCS5B01G398100 chr5D 89.757 2304 132 47 2389 4644 469059962 469057715 0.000000e+00 2852.0
12 TraesCS5B01G398100 chr5D 87.122 1522 101 40 1 1468 469062370 469060890 0.000000e+00 1637.0
13 TraesCS5B01G398100 chr5D 89.097 853 44 19 1523 2341 469060797 469059960 0.000000e+00 1014.0
14 TraesCS5B01G398100 chr5D 88.350 103 11 1 2104 2205 553507083 553507185 6.310000e-24 122.0
15 TraesCS5B01G398100 chr5D 81.560 141 22 2 2061 2197 553483873 553484013 3.800000e-21 113.0
16 TraesCS5B01G398100 chr5D 89.286 84 6 3 1387 1470 469060889 469060809 8.220000e-18 102.0
17 TraesCS5B01G398100 chr2A 83.154 279 38 7 4326 4599 104867696 104867970 3.590000e-61 246.0
18 TraesCS5B01G398100 chr2B 82.007 289 41 10 4314 4597 354071733 354072015 7.770000e-58 235.0
19 TraesCS5B01G398100 chr2B 77.468 395 57 20 4246 4623 162871807 162872186 1.690000e-49 207.0
20 TraesCS5B01G398100 chr4D 78.358 402 50 18 4227 4623 37521129 37520760 4.680000e-55 226.0
21 TraesCS5B01G398100 chr4D 77.904 353 55 15 4279 4623 44758871 44758534 1.020000e-46 198.0
22 TraesCS5B01G398100 chr7B 76.683 416 64 19 4223 4623 84488898 84488501 2.830000e-47 200.0
23 TraesCS5B01G398100 chr6D 81.933 238 34 9 4324 4554 409339580 409339345 4.740000e-45 193.0
24 TraesCS5B01G398100 chr6B 77.536 276 37 14 4369 4626 614304706 614304438 4.840000e-30 143.0


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 TraesCS5B01G398100 chr5B 575778837 575783480 4643 True 8576.00 8576 100.000000 1 4644 1 chr5B.!!$R1 4643
1 TraesCS5B01G398100 chr5A 589218710 589223716 5006 True 1875.00 4065 87.779667 1 4644 3 chr5A.!!$R2 4643
2 TraesCS5B01G398100 chr5D 469057715 469062370 4655 True 1401.25 2852 88.815500 1 4644 4 chr5D.!!$R1 4643

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
578 881 0.035598 TCTTTTCCCGTTCGCCATCA 59.964 50.0 0.0 0.00 0.00 3.07 F
663 971 0.595095 GTTGCTGCCCAGTCAGAAAG 59.405 55.0 0.0 0.00 32.51 2.62 F
1373 1742 0.713883 CCGTCACCATTCGAAACTCG 59.286 55.0 0.0 2.05 42.10 4.18 F
1378 1747 0.872388 ACCATTCGAAACTCGGTTGC 59.128 50.0 0.0 0.00 40.88 4.17 F
3190 3670 0.179111 TTATTCTGCACCCGAGAGCG 60.179 55.0 0.0 0.00 31.34 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1515 1910 1.168714 GTAACCTTCCTTGCAGCTGG 58.831 55.000 17.12 0.0 0.00 4.85 R
1615 2048 1.482593 ACCCAACTATTCAGCTCCTCG 59.517 52.381 0.00 0.0 0.00 4.63 R
3101 3581 0.038599 ATCCAGCTCCACATGCAACA 59.961 50.000 0.00 0.0 0.00 3.33 R
3283 3763 1.066071 GGTACCTGGAAGAAGTCTGCC 60.066 57.143 4.06 0.0 42.39 4.85 R
4225 4762 1.135575 CAAAGCCGAGAAACTCCATGC 60.136 52.381 0.00 0.0 0.00 4.06 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
23 24 6.057627 GCAGATGGATTGTCTGATAACTTG 57.942 41.667 7.28 0.00 44.57 3.16
58 59 2.281762 CGGCTTTGTACGATAAGAGTGC 59.718 50.000 0.00 0.00 0.00 4.40
82 83 5.404066 CGACATGCGTATGAATAATGTGGTA 59.596 40.000 20.86 0.00 37.73 3.25
169 173 4.956075 ACTTGTGTTGTTTCCAATCCTTCT 59.044 37.500 0.00 0.00 32.11 2.85
170 174 4.916983 TGTGTTGTTTCCAATCCTTCTG 57.083 40.909 0.00 0.00 32.11 3.02
191 195 8.413309 TTCTGTCATGATGAATTTTTCCTCTT 57.587 30.769 0.00 0.00 0.00 2.85
192 196 8.048534 TCTGTCATGATGAATTTTTCCTCTTC 57.951 34.615 0.00 0.00 0.00 2.87
193 197 7.121759 TCTGTCATGATGAATTTTTCCTCTTCC 59.878 37.037 0.00 0.00 0.00 3.46
194 198 6.950041 TGTCATGATGAATTTTTCCTCTTCCT 59.050 34.615 0.00 0.00 0.00 3.36
209 213 0.684535 TTCCTCCATGACGTTGAGCA 59.315 50.000 0.00 0.00 0.00 4.26
214 218 1.344438 TCCATGACGTTGAGCAAGAGT 59.656 47.619 0.00 0.00 0.00 3.24
225 229 8.149973 ACGTTGAGCAAGAGTAAATTTTCTTA 57.850 30.769 5.09 0.00 32.62 2.10
233 237 9.463443 GCAAGAGTAAATTTTCTTATTGTGTGT 57.537 29.630 17.25 0.00 32.62 3.72
241 245 6.691754 TTTTCTTATTGTGTGTTGCAGAGA 57.308 33.333 0.00 0.00 0.00 3.10
242 246 6.691754 TTTCTTATTGTGTGTTGCAGAGAA 57.308 33.333 0.00 0.00 0.00 2.87
243 247 6.691754 TTCTTATTGTGTGTTGCAGAGAAA 57.308 33.333 0.00 0.00 0.00 2.52
244 248 6.691754 TCTTATTGTGTGTTGCAGAGAAAA 57.308 33.333 0.00 0.00 0.00 2.29
245 249 7.094508 TCTTATTGTGTGTTGCAGAGAAAAA 57.905 32.000 0.00 0.00 0.00 1.94
246 250 7.195646 TCTTATTGTGTGTTGCAGAGAAAAAG 58.804 34.615 0.00 0.00 0.00 2.27
247 251 5.581126 ATTGTGTGTTGCAGAGAAAAAGA 57.419 34.783 0.00 0.00 0.00 2.52
248 252 5.384063 TTGTGTGTTGCAGAGAAAAAGAA 57.616 34.783 0.00 0.00 0.00 2.52
249 253 5.384063 TGTGTGTTGCAGAGAAAAAGAAA 57.616 34.783 0.00 0.00 0.00 2.52
250 254 5.964758 TGTGTGTTGCAGAGAAAAAGAAAT 58.035 33.333 0.00 0.00 0.00 2.17
251 255 6.035843 TGTGTGTTGCAGAGAAAAAGAAATC 58.964 36.000 0.00 0.00 0.00 2.17
252 256 6.127647 TGTGTGTTGCAGAGAAAAAGAAATCT 60.128 34.615 0.00 0.00 0.00 2.40
253 257 6.416161 GTGTGTTGCAGAGAAAAAGAAATCTC 59.584 38.462 0.00 0.00 41.92 2.75
285 289 3.374506 TCTCCGCTGAGATGCAATG 57.625 52.632 3.40 0.00 42.73 2.82
286 290 0.179065 TCTCCGCTGAGATGCAATGG 60.179 55.000 3.40 0.00 42.73 3.16
287 291 0.179065 CTCCGCTGAGATGCAATGGA 60.179 55.000 0.00 0.00 41.42 3.41
288 292 0.462581 TCCGCTGAGATGCAATGGAC 60.463 55.000 0.00 0.00 0.00 4.02
294 298 4.201940 CGCTGAGATGCAATGGACAAATTA 60.202 41.667 0.00 0.00 0.00 1.40
297 301 6.405065 GCTGAGATGCAATGGACAAATTAGAA 60.405 38.462 0.00 0.00 0.00 2.10
298 302 7.092137 TGAGATGCAATGGACAAATTAGAAG 57.908 36.000 0.00 0.00 0.00 2.85
300 304 7.093322 AGATGCAATGGACAAATTAGAAGAC 57.907 36.000 0.00 0.00 0.00 3.01
386 390 5.634859 GGTGCCATTTGAACAGTTTGAATAG 59.365 40.000 0.00 0.00 0.00 1.73
394 398 3.928727 ACAGTTTGAATAGACGTCCGA 57.071 42.857 13.01 0.16 0.00 4.55
396 400 4.817517 ACAGTTTGAATAGACGTCCGATT 58.182 39.130 13.01 12.37 0.00 3.34
419 720 4.277174 TCAAGCTTATTTTTCTTGGCACGA 59.723 37.500 0.00 0.00 38.13 4.35
422 723 3.833442 CTTATTTTTCTTGGCACGACCC 58.167 45.455 0.00 0.00 37.83 4.46
432 733 3.706600 TGGCACGACCCTAATTTTACT 57.293 42.857 0.00 0.00 37.83 2.24
461 762 1.263217 GATGAAACTCCGCAACGTGTT 59.737 47.619 0.00 0.00 0.00 3.32
462 763 0.375454 TGAAACTCCGCAACGTGTTG 59.625 50.000 8.35 8.35 43.14 3.33
486 787 2.795175 GCATCTGCTTTCATCCATGG 57.205 50.000 4.97 4.97 38.21 3.66
491 792 2.041485 TCTGCTTTCATCCATGGTTCCA 59.959 45.455 12.58 0.00 0.00 3.53
547 850 5.044428 GTAGTGACGACATGTAGTGTTCT 57.956 43.478 16.82 12.76 42.36 3.01
548 851 4.585955 AGTGACGACATGTAGTGTTCTT 57.414 40.909 16.82 0.00 42.36 2.52
549 852 5.700722 AGTGACGACATGTAGTGTTCTTA 57.299 39.130 16.82 0.00 42.36 2.10
567 870 8.127327 GTGTTCTTAGTACAACTTTCTTTTCCC 58.873 37.037 0.00 0.00 0.00 3.97
568 871 7.011669 TGTTCTTAGTACAACTTTCTTTTCCCG 59.988 37.037 0.00 0.00 0.00 5.14
569 872 6.585416 TCTTAGTACAACTTTCTTTTCCCGT 58.415 36.000 0.00 0.00 0.00 5.28
570 873 7.049754 TCTTAGTACAACTTTCTTTTCCCGTT 58.950 34.615 0.00 0.00 0.00 4.44
571 874 5.746307 AGTACAACTTTCTTTTCCCGTTC 57.254 39.130 0.00 0.00 0.00 3.95
572 875 3.685836 ACAACTTTCTTTTCCCGTTCG 57.314 42.857 0.00 0.00 0.00 3.95
573 876 2.223409 ACAACTTTCTTTTCCCGTTCGC 60.223 45.455 0.00 0.00 0.00 4.70
574 877 0.949397 ACTTTCTTTTCCCGTTCGCC 59.051 50.000 0.00 0.00 0.00 5.54
575 878 0.948678 CTTTCTTTTCCCGTTCGCCA 59.051 50.000 0.00 0.00 0.00 5.69
578 881 0.035598 TCTTTTCCCGTTCGCCATCA 59.964 50.000 0.00 0.00 0.00 3.07
579 882 1.094785 CTTTTCCCGTTCGCCATCAT 58.905 50.000 0.00 0.00 0.00 2.45
580 883 1.064060 CTTTTCCCGTTCGCCATCATC 59.936 52.381 0.00 0.00 0.00 2.92
603 911 5.242838 TCCATTCTGCTTTCGTAAATGGTTT 59.757 36.000 11.10 0.00 44.32 3.27
663 971 0.595095 GTTGCTGCCCAGTCAGAAAG 59.405 55.000 0.00 0.00 32.51 2.62
704 1012 1.408702 TGGAACAAAAGGAGCAAGTGC 59.591 47.619 0.00 0.00 36.85 4.40
793 1133 1.000938 CACACAAAGAGCAAGGAAGCC 60.001 52.381 0.00 0.00 34.23 4.35
833 1173 4.035102 GGGCCGTCCAAAGCTCCT 62.035 66.667 0.00 0.00 35.00 3.69
834 1174 2.747855 GGCCGTCCAAAGCTCCTG 60.748 66.667 0.00 0.00 0.00 3.86
849 1189 3.252284 CTGACAGGTGGGCCCACT 61.252 66.667 45.38 31.64 45.52 4.00
879 1219 1.348250 CAATCGCAATCCACCGACG 59.652 57.895 0.00 0.00 36.18 5.12
880 1220 1.079405 AATCGCAATCCACCGACGT 60.079 52.632 0.00 0.00 36.18 4.34
881 1221 1.082117 AATCGCAATCCACCGACGTC 61.082 55.000 5.18 5.18 36.18 4.34
1149 1517 4.329545 CCTGTGGTGGGTGTCCGG 62.330 72.222 0.00 0.00 35.24 5.14
1333 1701 1.197430 ACCTCCTCTGGTGCTTCCTG 61.197 60.000 0.00 0.67 39.17 3.86
1367 1736 4.090588 GCCCCCGTCACCATTCGA 62.091 66.667 0.00 0.00 0.00 3.71
1373 1742 0.713883 CCGTCACCATTCGAAACTCG 59.286 55.000 0.00 2.05 42.10 4.18
1375 1744 1.792006 GTCACCATTCGAAACTCGGT 58.208 50.000 0.00 3.95 40.88 4.69
1377 1746 2.096417 GTCACCATTCGAAACTCGGTTG 60.096 50.000 0.00 0.00 40.88 3.77
1378 1747 0.872388 ACCATTCGAAACTCGGTTGC 59.128 50.000 0.00 0.00 40.88 4.17
1379 1748 1.156736 CCATTCGAAACTCGGTTGCT 58.843 50.000 0.00 0.00 40.88 3.91
1380 1749 1.135972 CCATTCGAAACTCGGTTGCTG 60.136 52.381 0.00 0.00 40.88 4.41
1381 1750 1.531149 CATTCGAAACTCGGTTGCTGT 59.469 47.619 0.00 0.00 40.88 4.40
1382 1751 1.658994 TTCGAAACTCGGTTGCTGTT 58.341 45.000 0.00 0.00 40.88 3.16
1434 1803 7.710907 GCATAAATGATGTGGAGTAACTAGTGA 59.289 37.037 0.00 0.00 37.90 3.41
1443 1838 9.654663 ATGTGGAGTAACTAGTGATAGTTTTTC 57.345 33.333 6.02 5.04 40.43 2.29
1468 1863 5.008316 GTGACTTCTTCTAGTAGAGGCTAGC 59.992 48.000 6.04 6.04 38.58 3.42
1469 1864 5.118729 ACTTCTTCTAGTAGAGGCTAGCA 57.881 43.478 18.24 0.00 38.58 3.49
1501 1896 7.116519 GGTAGCCGAGTTCAATTAGTTATCATC 59.883 40.741 0.00 0.00 0.00 2.92
1515 1910 2.981859 ATCATCACGTTGGGTAGGAC 57.018 50.000 0.00 0.00 0.00 3.85
1552 1985 4.135153 AGCTACGGCACCGCTGAG 62.135 66.667 9.43 5.47 44.19 3.35
1605 2038 7.767261 ACAGTTCAACTTTTGTATGCTTGTTA 58.233 30.769 0.00 0.00 0.00 2.41
1615 2048 8.795786 TTTTGTATGCTTGTTAGTGTTTGATC 57.204 30.769 0.00 0.00 0.00 2.92
1623 2056 3.258372 TGTTAGTGTTTGATCGAGGAGCT 59.742 43.478 0.00 0.00 0.00 4.09
1629 2062 4.505922 GTGTTTGATCGAGGAGCTGAATAG 59.494 45.833 0.00 0.00 0.00 1.73
1699 2141 6.145371 GTGTACATATGGTTTGCCTTTTGTTG 59.855 38.462 7.80 0.00 36.24 3.33
1921 2379 9.760077 CCTGGTTACTAAGGTATATGTGTTTAG 57.240 37.037 0.00 0.00 0.00 1.85
1928 2395 8.104566 ACTAAGGTATATGTGTTTAGTTGCCAA 58.895 33.333 0.00 0.00 32.30 4.52
2023 2501 9.502091 GTAATGTTGCCCATTGTATATTCTCTA 57.498 33.333 8.52 0.00 43.63 2.43
2068 2546 2.028839 CAGTTTCATTGATTGGCAGGCA 60.029 45.455 0.00 0.00 0.00 4.75
2279 2757 1.681229 ATGTTACCCCTCCATGGTGT 58.319 50.000 12.58 7.82 36.57 4.16
2296 2775 6.699642 CCATGGTGTGACGTTTCTTTATTTTT 59.300 34.615 2.57 0.00 0.00 1.94
2356 2835 6.816134 GTAAGTATTACCCCCGTTTGAAAA 57.184 37.500 0.00 0.00 45.64 2.29
2357 2836 7.395190 GTAAGTATTACCCCCGTTTGAAAAT 57.605 36.000 0.00 0.00 45.64 1.82
2358 2837 8.504812 GTAAGTATTACCCCCGTTTGAAAATA 57.495 34.615 0.00 0.00 45.64 1.40
2359 2838 8.955388 GTAAGTATTACCCCCGTTTGAAAATAA 58.045 33.333 0.00 0.00 45.64 1.40
2360 2839 7.634671 AGTATTACCCCCGTTTGAAAATAAG 57.365 36.000 0.00 0.00 0.00 1.73
2361 2840 7.177184 AGTATTACCCCCGTTTGAAAATAAGT 58.823 34.615 0.00 0.00 0.00 2.24
2362 2841 6.921486 ATTACCCCCGTTTGAAAATAAGTT 57.079 33.333 0.00 0.00 0.00 2.66
2363 2842 8.955388 GTATTACCCCCGTTTGAAAATAAGTTA 58.045 33.333 0.00 0.00 0.00 2.24
2364 2843 5.710513 ACCCCCGTTTGAAAATAAGTTAC 57.289 39.130 0.00 0.00 0.00 2.50
2365 2844 4.216042 ACCCCCGTTTGAAAATAAGTTACG 59.784 41.667 0.00 0.00 0.00 3.18
2447 2926 7.861176 TGCAACGGAAACAAATTAACTATTC 57.139 32.000 0.00 0.00 0.00 1.75
2582 3061 6.234177 CAGGGTCTTATCTCTTGAAAGTTGT 58.766 40.000 0.00 0.00 0.00 3.32
2607 3086 8.520351 GTTACTATAAAATGAGTTTTGGGCTGT 58.480 33.333 0.00 0.00 38.01 4.40
2666 3145 6.845302 TCACTCTATGTTGTTTCATTGCATC 58.155 36.000 0.00 0.00 0.00 3.91
2694 3173 2.629137 TGCTGCAGGTTGATGTTTGAAT 59.371 40.909 17.12 0.00 0.00 2.57
2704 3183 9.132521 CAGGTTGATGTTTGAATGATAGTTTTC 57.867 33.333 0.00 0.00 0.00 2.29
2705 3184 9.082313 AGGTTGATGTTTGAATGATAGTTTTCT 57.918 29.630 0.00 0.00 0.00 2.52
2706 3185 9.346725 GGTTGATGTTTGAATGATAGTTTTCTC 57.653 33.333 0.00 0.00 0.00 2.87
2707 3186 9.897744 GTTGATGTTTGAATGATAGTTTTCTCA 57.102 29.630 0.00 0.00 0.00 3.27
2710 3189 8.922058 ATGTTTGAATGATAGTTTTCTCATGC 57.078 30.769 0.00 0.00 32.56 4.06
2711 3190 8.114331 TGTTTGAATGATAGTTTTCTCATGCT 57.886 30.769 0.00 0.00 32.56 3.79
2712 3191 8.579006 TGTTTGAATGATAGTTTTCTCATGCTT 58.421 29.630 0.00 0.00 32.56 3.91
2745 3224 4.288626 AGGGAACTGTATGTTAGCTTTGGA 59.711 41.667 0.00 0.00 41.13 3.53
2888 3367 6.463049 GCTTACAGGAGTCTATGGCTTGATTA 60.463 42.308 0.00 0.00 0.00 1.75
2938 3417 1.212935 AGGCTACCTGGTAATTGGCTG 59.787 52.381 16.57 2.09 29.57 4.85
2945 3424 2.423538 CCTGGTAATTGGCTGCACTAAC 59.576 50.000 0.50 0.00 0.00 2.34
3056 3536 4.214119 CCAGCATATTACCAGTATGTGTGC 59.786 45.833 0.00 0.00 33.19 4.57
3101 3581 0.385390 CGCTGTTTGGCTGTTTCCTT 59.615 50.000 0.00 0.00 0.00 3.36
3102 3582 1.856802 GCTGTTTGGCTGTTTCCTTG 58.143 50.000 0.00 0.00 0.00 3.61
3182 3662 7.442364 TCATATTGTTCTAGCTTATTCTGCACC 59.558 37.037 0.00 0.00 0.00 5.01
3183 3663 3.873910 TGTTCTAGCTTATTCTGCACCC 58.126 45.455 0.00 0.00 0.00 4.61
3190 3670 0.179111 TTATTCTGCACCCGAGAGCG 60.179 55.000 0.00 0.00 31.34 5.03
3223 3703 2.972625 TGTCTATTGTGCAGGCTGTAC 58.027 47.619 26.19 26.19 33.42 2.90
3233 3713 1.800805 CAGGCTGTACAACCTCACTG 58.199 55.000 15.07 1.47 32.56 3.66
3250 3730 1.349026 ACTGCTGTCTGTTACCATGCT 59.651 47.619 0.00 0.00 0.00 3.79
3281 3761 5.545063 TCCACTTCTGTATGTGACTTTCA 57.455 39.130 0.00 0.00 36.38 2.69
3283 3763 5.934043 TCCACTTCTGTATGTGACTTTCATG 59.066 40.000 0.00 0.00 36.38 3.07
3292 3772 3.141398 TGTGACTTTCATGGCAGACTTC 58.859 45.455 0.00 0.00 0.00 3.01
3349 3853 6.069556 ACCTCTCTGTACTTGTATCTGGAGTA 60.070 42.308 0.00 0.00 0.00 2.59
3354 3858 9.522804 CTCTGTACTTGTATCTGGAGTATTTTC 57.477 37.037 0.00 0.00 0.00 2.29
3374 3878 1.605710 CTGTGCCTTCTTGTTCCTGTG 59.394 52.381 0.00 0.00 0.00 3.66
3510 4015 2.620585 GGATTAAACCTGCCTGCAGATC 59.379 50.000 20.29 13.50 46.30 2.75
3571 4076 1.339610 CGGAGTAGCTTCATCCTGGAG 59.660 57.143 1.52 0.00 0.00 3.86
3573 4078 3.238597 GGAGTAGCTTCATCCTGGAGAT 58.761 50.000 1.52 0.00 34.66 2.75
3693 4200 2.756760 CCTTTGTCATCATCTGTTGGGG 59.243 50.000 0.00 0.00 0.00 4.96
3741 4251 1.295792 CCAATTACCCATCACGACGG 58.704 55.000 0.00 0.00 0.00 4.79
3832 4342 1.803555 GTTCTGGCAGCTCTCTTGAAC 59.196 52.381 10.34 2.85 0.00 3.18
3836 4346 0.392327 GGCAGCTCTCTTGAACCTCC 60.392 60.000 0.00 0.00 0.00 4.30
3857 4367 2.033550 CCTCGCTGCTAGTGTTACTAGG 59.966 54.545 15.53 3.81 46.31 3.02
3858 4368 2.022195 TCGCTGCTAGTGTTACTAGGG 58.978 52.381 15.53 3.78 46.31 3.53
3859 4369 1.749634 CGCTGCTAGTGTTACTAGGGT 59.250 52.381 15.53 0.00 46.31 4.34
3860 4370 2.947652 CGCTGCTAGTGTTACTAGGGTA 59.052 50.000 15.53 0.00 46.31 3.69
3863 4380 5.334724 CGCTGCTAGTGTTACTAGGGTATAC 60.335 48.000 15.53 0.00 46.31 1.47
3866 4383 7.201893 GCTGCTAGTGTTACTAGGGTATACTTT 60.202 40.741 15.53 0.00 46.31 2.66
3932 4452 0.171903 GCACACATGGCATCCTTGTC 59.828 55.000 0.00 0.00 39.41 3.18
4013 4542 6.129247 GCGACAGTAGTTATTTATTACGGCTC 60.129 42.308 0.00 0.00 0.00 4.70
4048 4584 0.734253 CGCTGAAGTTCCGTGAGAGG 60.734 60.000 1.94 0.00 0.00 3.69
4055 4591 2.943449 GTTCCGTGAGAGGGACTTAG 57.057 55.000 0.00 0.00 41.55 2.18
4056 4592 2.444421 GTTCCGTGAGAGGGACTTAGA 58.556 52.381 0.00 0.00 41.55 2.10
4057 4593 2.125773 TCCGTGAGAGGGACTTAGAC 57.874 55.000 0.00 0.00 41.55 2.59
4058 4594 0.733729 CCGTGAGAGGGACTTAGACG 59.266 60.000 0.00 0.00 41.55 4.18
4060 4596 2.082231 CGTGAGAGGGACTTAGACGAA 58.918 52.381 0.00 0.00 41.55 3.85
4062 4598 2.424246 GTGAGAGGGACTTAGACGAAGG 59.576 54.545 0.21 0.00 41.55 3.46
4063 4599 2.041350 TGAGAGGGACTTAGACGAAGGT 59.959 50.000 0.21 0.00 41.55 3.50
4112 4648 0.317854 GCTTCAACGGGCTGAAACAC 60.318 55.000 0.00 0.00 34.96 3.32
4113 4649 0.041312 CTTCAACGGGCTGAAACACG 60.041 55.000 0.00 0.00 34.96 4.49
4114 4650 2.051345 CAACGGGCTGAAACACGC 60.051 61.111 0.00 0.00 0.00 5.34
4171 4708 1.666553 TTAGCTGCGTTCACCCGTG 60.667 57.895 0.00 0.00 0.00 4.94
4225 4762 0.523072 CAAATGCTCTTGGACACGGG 59.477 55.000 0.00 0.00 0.00 5.28
4243 4780 0.678048 GGCATGGAGTTTCTCGGCTT 60.678 55.000 0.00 0.00 0.00 4.35
4274 4812 7.177216 TCAAATGAGCCAGATGAACAGTAAAAT 59.823 33.333 0.00 0.00 0.00 1.82
4378 4922 4.401022 AGTTTCAGCTGGAATCACATTCA 58.599 39.130 11.48 0.00 41.03 2.57
4381 4925 3.284617 TCAGCTGGAATCACATTCATGG 58.715 45.455 15.13 0.00 41.03 3.66
4386 4930 4.883585 GCTGGAATCACATTCATGGAAGTA 59.116 41.667 0.00 0.00 41.03 2.24
4422 4966 6.506500 AAAAGATTGATGCTTCGAAGATGT 57.493 33.333 28.95 12.80 35.04 3.06
4430 4974 5.931724 TGATGCTTCGAAGATGTTACTTTCA 59.068 36.000 28.95 12.66 35.04 2.69
4511 5055 4.691685 TGATGATGAAAATTTGCAAGCACC 59.308 37.500 2.14 0.00 0.00 5.01
4527 5071 5.469479 CAAGCACCCGAAACATTTCTTAAT 58.531 37.500 3.04 0.00 35.07 1.40
4528 5072 5.059404 AGCACCCGAAACATTTCTTAATG 57.941 39.130 3.04 0.00 45.39 1.90
4625 5172 6.551385 AGCTCATATTAGGATTTTCGCTTG 57.449 37.500 0.00 0.00 0.00 4.01
4629 5176 5.465390 TCATATTAGGATTTTCGCTTGGACG 59.535 40.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 4.211164 ACCACATTATTCATACGCATGTCG 59.789 41.667 7.79 7.79 45.38 4.35
82 83 6.653320 TCTGAAAATGGCGAACAAAGTATAGT 59.347 34.615 0.00 0.00 0.00 2.12
169 173 6.950041 AGGAAGAGGAAAAATTCATCATGACA 59.050 34.615 0.00 0.00 42.56 3.58
170 174 7.401955 AGGAAGAGGAAAAATTCATCATGAC 57.598 36.000 0.00 0.00 42.56 3.06
191 195 0.684535 TTGCTCAACGTCATGGAGGA 59.315 50.000 0.00 0.00 0.00 3.71
192 196 1.081892 CTTGCTCAACGTCATGGAGG 58.918 55.000 0.00 0.00 0.00 4.30
193 197 1.998315 CTCTTGCTCAACGTCATGGAG 59.002 52.381 0.00 0.00 0.00 3.86
194 198 1.344438 ACTCTTGCTCAACGTCATGGA 59.656 47.619 0.00 0.00 0.00 3.41
214 218 9.462174 CTCTGCAACACACAATAAGAAAATTTA 57.538 29.630 0.00 0.00 0.00 1.40
225 229 5.581126 TCTTTTTCTCTGCAACACACAAT 57.419 34.783 0.00 0.00 0.00 2.71
228 232 6.268566 AGATTTCTTTTTCTCTGCAACACAC 58.731 36.000 0.00 0.00 0.00 3.82
270 274 0.745486 TGTCCATTGCATCTCAGCGG 60.745 55.000 0.00 0.00 37.31 5.52
322 326 8.834465 GTGTACTCCAAGACGAGTAAGATAATA 58.166 37.037 0.23 0.00 44.79 0.98
324 328 6.883217 AGTGTACTCCAAGACGAGTAAGATAA 59.117 38.462 0.23 0.00 44.79 1.75
386 390 4.859629 AAATAAGCTTGAATCGGACGTC 57.140 40.909 9.86 7.13 0.00 4.34
394 398 5.634859 CGTGCCAAGAAAAATAAGCTTGAAT 59.365 36.000 9.86 0.00 41.03 2.57
396 400 4.277174 TCGTGCCAAGAAAAATAAGCTTGA 59.723 37.500 9.86 0.00 41.03 3.02
419 720 3.340928 GACGGCACAGTAAAATTAGGGT 58.659 45.455 0.00 0.00 0.00 4.34
422 723 4.565166 TCATCGACGGCACAGTAAAATTAG 59.435 41.667 0.00 0.00 0.00 1.73
432 733 0.669318 GGAGTTTCATCGACGGCACA 60.669 55.000 0.00 0.00 0.00 4.57
469 770 3.294214 GGAACCATGGATGAAAGCAGAT 58.706 45.455 21.47 0.00 0.00 2.90
491 792 9.757227 TCGTGTTTTATTTCATTTTCAAGGAAT 57.243 25.926 0.00 0.00 30.58 3.01
515 818 1.368493 CGTCACTACGCGGGTATCG 60.368 63.158 12.47 12.41 43.12 2.92
534 837 9.257651 GAAAGTTGTACTAAGAACACTACATGT 57.742 33.333 2.69 2.69 46.42 3.21
537 840 9.880157 AAAGAAAGTTGTACTAAGAACACTACA 57.120 29.630 0.00 0.00 31.39 2.74
541 844 8.127327 GGGAAAAGAAAGTTGTACTAAGAACAC 58.873 37.037 0.00 0.00 31.39 3.32
542 845 7.011669 CGGGAAAAGAAAGTTGTACTAAGAACA 59.988 37.037 0.00 0.00 31.39 3.18
543 846 7.011763 ACGGGAAAAGAAAGTTGTACTAAGAAC 59.988 37.037 0.00 0.00 0.00 3.01
545 848 6.585416 ACGGGAAAAGAAAGTTGTACTAAGA 58.415 36.000 0.00 0.00 0.00 2.10
547 850 6.018832 CGAACGGGAAAAGAAAGTTGTACTAA 60.019 38.462 0.00 0.00 0.00 2.24
548 851 5.463061 CGAACGGGAAAAGAAAGTTGTACTA 59.537 40.000 0.00 0.00 0.00 1.82
549 852 4.271776 CGAACGGGAAAAGAAAGTTGTACT 59.728 41.667 0.00 0.00 0.00 2.73
567 870 1.262417 CAGAATGGATGATGGCGAACG 59.738 52.381 0.00 0.00 0.00 3.95
568 871 1.002033 GCAGAATGGATGATGGCGAAC 60.002 52.381 0.00 0.00 35.86 3.95
569 872 1.134007 AGCAGAATGGATGATGGCGAA 60.134 47.619 0.00 0.00 35.86 4.70
570 873 0.471191 AGCAGAATGGATGATGGCGA 59.529 50.000 0.00 0.00 35.86 5.54
571 874 1.315690 AAGCAGAATGGATGATGGCG 58.684 50.000 0.00 0.00 35.86 5.69
572 875 2.287427 CGAAAGCAGAATGGATGATGGC 60.287 50.000 0.00 0.00 35.86 4.40
573 876 2.947652 ACGAAAGCAGAATGGATGATGG 59.052 45.455 0.00 0.00 35.86 3.51
574 877 5.739752 TTACGAAAGCAGAATGGATGATG 57.260 39.130 0.00 0.00 35.86 3.07
575 878 6.238842 CCATTTACGAAAGCAGAATGGATGAT 60.239 38.462 7.46 0.00 44.26 2.45
578 881 4.949856 ACCATTTACGAAAGCAGAATGGAT 59.050 37.500 17.50 2.72 44.26 3.41
579 882 4.331968 ACCATTTACGAAAGCAGAATGGA 58.668 39.130 17.50 0.00 44.26 3.41
580 883 4.701956 ACCATTTACGAAAGCAGAATGG 57.298 40.909 10.87 10.87 45.62 3.16
603 911 1.741028 TTGTGGGGAATGACTGGAGA 58.259 50.000 0.00 0.00 0.00 3.71
613 921 0.178967 TGCTCATGCTTTGTGGGGAA 60.179 50.000 0.00 0.00 40.48 3.97
793 1133 1.480219 GCGAACCGATCCGCTACTTG 61.480 60.000 6.80 0.00 46.96 3.16
879 1219 1.268133 CGATCGGAAGGAAGAGACGAC 60.268 57.143 7.38 0.00 36.32 4.34
880 1220 1.015109 CGATCGGAAGGAAGAGACGA 58.985 55.000 7.38 0.00 38.00 4.20
881 1221 1.015109 TCGATCGGAAGGAAGAGACG 58.985 55.000 16.41 0.00 0.00 4.18
1358 1727 1.399727 GCAACCGAGTTTCGAATGGTG 60.400 52.381 0.00 0.00 43.74 4.17
1362 1731 1.878953 ACAGCAACCGAGTTTCGAAT 58.121 45.000 0.00 0.00 43.74 3.34
1387 1756 3.553922 GCATCCGAATTCACCCAAAACAA 60.554 43.478 6.22 0.00 0.00 2.83
1389 1758 2.029470 TGCATCCGAATTCACCCAAAAC 60.029 45.455 6.22 0.00 0.00 2.43
1404 1773 6.488006 AGTTACTCCACATCATTTATGCATCC 59.512 38.462 0.19 0.00 39.39 3.51
1434 1803 9.843334 CTACTAGAAGAAGTCACGAAAAACTAT 57.157 33.333 0.00 0.00 0.00 2.12
1443 1838 3.942748 AGCCTCTACTAGAAGAAGTCACG 59.057 47.826 0.00 0.00 0.00 4.35
1468 1863 3.587797 TGAACTCGGCTACCTACTTTG 57.412 47.619 0.00 0.00 0.00 2.77
1469 1864 4.820894 ATTGAACTCGGCTACCTACTTT 57.179 40.909 0.00 0.00 0.00 2.66
1480 1875 6.475727 ACGTGATGATAACTAATTGAACTCGG 59.524 38.462 0.00 0.00 0.00 4.63
1501 1896 1.375523 GCTGGTCCTACCCAACGTG 60.376 63.158 0.00 0.00 37.50 4.49
1515 1910 1.168714 GTAACCTTCCTTGCAGCTGG 58.831 55.000 17.12 0.00 0.00 4.85
1552 1985 5.358298 AAGACTAAGAACGCAAATTCACC 57.642 39.130 0.00 0.00 0.00 4.02
1605 2038 1.895798 TCAGCTCCTCGATCAAACACT 59.104 47.619 0.00 0.00 0.00 3.55
1615 2048 1.482593 ACCCAACTATTCAGCTCCTCG 59.517 52.381 0.00 0.00 0.00 4.63
1623 2056 6.691255 ACCTAACTTGTACCCAACTATTCA 57.309 37.500 0.00 0.00 0.00 2.57
1629 2062 5.735285 AGTCTACCTAACTTGTACCCAAC 57.265 43.478 0.00 0.00 0.00 3.77
1689 2131 3.181511 GCCAAGTTGAAACAACAAAAGGC 60.182 43.478 15.29 16.06 36.69 4.35
1699 2141 4.545610 TCATTCGATTGCCAAGTTGAAAC 58.454 39.130 3.87 0.00 0.00 2.78
1921 2379 2.456577 ACCCCATAGAACATTGGCAAC 58.543 47.619 0.00 0.00 0.00 4.17
1928 2395 6.491403 GCTCATTCAATTACCCCATAGAACAT 59.509 38.462 0.00 0.00 0.00 2.71
2001 2470 8.995027 AAATAGAGAATATACAATGGGCAACA 57.005 30.769 0.00 0.00 39.74 3.33
2086 2564 1.642762 ACATTCCATGAGAAGGCCCTT 59.357 47.619 0.00 0.00 39.95 3.95
2279 2757 7.763356 TGAACTGGAAAAATAAAGAAACGTCA 58.237 30.769 0.00 0.00 0.00 4.35
2296 2775 6.777091 CCCCATCATACATTATTTGAACTGGA 59.223 38.462 0.00 0.00 0.00 3.86
2346 2825 5.750650 ACCACGTAACTTATTTTCAAACGG 58.249 37.500 0.00 0.00 33.44 4.44
2347 2826 7.667984 AAACCACGTAACTTATTTTCAAACG 57.332 32.000 0.00 0.00 35.17 3.60
2351 2830 9.934190 GAACTAAAACCACGTAACTTATTTTCA 57.066 29.630 0.00 0.00 0.00 2.69
2352 2831 9.934190 TGAACTAAAACCACGTAACTTATTTTC 57.066 29.630 0.00 0.00 0.00 2.29
2354 2833 9.940166 CTTGAACTAAAACCACGTAACTTATTT 57.060 29.630 0.00 0.00 0.00 1.40
2355 2834 8.562052 CCTTGAACTAAAACCACGTAACTTATT 58.438 33.333 0.00 0.00 0.00 1.40
2356 2835 7.933033 TCCTTGAACTAAAACCACGTAACTTAT 59.067 33.333 0.00 0.00 0.00 1.73
2357 2836 7.271511 TCCTTGAACTAAAACCACGTAACTTA 58.728 34.615 0.00 0.00 0.00 2.24
2358 2837 6.114767 TCCTTGAACTAAAACCACGTAACTT 58.885 36.000 0.00 0.00 0.00 2.66
2359 2838 5.673514 TCCTTGAACTAAAACCACGTAACT 58.326 37.500 0.00 0.00 0.00 2.24
2360 2839 5.049886 CCTCCTTGAACTAAAACCACGTAAC 60.050 44.000 0.00 0.00 0.00 2.50
2361 2840 5.058490 CCTCCTTGAACTAAAACCACGTAA 58.942 41.667 0.00 0.00 0.00 3.18
2362 2841 4.503643 CCCTCCTTGAACTAAAACCACGTA 60.504 45.833 0.00 0.00 0.00 3.57
2363 2842 3.473625 CCTCCTTGAACTAAAACCACGT 58.526 45.455 0.00 0.00 0.00 4.49
2364 2843 2.812011 CCCTCCTTGAACTAAAACCACG 59.188 50.000 0.00 0.00 0.00 4.94
2365 2844 4.072839 CTCCCTCCTTGAACTAAAACCAC 58.927 47.826 0.00 0.00 0.00 4.16
2417 2896 9.915629 AGTTAATTTGTTTCCGTTGCATATTTA 57.084 25.926 0.00 0.00 0.00 1.40
2447 2926 2.795231 AGGACATGGTGAACCTGATG 57.205 50.000 0.00 0.00 36.82 3.07
2582 3061 8.644374 ACAGCCCAAAACTCATTTTATAGTAA 57.356 30.769 0.00 0.00 35.79 2.24
2607 3086 9.256228 ACTATGGAGTATGTTTTCTCTCTGTAA 57.744 33.333 0.00 0.00 32.65 2.41
2666 3145 3.630769 ACATCAACCTGCAGCATAATCTG 59.369 43.478 8.66 1.99 37.15 2.90
2704 3183 7.763528 CAGTTCCCTAGCTATAATAAGCATGAG 59.236 40.741 0.00 0.00 45.30 2.90
2705 3184 7.235606 ACAGTTCCCTAGCTATAATAAGCATGA 59.764 37.037 0.00 0.00 45.30 3.07
2706 3185 7.390027 ACAGTTCCCTAGCTATAATAAGCATG 58.610 38.462 0.00 0.00 45.30 4.06
2707 3186 7.560796 ACAGTTCCCTAGCTATAATAAGCAT 57.439 36.000 0.00 0.00 45.30 3.79
2708 3187 6.996180 ACAGTTCCCTAGCTATAATAAGCA 57.004 37.500 0.00 0.00 45.30 3.91
2709 3188 8.532819 ACATACAGTTCCCTAGCTATAATAAGC 58.467 37.037 0.00 0.00 43.11 3.09
2713 3192 8.532819 GCTAACATACAGTTCCCTAGCTATAAT 58.467 37.037 0.00 0.00 41.64 1.28
2737 3216 3.416156 GAGGAAATGTGAGTCCAAAGCT 58.584 45.455 0.00 0.00 36.28 3.74
2738 3217 2.489722 GGAGGAAATGTGAGTCCAAAGC 59.510 50.000 0.00 0.00 36.28 3.51
2745 3224 1.280421 GCAGAGGGAGGAAATGTGAGT 59.720 52.381 0.00 0.00 0.00 3.41
2936 3415 5.063438 ACACAATTATACAGCGTTAGTGCAG 59.937 40.000 0.00 0.00 37.31 4.41
2938 3417 5.163893 ACACACAATTATACAGCGTTAGTGC 60.164 40.000 0.00 0.00 0.00 4.40
2945 3424 5.684850 TGAAACACACACAATTATACAGCG 58.315 37.500 0.00 0.00 0.00 5.18
3056 3536 0.794229 CGTTAAGTGCCAGCATTGCG 60.794 55.000 2.38 0.00 0.00 4.85
3080 3560 0.317854 GGAAACAGCCAAACAGCGAC 60.318 55.000 0.00 0.00 38.01 5.19
3101 3581 0.038599 ATCCAGCTCCACATGCAACA 59.961 50.000 0.00 0.00 0.00 3.33
3102 3582 1.180029 AATCCAGCTCCACATGCAAC 58.820 50.000 0.00 0.00 0.00 4.17
3150 3630 9.698309 GAATAAGCTAGAACAATATGAGCTGTA 57.302 33.333 0.00 0.00 42.56 2.74
3182 3662 3.813529 AAACTCAAATTTCGCTCTCGG 57.186 42.857 0.00 0.00 36.13 4.63
3183 3663 4.527564 ACAAAACTCAAATTTCGCTCTCG 58.472 39.130 0.00 0.00 0.00 4.04
3190 3670 8.351495 TGCACAATAGACAAAACTCAAATTTC 57.649 30.769 0.00 0.00 0.00 2.17
3223 3703 1.959042 AACAGACAGCAGTGAGGTTG 58.041 50.000 0.00 0.00 0.00 3.77
3250 3730 6.269077 TCACATACAGAAGTGGAAGGTAAAGA 59.731 38.462 0.00 0.00 36.43 2.52
3283 3763 1.066071 GGTACCTGGAAGAAGTCTGCC 60.066 57.143 4.06 0.00 42.39 4.85
3332 3815 9.088512 CACAGAAAATACTCCAGATACAAGTAC 57.911 37.037 0.00 0.00 0.00 2.73
3334 3817 6.595716 GCACAGAAAATACTCCAGATACAAGT 59.404 38.462 0.00 0.00 0.00 3.16
3335 3818 6.037610 GGCACAGAAAATACTCCAGATACAAG 59.962 42.308 0.00 0.00 0.00 3.16
3336 3819 5.880332 GGCACAGAAAATACTCCAGATACAA 59.120 40.000 0.00 0.00 0.00 2.41
3338 3821 5.675538 AGGCACAGAAAATACTCCAGATAC 58.324 41.667 0.00 0.00 0.00 2.24
3339 3822 5.957771 AGGCACAGAAAATACTCCAGATA 57.042 39.130 0.00 0.00 0.00 1.98
3340 3823 4.851639 AGGCACAGAAAATACTCCAGAT 57.148 40.909 0.00 0.00 0.00 2.90
3341 3824 4.287067 AGAAGGCACAGAAAATACTCCAGA 59.713 41.667 0.00 0.00 0.00 3.86
3349 3853 4.038402 CAGGAACAAGAAGGCACAGAAAAT 59.962 41.667 0.00 0.00 0.00 1.82
3354 3858 1.605710 CACAGGAACAAGAAGGCACAG 59.394 52.381 0.00 0.00 0.00 3.66
3374 3878 4.218417 ACAGGCAAGACATAAACAATCACC 59.782 41.667 0.00 0.00 0.00 4.02
3573 4078 9.730705 ACAATCTCTGTTCTAAGATTCATTCAA 57.269 29.630 0.00 0.00 39.59 2.69
3693 4200 3.879892 GAGGTATGGCAATTCTTGAGGTC 59.120 47.826 0.00 0.00 0.00 3.85
3741 4251 3.363178 CTTTCAAGTTTCAACAGCGTCC 58.637 45.455 0.00 0.00 0.00 4.79
3750 4260 3.888930 CCAGTTAGGGCTTTCAAGTTTCA 59.111 43.478 0.00 0.00 0.00 2.69
3804 4314 1.678101 GAGCTGCCAGAACAAAACACT 59.322 47.619 0.00 0.00 0.00 3.55
3805 4315 1.678101 AGAGCTGCCAGAACAAAACAC 59.322 47.619 0.00 0.00 0.00 3.32
3832 4342 1.608717 AACACTAGCAGCGAGGGAGG 61.609 60.000 12.36 0.00 0.00 4.30
3836 4346 2.033550 CCTAGTAACACTAGCAGCGAGG 59.966 54.545 7.51 0.00 45.21 4.63
3856 4366 3.689649 CACTGGCAACTCAAAGTATACCC 59.310 47.826 0.00 0.00 37.61 3.69
3857 4367 3.127030 GCACTGGCAACTCAAAGTATACC 59.873 47.826 0.00 0.00 40.72 2.73
3858 4368 4.342352 GCACTGGCAACTCAAAGTATAC 57.658 45.455 0.00 0.00 40.72 1.47
3923 4443 6.091849 CAGTACACAGAAATGAGACAAGGATG 59.908 42.308 0.00 0.00 0.00 3.51
3932 4452 2.688507 ACGCCAGTACACAGAAATGAG 58.311 47.619 0.00 0.00 0.00 2.90
4048 4584 3.655276 TGTCAACCTTCGTCTAAGTCC 57.345 47.619 0.00 0.00 32.89 3.85
4053 4589 4.279922 TGAACTCATGTCAACCTTCGTCTA 59.720 41.667 0.00 0.00 0.00 2.59
4054 4590 3.069586 TGAACTCATGTCAACCTTCGTCT 59.930 43.478 0.00 0.00 0.00 4.18
4055 4591 3.390135 TGAACTCATGTCAACCTTCGTC 58.610 45.455 0.00 0.00 0.00 4.20
4056 4592 3.469008 TGAACTCATGTCAACCTTCGT 57.531 42.857 0.00 0.00 0.00 3.85
4057 4593 4.332186 CATGAACTCATGTCAACCTTCG 57.668 45.455 10.92 0.00 46.40 3.79
4112 4648 2.083167 ATCAAAAACAATGGCCTGCG 57.917 45.000 3.32 0.00 0.00 5.18
4113 4649 4.392754 CCTAAATCAAAAACAATGGCCTGC 59.607 41.667 3.32 0.00 0.00 4.85
4114 4650 4.937015 CCCTAAATCAAAAACAATGGCCTG 59.063 41.667 3.32 0.00 0.00 4.85
4186 4723 2.359478 GGCGTCCGTTTGATGGGT 60.359 61.111 0.00 0.00 0.00 4.51
4225 4762 1.135575 CAAAGCCGAGAAACTCCATGC 60.136 52.381 0.00 0.00 0.00 4.06
4285 4828 8.831715 ACAAGAACTTTTGTGATTTGTTTCTT 57.168 26.923 0.00 0.00 39.68 2.52
4286 4829 8.831715 AACAAGAACTTTTGTGATTTGTTTCT 57.168 26.923 0.00 0.00 40.24 2.52
4287 4830 9.877137 AAAACAAGAACTTTTGTGATTTGTTTC 57.123 25.926 11.38 0.00 42.81 2.78
4334 4877 2.559440 TGCAAGCACCCAAAACATTTC 58.441 42.857 0.00 0.00 0.00 2.17
4345 4888 1.202452 AGCTGAAACTTTGCAAGCACC 60.202 47.619 7.03 0.00 0.00 5.01
4367 4911 5.220931 GCCACTACTTCCATGAATGTGATTC 60.221 44.000 0.00 0.00 39.70 2.52
4400 4944 6.506500 AACATCTTCGAAGCATCAATCTTT 57.493 33.333 20.56 1.63 0.00 2.52
4401 4945 6.820656 AGTAACATCTTCGAAGCATCAATCTT 59.179 34.615 20.56 5.12 0.00 2.40
4402 4946 6.344500 AGTAACATCTTCGAAGCATCAATCT 58.656 36.000 20.56 9.80 0.00 2.40
4403 4947 6.595772 AGTAACATCTTCGAAGCATCAATC 57.404 37.500 20.56 7.84 0.00 2.67
4404 4948 6.992063 AAGTAACATCTTCGAAGCATCAAT 57.008 33.333 20.56 5.39 0.00 2.57
4562 5108 7.984050 TCTTGGCATGAACAGTAAATTCAAAAA 59.016 29.630 0.00 0.00 39.43 1.94
4600 5146 4.926238 AGCGAAAATCCTAATATGAGCTCG 59.074 41.667 9.64 0.00 0.00 5.03
4625 5172 2.070650 ACAATAGGAGGGGGCGTCC 61.071 63.158 0.00 0.00 38.54 4.79


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

AutoCloner maintained by Alex Coulton.