Multiple sequence alignment - TraesCS3B01G113000

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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 TraesCS3B01G113000 chr3B 100.000 4391 0 0 1 4391 79132464 79128074 0.000000e+00 8109.0
1 TraesCS3B01G113000 chr3B 100.000 28 0 0 184 211 46363670 46363643 8.000000e-03 52.8
2 TraesCS3B01G113000 chr3B 88.372 43 5 0 169 211 47123412 47123454 8.000000e-03 52.8
3 TraesCS3B01G113000 chr3A 92.299 2558 144 25 1868 4391 63078166 63075628 0.000000e+00 3583.0
4 TraesCS3B01G113000 chr3A 88.160 1478 107 38 416 1845 63079816 63078359 0.000000e+00 1698.0
5 TraesCS3B01G113000 chr3A 89.429 350 26 3 1 341 63080205 63079858 8.720000e-117 431.0
6 TraesCS3B01G113000 chr3A 79.692 325 56 9 1869 2190 63078798 63078481 4.420000e-55 226.0
7 TraesCS3B01G113000 chr3A 95.413 109 5 0 1746 1854 63078258 63078150 1.620000e-39 174.0
8 TraesCS3B01G113000 chr3A 93.878 49 3 0 1774 1822 63078356 63078308 1.690000e-09 75.0
9 TraesCS3B01G113000 chr3D 88.202 1746 117 38 116 1815 49650642 49648940 0.000000e+00 2001.0
10 TraesCS3B01G113000 chr3D 90.484 1219 63 23 3201 4391 49647265 49646072 0.000000e+00 1559.0
11 TraesCS3B01G113000 chr3D 87.426 1177 107 14 1865 3019 49648569 49647412 0.000000e+00 1315.0
12 TraesCS3B01G113000 chr3D 93.151 365 25 0 1395 1759 49648945 49648581 1.800000e-148 536.0
13 TraesCS3B01G113000 chr3D 91.892 37 3 0 175 211 27950616 27950652 8.000000e-03 52.8
14 TraesCS3B01G113000 chr6D 88.350 206 13 4 1156 1350 441776449 441776654 2.040000e-58 237.0
15 TraesCS3B01G113000 chr6D 93.617 47 2 1 1476 1521 204628695 204628741 7.880000e-08 69.4
16 TraesCS3B01G113000 chr2D 87.864 206 14 4 1156 1350 127410076 127410281 9.500000e-57 231.0
17 TraesCS3B01G113000 chr2D 86.408 206 17 4 1156 1350 391511974 391512179 9.560000e-52 215.0
18 TraesCS3B01G113000 chr2D 93.750 48 2 1 1475 1521 167143036 167143083 2.190000e-08 71.3
19 TraesCS3B01G113000 chr2D 93.617 47 2 1 1476 1521 127410929 127410975 7.880000e-08 69.4
20 TraesCS3B01G113000 chr7A 86.893 206 16 5 1156 1350 431936374 431936169 2.060000e-53 220.0
21 TraesCS3B01G113000 chr4D 86.893 206 16 4 1156 1350 407722673 407722878 2.060000e-53 220.0
22 TraesCS3B01G113000 chr4D 93.617 47 2 1 1476 1521 407723481 407723527 7.880000e-08 69.4
23 TraesCS3B01G113000 chr1D 87.437 199 14 6 1163 1350 56944994 56945192 7.390000e-53 219.0
24 TraesCS3B01G113000 chr1A 91.241 137 12 0 1182 1318 1415299 1415435 2.090000e-43 187.0
25 TraesCS3B01G113000 chr7D 93.617 47 2 1 1476 1521 250466273 250466227 7.880000e-08 69.4
26 TraesCS3B01G113000 chr7D 93.617 47 2 1 1476 1521 575044474 575044428 7.880000e-08 69.4


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 TraesCS3B01G113000 chr3B 79128074 79132464 4390 True 8109.000000 8109 100.000000 1 4391 1 chr3B.!!$R2 4390
1 TraesCS3B01G113000 chr3A 63075628 63080205 4577 True 1031.166667 3583 89.811833 1 4391 6 chr3A.!!$R1 4390
2 TraesCS3B01G113000 chr3D 49646072 49650642 4570 True 1352.750000 2001 89.815750 116 4391 4 chr3D.!!$R1 4275

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
583 622 0.449388 CCAAGAGCAAATCAGACGCC 59.551 55.000 0.00 0.0 0.00 5.68 F
675 714 0.597568 TTGTTGATTTGCTCTGCCCG 59.402 50.000 0.00 0.0 0.00 6.13 F
762 802 1.059657 CGCTGCACGTTTTTGGATCG 61.060 55.000 0.00 0.0 36.87 3.69 F
1681 1789 1.073199 AAACACCCCTCTCCTTGCG 59.927 57.895 0.00 0.0 0.00 4.85 F
2713 3315 0.661780 CCATCTTCTCGATCGCCGTC 60.662 60.000 11.09 0.0 39.75 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2193 2783 0.237761 CAGCAGAGCAGTTTGAGCAC 59.762 55.000 0.00 0.00 0.00 4.40 R
2620 3222 0.536006 GATGGCATAGACCACAGGCC 60.536 60.000 0.00 0.00 44.17 5.19 R
2694 3296 0.661780 GACGGCGATCGAGAAGATGG 60.662 60.000 21.57 0.12 40.26 3.51 R
2977 3579 0.375106 GCATTAGAACAGGTCAGCGC 59.625 55.000 0.00 0.00 0.00 5.92 R
4282 4950 1.209747 ACCTCCATCCCGCTAACTTTC 59.790 52.381 0.00 0.00 0.00 2.62 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
55 56 5.784578 ACCAAACTTTAAGACCCATTGAC 57.215 39.130 0.00 0.00 0.00 3.18
57 58 4.277423 CCAAACTTTAAGACCCATTGACGT 59.723 41.667 0.00 0.00 0.00 4.34
83 84 6.220930 ACAGTTTGACGTGTATGTGAAGTAT 58.779 36.000 0.00 0.00 0.00 2.12
84 85 7.372714 ACAGTTTGACGTGTATGTGAAGTATA 58.627 34.615 0.00 0.00 0.00 1.47
88 89 9.866936 GTTTGACGTGTATGTGAAGTATAAAAA 57.133 29.630 0.00 0.00 0.00 1.94
359 389 4.832266 TGGACACCATTTTGCTAGTTTGAT 59.168 37.500 0.00 0.00 0.00 2.57
386 416 4.326504 AAACATGAAAAAGGACAGGCTG 57.673 40.909 14.16 14.16 0.00 4.85
391 421 2.158682 TGAAAAAGGACAGGCTGCTACA 60.159 45.455 15.89 1.31 0.00 2.74
393 423 1.059913 AAAGGACAGGCTGCTACACT 58.940 50.000 15.89 2.75 0.00 3.55
394 424 1.938585 AAGGACAGGCTGCTACACTA 58.061 50.000 15.89 0.00 0.00 2.74
395 425 1.187087 AGGACAGGCTGCTACACTAC 58.813 55.000 15.89 0.00 0.00 2.73
396 426 0.895530 GGACAGGCTGCTACACTACA 59.104 55.000 15.89 0.00 0.00 2.74
397 427 1.275291 GGACAGGCTGCTACACTACAA 59.725 52.381 15.89 0.00 0.00 2.41
398 428 2.338500 GACAGGCTGCTACACTACAAC 58.662 52.381 15.89 0.00 0.00 3.32
399 429 1.691976 ACAGGCTGCTACACTACAACA 59.308 47.619 15.89 0.00 0.00 3.33
400 430 2.104111 ACAGGCTGCTACACTACAACAA 59.896 45.455 15.89 0.00 0.00 2.83
401 431 3.138304 CAGGCTGCTACACTACAACAAA 58.862 45.455 0.00 0.00 0.00 2.83
402 432 3.753272 CAGGCTGCTACACTACAACAAAT 59.247 43.478 0.00 0.00 0.00 2.32
403 433 3.753272 AGGCTGCTACACTACAACAAATG 59.247 43.478 0.00 0.00 0.00 2.32
437 467 6.653320 ACACAGTTCAGTTCAGTCTTTTTACA 59.347 34.615 0.00 0.00 0.00 2.41
444 474 7.272978 TCAGTTCAGTCTTTTTACAGCTTACT 58.727 34.615 0.00 0.00 0.00 2.24
445 475 7.438459 TCAGTTCAGTCTTTTTACAGCTTACTC 59.562 37.037 0.00 0.00 0.00 2.59
446 476 6.706716 AGTTCAGTCTTTTTACAGCTTACTCC 59.293 38.462 0.00 0.00 0.00 3.85
447 477 6.420913 TCAGTCTTTTTACAGCTTACTCCT 57.579 37.500 0.00 0.00 0.00 3.69
448 478 7.534723 TCAGTCTTTTTACAGCTTACTCCTA 57.465 36.000 0.00 0.00 0.00 2.94
449 479 7.376615 TCAGTCTTTTTACAGCTTACTCCTAC 58.623 38.462 0.00 0.00 0.00 3.18
450 480 6.590677 CAGTCTTTTTACAGCTTACTCCTACC 59.409 42.308 0.00 0.00 0.00 3.18
451 481 6.497606 AGTCTTTTTACAGCTTACTCCTACCT 59.502 38.462 0.00 0.00 0.00 3.08
452 482 7.016366 AGTCTTTTTACAGCTTACTCCTACCTT 59.984 37.037 0.00 0.00 0.00 3.50
453 483 7.117956 GTCTTTTTACAGCTTACTCCTACCTTG 59.882 40.741 0.00 0.00 0.00 3.61
454 484 6.429521 TTTTACAGCTTACTCCTACCTTGT 57.570 37.500 0.00 0.00 0.00 3.16
510 549 1.693062 CCATCCATCCTCAGGAGTCAG 59.307 57.143 0.00 0.00 38.83 3.51
583 622 0.449388 CCAAGAGCAAATCAGACGCC 59.551 55.000 0.00 0.00 0.00 5.68
649 688 4.646572 GCGATTCCCCTGAGAGAATATTT 58.353 43.478 0.00 0.00 32.91 1.40
657 696 8.855804 TCCCCTGAGAGAATATTTTACTACTT 57.144 34.615 0.00 0.00 0.00 2.24
659 698 8.487028 CCCCTGAGAGAATATTTTACTACTTGT 58.513 37.037 0.00 0.00 0.00 3.16
675 714 0.597568 TTGTTGATTTGCTCTGCCCG 59.402 50.000 0.00 0.00 0.00 6.13
762 802 1.059657 CGCTGCACGTTTTTGGATCG 61.060 55.000 0.00 0.00 36.87 3.69
799 839 3.056328 GTGGGGACGGAAGCTTGC 61.056 66.667 2.10 5.53 0.00 4.01
822 862 1.659794 GCGGTGCCACAAGAACAAT 59.340 52.632 0.00 0.00 0.00 2.71
826 866 2.811431 CGGTGCCACAAGAACAATTCTA 59.189 45.455 0.00 0.00 39.61 2.10
838 878 6.305272 AGAACAATTCTAGCTGAATCTGGA 57.695 37.500 10.52 0.00 43.99 3.86
844 884 2.957680 TCTAGCTGAATCTGGAGCTCAG 59.042 50.000 17.19 11.13 44.55 3.35
854 894 1.269723 CTGGAGCTCAGAACGTGTGTA 59.730 52.381 17.19 0.00 46.18 2.90
855 895 1.893137 TGGAGCTCAGAACGTGTGTAT 59.107 47.619 17.19 0.00 0.00 2.29
899 947 2.729028 TAGGAATTGGGGTTAGCTGC 57.271 50.000 0.00 0.00 0.00 5.25
948 1019 2.814336 GGACATCTCCCTGTTTTGTGTC 59.186 50.000 0.00 0.00 35.11 3.67
949 1020 3.476552 GACATCTCCCTGTTTTGTGTCA 58.523 45.455 0.00 0.00 35.72 3.58
971 1042 6.428159 GTCATGAGTCTCCAAATTAACTGTGT 59.572 38.462 0.00 0.00 0.00 3.72
1096 1176 2.837532 TGCATATATGAGGAGCGCAA 57.162 45.000 17.10 0.00 0.00 4.85
1128 1208 4.820897 CCTGCATACTGAGTAAGTTGTGA 58.179 43.478 0.00 0.00 40.56 3.58
1151 1231 7.375280 GTGAATTCATTACAAGATCGAATGCTG 59.625 37.037 12.12 0.00 31.86 4.41
1161 1241 5.290493 AGATCGAATGCTGGTATTGGTTA 57.710 39.130 0.00 0.00 0.00 2.85
1171 1251 6.919721 TGCTGGTATTGGTTATTCTTGTTTC 58.080 36.000 0.00 0.00 0.00 2.78
1237 1317 1.535833 ATGCTAGGTAGATCGACCGG 58.464 55.000 18.05 15.49 44.88 5.28
1246 1326 3.950794 GATCGACCGGGTGCAGCAA 62.951 63.158 19.06 0.00 0.00 3.91
1259 1339 1.372004 CAGCAATTGTGTGCCACCG 60.372 57.895 7.40 0.00 46.14 4.94
1260 1340 2.049248 GCAATTGTGTGCCACCGG 60.049 61.111 7.40 0.00 38.66 5.28
1280 1360 4.156008 CCGGTCCACTTTTCTGGAAAATAG 59.844 45.833 8.64 2.05 42.22 1.73
1302 1382 6.566197 AGTTGCTAGAAAACCATCTGAAAG 57.434 37.500 0.00 0.00 0.00 2.62
1303 1383 5.048434 AGTTGCTAGAAAACCATCTGAAAGC 60.048 40.000 0.00 0.00 31.91 3.51
1310 1390 5.182760 AGAAAACCATCTGAAAGCTGTGATC 59.817 40.000 0.00 0.00 0.00 2.92
1311 1391 3.996921 ACCATCTGAAAGCTGTGATCT 57.003 42.857 0.00 0.00 0.00 2.75
1318 1398 5.494724 TCTGAAAGCTGTGATCTTTGCTAT 58.505 37.500 7.19 0.00 34.24 2.97
1319 1399 6.643388 TCTGAAAGCTGTGATCTTTGCTATA 58.357 36.000 7.19 0.00 34.24 1.31
1320 1400 7.105588 TCTGAAAGCTGTGATCTTTGCTATAA 58.894 34.615 7.19 0.00 34.24 0.98
1356 1446 4.237349 ACTGCCACTTAATTTTTGACCG 57.763 40.909 0.00 0.00 0.00 4.79
1373 1471 9.545105 TTTTTGACCGAAATACTACTGTCTTTA 57.455 29.630 0.00 0.00 0.00 1.85
1374 1472 8.752766 TTTGACCGAAATACTACTGTCTTTAG 57.247 34.615 0.00 0.00 0.00 1.85
1387 1485 9.185680 ACTACTGTCTTTAGATTTGGTTTTGTT 57.814 29.630 0.00 0.00 0.00 2.83
1432 1530 6.426633 TGCGTCTATTTTTCTGTTTCATCTGA 59.573 34.615 0.00 0.00 0.00 3.27
1449 1547 3.917988 TCTGAGTTGCACAGACACATAG 58.082 45.455 1.56 0.00 39.10 2.23
1566 1668 2.243221 AGGGCATGTTATTCTGCTTCCT 59.757 45.455 0.00 0.00 38.45 3.36
1610 1718 9.383519 TCTGAATTATCACTTATGGTTTCTCAC 57.616 33.333 0.00 0.00 0.00 3.51
1629 1737 6.356556 TCTCACAAAGAAAACTCAGATCCAA 58.643 36.000 0.00 0.00 0.00 3.53
1662 1770 1.896220 TGTTCACCACATCTTCAGCC 58.104 50.000 0.00 0.00 0.00 4.85
1681 1789 1.073199 AAACACCCCTCTCCTTGCG 59.927 57.895 0.00 0.00 0.00 4.85
1693 1801 5.392057 CCCTCTCCTTGCGAAAATTAAAGTC 60.392 44.000 0.00 0.00 0.00 3.01
1726 1835 9.567776 TTTTTGAGTGTTCACCTTATGATAAGA 57.432 29.630 13.56 0.00 37.11 2.10
1772 1883 9.455847 CCAGAAGACTGTCTTTTTATTTTTGAG 57.544 33.333 22.80 3.93 42.05 3.02
1816 1927 3.706594 TCCTGCATCTACTTACCAGAAGG 59.293 47.826 0.00 0.00 42.21 3.46
1845 2357 9.289782 GTCCATAAATAATCCTGCATCTACTTT 57.710 33.333 0.00 0.00 0.00 2.66
1846 2358 9.866655 TCCATAAATAATCCTGCATCTACTTTT 57.133 29.630 0.00 0.00 0.00 2.27
1850 2362 6.874288 ATAATCCTGCATCTACTTTTCTGC 57.126 37.500 0.00 0.00 35.21 4.26
1851 2363 3.988976 TCCTGCATCTACTTTTCTGCT 57.011 42.857 0.00 0.00 35.66 4.24
1852 2364 4.292186 TCCTGCATCTACTTTTCTGCTT 57.708 40.909 0.00 0.00 35.66 3.91
1853 2365 4.655963 TCCTGCATCTACTTTTCTGCTTT 58.344 39.130 0.00 0.00 35.66 3.51
1854 2366 5.072741 TCCTGCATCTACTTTTCTGCTTTT 58.927 37.500 0.00 0.00 35.66 2.27
1895 2477 9.862371 CTACTTTTCTGCTTTGATCTAAGTAGA 57.138 33.333 25.45 25.45 42.94 2.59
1907 2489 8.777865 TTGATCTAAGTAGAAAAGACACATGG 57.222 34.615 0.00 0.00 35.69 3.66
1920 2502 7.849804 AAAGACACATGGTAGTATGAATCAC 57.150 36.000 0.00 0.00 0.00 3.06
1980 2570 5.220681 GCTTTACTTGCTGCCTGTTAGATAC 60.221 44.000 0.00 0.00 0.00 2.24
2070 2660 7.281324 GTCTGAACTCTCACTTATAGCTACTCA 59.719 40.741 0.00 0.00 0.00 3.41
2071 2661 7.996066 TCTGAACTCTCACTTATAGCTACTCAT 59.004 37.037 0.00 0.00 0.00 2.90
2072 2662 9.278978 CTGAACTCTCACTTATAGCTACTCATA 57.721 37.037 0.00 0.00 0.00 2.15
2073 2663 9.628500 TGAACTCTCACTTATAGCTACTCATAA 57.372 33.333 0.00 0.00 0.00 1.90
2076 2666 9.635404 ACTCTCACTTATAGCTACTCATAAAGT 57.365 33.333 0.00 0.00 42.33 2.66
2077 2667 9.891828 CTCTCACTTATAGCTACTCATAAAGTG 57.108 37.037 16.74 16.74 39.11 3.16
2193 2783 3.930336 TGAGTGCTGACCTTATGAGTTG 58.070 45.455 0.00 0.00 0.00 3.16
2196 2786 2.160417 GTGCTGACCTTATGAGTTGTGC 59.840 50.000 0.00 0.00 0.00 4.57
2207 2797 2.677559 GAGTTGTGCTCAAACTGCTC 57.322 50.000 2.18 2.29 43.58 4.26
2257 2859 1.378250 CCTCTTGCAAGCAGAGGGG 60.378 63.158 21.99 15.87 43.98 4.79
2304 2906 2.926200 GCTGTGTGTACTATGTGAGCAG 59.074 50.000 0.00 0.00 0.00 4.24
2388 2990 2.112198 CCACCACACGTGTGCAAGT 61.112 57.895 37.33 27.89 44.34 3.16
2484 3086 4.363991 ACTGACTGGCTTTCATCTTCTT 57.636 40.909 0.00 0.00 0.00 2.52
2661 3263 7.805071 CCATCATGTTCTTGTTGAAGTTCTTAC 59.195 37.037 4.17 3.37 35.01 2.34
2662 3264 7.259290 TCATGTTCTTGTTGAAGTTCTTACC 57.741 36.000 4.17 0.00 35.01 2.85
2710 3312 0.943359 CTGCCATCTTCTCGATCGCC 60.943 60.000 11.09 0.00 35.65 5.54
2713 3315 0.661780 CCATCTTCTCGATCGCCGTC 60.662 60.000 11.09 0.00 39.75 4.79
2715 3317 0.955178 ATCTTCTCGATCGCCGTCAT 59.045 50.000 11.09 0.00 39.75 3.06
2723 3325 3.967886 ATCGCCGTCATCGATCTTT 57.032 47.368 0.00 0.00 42.28 2.52
2741 3343 2.237393 TTTGTGCAATGGTTGGCTTC 57.763 45.000 0.00 0.00 0.00 3.86
2781 3383 1.298788 GTTTTTGTGGGTGTCGCGG 60.299 57.895 6.13 0.00 0.00 6.46
2914 3516 6.478588 CAGACGAATCTGCCTGTAATTAAAC 58.521 40.000 0.00 0.00 45.83 2.01
2954 3556 5.407407 TCACCTAGTTCTCATGGTCTTTC 57.593 43.478 0.00 0.00 0.00 2.62
2955 3557 4.838423 TCACCTAGTTCTCATGGTCTTTCA 59.162 41.667 0.00 0.00 0.00 2.69
2979 3581 5.597813 ACAACAGAAATAACTGAGAAGCG 57.402 39.130 0.00 0.00 40.63 4.68
3011 3613 6.128553 TGTTCTAATGCTTCTGAAAGTTAGCG 60.129 38.462 9.47 0.00 42.63 4.26
3034 3638 5.869888 CGGTTCAATACTAGTGCTTTTCTCT 59.130 40.000 5.39 0.00 0.00 3.10
3036 3640 7.221067 CGGTTCAATACTAGTGCTTTTCTCTAG 59.779 40.741 5.39 0.00 41.99 2.43
3037 3641 7.010645 GGTTCAATACTAGTGCTTTTCTCTAGC 59.989 40.741 5.39 0.00 40.68 3.42
3045 3649 2.290514 TGCTTTTCTCTAGCATGCCAGT 60.291 45.455 15.66 0.00 43.30 4.00
3052 3656 1.065926 TCTAGCATGCCAGTTCCAGTG 60.066 52.381 15.66 0.00 0.00 3.66
3124 3762 9.559958 CTATTTCTGTAATTGGCTAACTTTGTG 57.440 33.333 0.00 0.00 0.00 3.33
3136 3774 5.221048 GGCTAACTTTGTGACAACTGAATGT 60.221 40.000 0.00 0.00 35.90 2.71
3137 3775 6.017440 GGCTAACTTTGTGACAACTGAATGTA 60.017 38.462 0.00 0.00 32.57 2.29
3155 3793 9.912634 CTGAATGTAACACATAAACCTTTTGAT 57.087 29.630 0.00 0.00 37.97 2.57
3321 3961 1.546961 ACTTCCTTGAGACGACGGAT 58.453 50.000 0.00 0.00 0.00 4.18
3375 4015 2.877097 TGCAAGCAACCATTCCTCTA 57.123 45.000 0.00 0.00 0.00 2.43
3415 4055 7.539712 AGAACAAATGTGTAGGAATCATACG 57.460 36.000 0.53 0.00 36.80 3.06
3416 4056 5.734855 ACAAATGTGTAGGAATCATACGC 57.265 39.130 11.17 11.17 35.72 4.42
3440 4081 5.126396 GCAAAGAAGCCTGTAAATGTTCT 57.874 39.130 0.00 0.00 0.00 3.01
3445 4086 6.374417 AGAAGCCTGTAAATGTTCTTCCTA 57.626 37.500 0.00 0.00 32.62 2.94
3447 4088 6.825721 AGAAGCCTGTAAATGTTCTTCCTATG 59.174 38.462 0.00 0.00 32.62 2.23
3451 4092 8.107095 AGCCTGTAAATGTTCTTCCTATGTTTA 58.893 33.333 0.00 0.00 0.00 2.01
3463 4104 5.932619 TCCTATGTTTAGCTCAAGCACTA 57.067 39.130 4.59 0.00 45.16 2.74
3480 4121 4.938226 AGCACTACCAAGCTATGAAACTTC 59.062 41.667 0.00 0.00 39.78 3.01
3481 4122 4.201724 GCACTACCAAGCTATGAAACTTCG 60.202 45.833 0.00 0.00 0.00 3.79
3485 4126 2.678336 CCAAGCTATGAAACTTCGGGTC 59.322 50.000 0.00 0.00 0.00 4.46
3489 4130 2.929592 GCTATGAAACTTCGGGTCGTGT 60.930 50.000 0.00 0.00 0.00 4.49
3492 4133 1.069513 TGAAACTTCGGGTCGTGTGAT 59.930 47.619 0.00 0.00 0.00 3.06
3494 4135 0.949105 AACTTCGGGTCGTGTGATGC 60.949 55.000 0.00 0.00 0.00 3.91
3520 4161 3.126000 GTCTGTACAATTTGAGCTCTGCC 59.874 47.826 16.19 0.11 0.00 4.85
3544 4185 2.490903 CTGAAGTTTATGCAGCAAGCCT 59.509 45.455 0.00 0.00 44.83 4.58
3561 4202 3.667497 GCCTGCAGCTGTACTATCATA 57.333 47.619 16.64 0.00 38.99 2.15
3562 4203 3.995199 GCCTGCAGCTGTACTATCATAA 58.005 45.455 16.64 0.00 38.99 1.90
3574 4215 7.177498 TGTACTATCATAAATTTGCTCAGCG 57.823 36.000 0.00 0.00 0.00 5.18
3601 4255 6.146837 ACAATCGTCTCAGAGAATTGTGAAAG 59.853 38.462 22.07 8.15 30.71 2.62
3602 4256 5.201713 TCGTCTCAGAGAATTGTGAAAGT 57.798 39.130 0.20 0.00 0.00 2.66
3604 4258 6.745116 TCGTCTCAGAGAATTGTGAAAGTTA 58.255 36.000 0.20 0.00 0.00 2.24
3629 4284 8.599055 AACATCACATTGTATCTACTGCTATG 57.401 34.615 0.00 0.00 0.00 2.23
3636 4291 8.870116 ACATTGTATCTACTGCTATGTATCCAA 58.130 33.333 0.00 0.00 0.00 3.53
3648 4303 7.864770 TGCTATGTATCCAATCATGATGGTAT 58.135 34.615 9.46 0.58 39.09 2.73
3694 4349 1.176527 TGGCATTAGCAAGTGAAGCC 58.823 50.000 0.00 0.00 44.61 4.35
3703 4358 7.464977 GCATTAGCAAGTGAAGCCATTTTTATG 60.465 37.037 0.00 0.00 41.58 1.90
3714 4369 4.962362 AGCCATTTTTATGGGGAAGGTAAG 59.038 41.667 6.33 0.00 41.94 2.34
3719 4374 2.579624 TATGGGGAAGGTAAGCCTGA 57.420 50.000 0.00 0.00 46.33 3.86
3750 4405 8.488668 TGATATGAAAAGATTGATGAGACTGGA 58.511 33.333 0.00 0.00 0.00 3.86
3754 4409 5.831702 AAAGATTGATGAGACTGGATTGC 57.168 39.130 0.00 0.00 0.00 3.56
3765 4420 6.341316 TGAGACTGGATTGCTAACATACTTC 58.659 40.000 0.00 0.00 0.00 3.01
3766 4421 6.155221 TGAGACTGGATTGCTAACATACTTCT 59.845 38.462 0.00 0.00 0.00 2.85
3767 4422 6.951971 AGACTGGATTGCTAACATACTTCTT 58.048 36.000 0.00 0.00 0.00 2.52
3835 4490 8.874744 AGTTAGAAGTGAACTGAAGAAACTAC 57.125 34.615 0.00 0.00 35.80 2.73
3841 4496 5.294552 AGTGAACTGAAGAAACTACAAGTGC 59.705 40.000 0.00 0.00 0.00 4.40
3865 4521 7.125811 TGCTAGATTTAGTAGTCATTCAAGGGT 59.874 37.037 0.00 0.00 0.00 4.34
3882 4538 3.928754 AGGGTAGAATAGCACCAGATGA 58.071 45.455 0.00 0.00 41.82 2.92
3900 4556 6.325028 CCAGATGACCTTAATTCTCCAGAGTA 59.675 42.308 0.00 0.00 0.00 2.59
3901 4557 7.147655 CCAGATGACCTTAATTCTCCAGAGTAA 60.148 40.741 0.00 0.00 0.00 2.24
3902 4558 7.708752 CAGATGACCTTAATTCTCCAGAGTAAC 59.291 40.741 0.00 0.00 0.00 2.50
3903 4559 7.621683 AGATGACCTTAATTCTCCAGAGTAACT 59.378 37.037 0.00 0.00 0.00 2.24
3911 4575 4.634184 TCTCCAGAGTAACTACGAATGC 57.366 45.455 0.00 0.00 0.00 3.56
3933 4597 7.994425 TGCTAGATTTAGTTGTCCATTCAAA 57.006 32.000 0.00 0.00 0.00 2.69
3946 4610 4.943705 GTCCATTCAAAGCCAGACAGAATA 59.056 41.667 0.00 0.00 0.00 1.75
3950 4614 6.769822 CCATTCAAAGCCAGACAGAATATAGT 59.230 38.462 0.00 0.00 0.00 2.12
3976 4640 4.505191 CCAGAGCACATTTCACAAAAACAG 59.495 41.667 0.00 0.00 0.00 3.16
4034 4698 3.004734 CCACAGGAAGGATCACAAACAAC 59.995 47.826 0.00 0.00 0.00 3.32
4053 4717 1.072331 ACGGTGCAGATCCAAGTCTTT 59.928 47.619 0.00 0.00 0.00 2.52
4277 4945 1.029947 CAGCCATCTGCACATCAGCA 61.030 55.000 0.00 0.00 44.83 4.41
4282 4950 2.415491 CCATCTGCACATCAGCACAAAG 60.415 50.000 0.00 0.00 42.56 2.77
4292 4960 3.878086 TCAGCACAAAGAAAGTTAGCG 57.122 42.857 0.00 0.00 0.00 4.26
4312 4980 3.886123 CGGGATGGAGGTTCATAAACTT 58.114 45.455 0.00 0.00 35.61 2.66
4314 4982 4.625324 CGGGATGGAGGTTCATAAACTTCA 60.625 45.833 0.00 0.00 41.86 3.02
4329 4997 8.293157 TCATAAACTTCAATGTTATCGCAAACA 58.707 29.630 5.10 5.10 43.16 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.363575 CGTCAAACTGTTACGTCAATGGG 60.364 47.826 7.49 0.00 32.16 4.00
55 56 4.441744 TCACATACACGTCAAACTGTTACG 59.558 41.667 12.77 12.77 42.17 3.18
57 58 6.044046 ACTTCACATACACGTCAAACTGTTA 58.956 36.000 0.00 0.00 0.00 2.41
88 89 5.010282 AGCAGGGTAAATTCACTCGATTTT 58.990 37.500 0.00 0.00 0.00 1.82
97 98 7.716799 AATGTCATTTAGCAGGGTAAATTCA 57.283 32.000 12.38 13.78 31.49 2.57
158 168 4.809673 AGCAGTTGCAGCCTAATTAAAAC 58.190 39.130 6.90 0.00 45.16 2.43
317 327 9.725019 GGTGTCCATTAATCATCTGTCATAATA 57.275 33.333 0.00 0.00 0.00 0.98
319 329 7.572814 TGGTGTCCATTAATCATCTGTCATAA 58.427 34.615 0.00 0.00 0.00 1.90
366 396 2.036346 GCAGCCTGTCCTTTTTCATGTT 59.964 45.455 0.00 0.00 0.00 2.71
367 397 1.615392 GCAGCCTGTCCTTTTTCATGT 59.385 47.619 0.00 0.00 0.00 3.21
370 400 2.158682 TGTAGCAGCCTGTCCTTTTTCA 60.159 45.455 0.00 0.00 0.00 2.69
379 409 1.691976 TGTTGTAGTGTAGCAGCCTGT 59.308 47.619 0.00 0.00 0.00 4.00
382 412 3.751175 TCATTTGTTGTAGTGTAGCAGCC 59.249 43.478 0.00 0.00 0.00 4.85
386 416 6.416750 GGTTTGTTCATTTGTTGTAGTGTAGC 59.583 38.462 0.00 0.00 0.00 3.58
391 421 6.096695 GTGTGGTTTGTTCATTTGTTGTAGT 58.903 36.000 0.00 0.00 0.00 2.73
393 423 6.025749 TGTGTGGTTTGTTCATTTGTTGTA 57.974 33.333 0.00 0.00 0.00 2.41
394 424 4.887748 TGTGTGGTTTGTTCATTTGTTGT 58.112 34.783 0.00 0.00 0.00 3.32
395 425 4.928615 ACTGTGTGGTTTGTTCATTTGTTG 59.071 37.500 0.00 0.00 0.00 3.33
396 426 5.146010 ACTGTGTGGTTTGTTCATTTGTT 57.854 34.783 0.00 0.00 0.00 2.83
397 427 4.799564 ACTGTGTGGTTTGTTCATTTGT 57.200 36.364 0.00 0.00 0.00 2.83
398 428 5.167121 TGAACTGTGTGGTTTGTTCATTTG 58.833 37.500 0.00 0.00 42.25 2.32
399 429 5.047377 ACTGAACTGTGTGGTTTGTTCATTT 60.047 36.000 7.67 0.00 44.79 2.32
400 430 4.462483 ACTGAACTGTGTGGTTTGTTCATT 59.538 37.500 7.67 0.84 44.79 2.57
401 431 4.016444 ACTGAACTGTGTGGTTTGTTCAT 58.984 39.130 7.67 0.00 44.79 2.57
402 432 3.417101 ACTGAACTGTGTGGTTTGTTCA 58.583 40.909 0.00 0.00 44.06 3.18
403 433 4.083003 TGAACTGAACTGTGTGGTTTGTTC 60.083 41.667 14.07 14.07 39.83 3.18
437 467 6.930068 TTCTTTACAAGGTAGGAGTAAGCT 57.070 37.500 0.00 0.00 0.00 3.74
449 479 7.334844 AGAAGACAACCTTTTCTTTACAAGG 57.665 36.000 0.00 0.00 44.68 3.61
450 480 8.678199 AGAAGAAGACAACCTTTTCTTTACAAG 58.322 33.333 0.86 0.00 40.27 3.16
451 481 8.575649 AGAAGAAGACAACCTTTTCTTTACAA 57.424 30.769 0.86 0.00 40.27 2.41
452 482 8.575649 AAGAAGAAGACAACCTTTTCTTTACA 57.424 30.769 0.86 0.00 40.27 2.41
453 483 7.851472 CGAAGAAGAAGACAACCTTTTCTTTAC 59.149 37.037 0.00 0.00 40.27 2.01
454 484 7.466860 GCGAAGAAGAAGACAACCTTTTCTTTA 60.467 37.037 0.00 0.00 40.27 1.85
510 549 1.275421 AAGAGGTTAGCTCAGGCCCC 61.275 60.000 14.09 0.00 39.73 5.80
649 688 5.181245 GGCAGAGCAAATCAACAAGTAGTAA 59.819 40.000 0.00 0.00 0.00 2.24
657 696 1.243342 CCGGGCAGAGCAAATCAACA 61.243 55.000 0.00 0.00 0.00 3.33
659 698 2.342650 GCCGGGCAGAGCAAATCAA 61.343 57.895 15.62 0.00 0.00 2.57
822 862 3.369175 TGAGCTCCAGATTCAGCTAGAA 58.631 45.455 12.15 0.00 46.31 2.10
838 878 1.000843 TGCATACACACGTTCTGAGCT 59.999 47.619 0.00 0.00 0.00 4.09
899 947 0.654683 GAAGGCTAGAATGCACGCAG 59.345 55.000 0.00 0.00 34.04 5.18
948 1019 6.808008 ACACAGTTAATTTGGAGACTCATG 57.192 37.500 4.53 0.00 0.00 3.07
949 1020 7.173907 CAGAACACAGTTAATTTGGAGACTCAT 59.826 37.037 4.53 0.00 0.00 2.90
971 1042 1.677576 CTGCTCACAAGTTTGCCAGAA 59.322 47.619 0.00 0.00 0.00 3.02
1096 1176 4.020751 ACTCAGTATGCAGGCATATCGATT 60.021 41.667 16.22 8.13 40.49 3.34
1128 1208 6.319658 ACCAGCATTCGATCTTGTAATGAATT 59.680 34.615 9.70 0.00 33.38 2.17
1143 1223 6.183360 ACAAGAATAACCAATACCAGCATTCG 60.183 38.462 0.00 0.00 0.00 3.34
1151 1231 9.516314 GCATAAGAAACAAGAATAACCAATACC 57.484 33.333 0.00 0.00 0.00 2.73
1161 1241 8.854117 AGAAACTCTTGCATAAGAAACAAGAAT 58.146 29.630 6.19 0.00 46.59 2.40
1171 1251 6.906659 ACATGAACAGAAACTCTTGCATAAG 58.093 36.000 0.00 0.00 35.16 1.73
1237 1317 1.665599 GGCACACAATTGCTGCACC 60.666 57.895 23.26 13.87 42.56 5.01
1259 1339 6.447162 CAACTATTTTCCAGAAAAGTGGACC 58.553 40.000 10.96 0.00 46.75 4.46
1260 1340 5.920840 GCAACTATTTTCCAGAAAAGTGGAC 59.079 40.000 10.96 0.00 46.75 4.02
1280 1360 5.048434 AGCTTTCAGATGGTTTTCTAGCAAC 60.048 40.000 0.00 0.00 37.87 4.17
1318 1398 7.948357 AGTGGCAGTTCTTCGTACATATATTA 58.052 34.615 0.00 0.00 0.00 0.98
1319 1399 6.817184 AGTGGCAGTTCTTCGTACATATATT 58.183 36.000 0.00 0.00 0.00 1.28
1320 1400 6.406692 AGTGGCAGTTCTTCGTACATATAT 57.593 37.500 0.00 0.00 0.00 0.86
1329 1419 6.142320 GTCAAAAATTAAGTGGCAGTTCTTCG 59.858 38.462 11.55 0.50 0.00 3.79
1367 1465 9.750125 AATCAGAACAAAACCAAATCTAAAGAC 57.250 29.630 0.00 0.00 0.00 3.01
1373 1471 6.550854 TCTGGAATCAGAACAAAACCAAATCT 59.449 34.615 0.00 0.00 46.08 2.40
1374 1472 6.748132 TCTGGAATCAGAACAAAACCAAATC 58.252 36.000 0.00 0.00 46.08 2.17
1432 1530 4.342862 ACTTCTATGTGTCTGTGCAACT 57.657 40.909 0.00 0.00 38.04 3.16
1449 1547 6.308766 GGCATCAACAACACAATTCATACTTC 59.691 38.462 0.00 0.00 0.00 3.01
1566 1668 8.455903 AATTCAGACTTTCAGAATCAGTGAAA 57.544 30.769 0.00 0.00 40.73 2.69
1610 1718 7.428020 TCACATTTGGATCTGAGTTTTCTTTG 58.572 34.615 0.00 0.00 0.00 2.77
1645 1753 2.622942 GTTTGGCTGAAGATGTGGTGAA 59.377 45.455 0.00 0.00 0.00 3.18
1662 1770 1.237285 CGCAAGGAGAGGGGTGTTTG 61.237 60.000 0.00 0.00 0.00 2.93
1681 1789 8.710835 TCAAAAACAGTGGGACTTTAATTTTC 57.289 30.769 0.00 0.00 0.00 2.29
1693 1801 3.428862 GGTGAACACTCAAAAACAGTGGG 60.429 47.826 4.92 0.00 44.86 4.61
1726 1835 6.872920 TCTGGTCAAAAATTAAGTTGCAGTT 58.127 32.000 0.00 0.00 0.00 3.16
1772 1883 5.760743 GGATTATTTAGGGACAGTCTTCTGC 59.239 44.000 0.00 0.00 44.77 4.26
1816 1927 5.709164 AGATGCAGGATTATTTATGGACAGC 59.291 40.000 0.00 0.00 0.00 4.40
1856 2368 4.215399 CAGAAAAGTAGATCACCCGCAAAA 59.785 41.667 0.00 0.00 0.00 2.44
1858 2370 3.334691 CAGAAAAGTAGATCACCCGCAA 58.665 45.455 0.00 0.00 0.00 4.85
1859 2371 2.935238 GCAGAAAAGTAGATCACCCGCA 60.935 50.000 0.00 0.00 0.00 5.69
1860 2372 1.666189 GCAGAAAAGTAGATCACCCGC 59.334 52.381 0.00 0.00 0.00 6.13
1861 2373 3.252974 AGCAGAAAAGTAGATCACCCG 57.747 47.619 0.00 0.00 0.00 5.28
1862 2374 5.003804 TCAAAGCAGAAAAGTAGATCACCC 58.996 41.667 0.00 0.00 0.00 4.61
1863 2375 6.597280 AGATCAAAGCAGAAAAGTAGATCACC 59.403 38.462 0.00 0.00 34.58 4.02
1864 2376 7.608308 AGATCAAAGCAGAAAAGTAGATCAC 57.392 36.000 0.00 0.00 34.58 3.06
1866 2378 9.377312 ACTTAGATCAAAGCAGAAAAGTAGATC 57.623 33.333 0.00 0.00 0.00 2.75
1893 2475 8.321353 TGATTCATACTACCATGTGTCTTTTCT 58.679 33.333 0.00 0.00 0.00 2.52
1895 2477 7.064609 CGTGATTCATACTACCATGTGTCTTTT 59.935 37.037 0.00 0.00 0.00 2.27
1907 2489 5.557136 GCATCAGCAACGTGATTCATACTAC 60.557 44.000 0.00 0.00 41.58 2.73
1920 2502 1.739466 ACAATACAGGCATCAGCAACG 59.261 47.619 0.00 0.00 44.61 4.10
1980 2570 6.992063 ATTGTGACTACTTCCAGCTAAATG 57.008 37.500 0.00 0.00 0.00 2.32
2072 2662 9.388506 CAGGATCACAGTTATCTTTATCACTTT 57.611 33.333 0.00 0.00 0.00 2.66
2073 2663 7.497249 GCAGGATCACAGTTATCTTTATCACTT 59.503 37.037 0.00 0.00 0.00 3.16
2074 2664 6.989169 GCAGGATCACAGTTATCTTTATCACT 59.011 38.462 0.00 0.00 0.00 3.41
2075 2665 6.989169 AGCAGGATCACAGTTATCTTTATCAC 59.011 38.462 0.00 0.00 0.00 3.06
2076 2666 6.988580 CAGCAGGATCACAGTTATCTTTATCA 59.011 38.462 0.00 0.00 0.00 2.15
2077 2667 6.989169 ACAGCAGGATCACAGTTATCTTTATC 59.011 38.462 0.00 0.00 0.00 1.75
2193 2783 0.237761 CAGCAGAGCAGTTTGAGCAC 59.762 55.000 0.00 0.00 0.00 4.40
2196 2786 2.935201 GGATACAGCAGAGCAGTTTGAG 59.065 50.000 0.00 0.00 29.63 3.02
2257 2859 2.727916 CGTTTGCCGAAGTTAATCCTGC 60.728 50.000 0.00 0.00 39.56 4.85
2304 2906 1.272769 ACCAGAGCTTCGGTTGAGTAC 59.727 52.381 2.25 0.00 28.43 2.73
2388 2990 2.828520 CTGCTGTCTTAGAGGACCAAGA 59.171 50.000 0.00 0.00 35.54 3.02
2459 3061 5.936956 AGAAGATGAAAGCCAGTCAGTTTAG 59.063 40.000 0.00 0.00 0.00 1.85
2503 3105 3.767673 AGAAAGCGGGAATGTAGTAGTCA 59.232 43.478 0.00 0.00 0.00 3.41
2620 3222 0.536006 GATGGCATAGACCACAGGCC 60.536 60.000 0.00 0.00 44.17 5.19
2661 3263 2.689983 GTGTTGGGATCCTTAAGCATGG 59.310 50.000 12.58 0.00 0.00 3.66
2662 3264 2.689983 GGTGTTGGGATCCTTAAGCATG 59.310 50.000 12.58 0.00 0.00 4.06
2694 3296 0.661780 GACGGCGATCGAGAAGATGG 60.662 60.000 21.57 0.12 40.26 3.51
2698 3300 0.994241 CGATGACGGCGATCGAGAAG 60.994 60.000 21.57 8.60 44.46 2.85
2710 3312 3.454042 TTGCACAAAAGATCGATGACG 57.546 42.857 0.54 0.00 41.26 4.35
2713 3315 4.100707 ACCATTGCACAAAAGATCGATG 57.899 40.909 0.54 0.00 0.00 3.84
2715 3317 3.305267 CCAACCATTGCACAAAAGATCGA 60.305 43.478 0.00 0.00 0.00 3.59
2723 3325 1.412079 AGAAGCCAACCATTGCACAA 58.588 45.000 0.00 0.00 0.00 3.33
2741 3343 4.970662 ACATTAGCCATGTGCAAAGTAG 57.029 40.909 8.58 0.00 45.12 2.57
2762 3364 1.429825 CGCGACACCCACAAAAACA 59.570 52.632 0.00 0.00 0.00 2.83
2763 3365 1.298788 CCGCGACACCCACAAAAAC 60.299 57.895 8.23 0.00 0.00 2.43
2766 3368 1.313812 AAAACCGCGACACCCACAAA 61.314 50.000 8.23 0.00 0.00 2.83
2833 3435 3.074412 CACCTGCGGTTCATAGTTCTTT 58.926 45.455 0.00 0.00 31.02 2.52
2908 3510 8.314021 TGATCCTGTGATATGCTATCGTTTAAT 58.686 33.333 0.00 0.00 0.00 1.40
2914 3516 4.159321 AGGTGATCCTGTGATATGCTATCG 59.841 45.833 0.00 0.00 43.33 2.92
2954 3556 7.176075 CGCTTCTCAGTTATTTCTGTTGTATG 58.824 38.462 0.00 0.00 36.85 2.39
2955 3557 6.183360 GCGCTTCTCAGTTATTTCTGTTGTAT 60.183 38.462 0.00 0.00 36.85 2.29
2977 3579 0.375106 GCATTAGAACAGGTCAGCGC 59.625 55.000 0.00 0.00 0.00 5.92
2979 3581 3.373439 CAGAAGCATTAGAACAGGTCAGC 59.627 47.826 0.00 0.00 0.00 4.26
3011 3613 7.010645 GCTAGAGAAAAGCACTAGTATTGAACC 59.989 40.741 0.00 0.00 39.24 3.62
3034 3638 0.983467 TCACTGGAACTGGCATGCTA 59.017 50.000 18.92 11.28 0.00 3.49
3036 3640 2.042686 TATCACTGGAACTGGCATGC 57.957 50.000 9.90 9.90 0.00 4.06
3037 3641 7.712639 GGTATATATATCACTGGAACTGGCATG 59.287 40.741 0.00 0.00 0.00 4.06
3039 3643 6.728632 TGGTATATATATCACTGGAACTGGCA 59.271 38.462 1.31 0.00 0.00 4.92
3040 3644 7.093289 ACTGGTATATATATCACTGGAACTGGC 60.093 40.741 1.31 0.00 0.00 4.85
3045 3649 9.035890 CCTGAACTGGTATATATATCACTGGAA 57.964 37.037 1.31 0.00 0.00 3.53
3124 3762 7.871853 AGGTTTATGTGTTACATTCAGTTGTC 58.128 34.615 0.00 0.00 39.88 3.18
3137 3775 9.442047 TCAAAAACATCAAAAGGTTTATGTGTT 57.558 25.926 0.00 0.00 38.36 3.32
3198 3837 5.064071 GTGAGCAGAACAAAACTAGATAGCC 59.936 44.000 0.00 0.00 0.00 3.93
3200 3839 6.093404 TCGTGAGCAGAACAAAACTAGATAG 58.907 40.000 0.00 0.00 0.00 2.08
3301 3941 1.325355 TCCGTCGTCTCAAGGAAGTT 58.675 50.000 0.00 0.00 0.00 2.66
3303 3943 1.202582 ACATCCGTCGTCTCAAGGAAG 59.797 52.381 0.00 0.00 36.25 3.46
3321 3961 0.587768 CATGTGTCGCAAAGCAGACA 59.412 50.000 10.82 10.82 38.74 3.41
3375 4015 0.605319 TTCTTCACAAAGCGGCGGAT 60.605 50.000 9.78 0.00 32.18 4.18
3400 4040 1.137513 GCCGCGTATGATTCCTACAC 58.862 55.000 4.92 0.00 0.00 2.90
3440 4081 5.165961 AGTGCTTGAGCTAAACATAGGAA 57.834 39.130 4.44 0.00 42.66 3.36
3445 4086 4.286297 TGGTAGTGCTTGAGCTAAACAT 57.714 40.909 4.44 0.00 42.66 2.71
3447 4088 3.120165 GCTTGGTAGTGCTTGAGCTAAAC 60.120 47.826 4.44 0.00 42.66 2.01
3451 4092 0.689623 AGCTTGGTAGTGCTTGAGCT 59.310 50.000 4.44 0.00 42.66 4.09
3463 4104 2.039879 ACCCGAAGTTTCATAGCTTGGT 59.960 45.455 0.00 0.00 0.00 3.67
3480 4121 1.227999 ACAAAGCATCACACGACCCG 61.228 55.000 0.00 0.00 0.00 5.28
3481 4122 0.517316 GACAAAGCATCACACGACCC 59.483 55.000 0.00 0.00 0.00 4.46
3485 4126 2.799978 TGTACAGACAAAGCATCACACG 59.200 45.455 0.00 0.00 30.68 4.49
3520 4161 3.427233 GCTTGCTGCATAAACTTCAGAGG 60.427 47.826 1.84 0.00 42.31 3.69
3544 4185 6.543465 AGCAAATTTATGATAGTACAGCTGCA 59.457 34.615 15.27 0.00 0.00 4.41
3574 4215 3.681897 ACAATTCTCTGAGACGATTGTGC 59.318 43.478 25.67 0.00 35.50 4.57
3577 4218 6.146837 ACTTTCACAATTCTCTGAGACGATTG 59.853 38.462 21.87 21.87 31.84 2.67
3601 4255 8.425577 AGCAGTAGATACAATGTGATGTTAAC 57.574 34.615 0.00 0.00 34.75 2.01
3604 4258 8.206867 ACATAGCAGTAGATACAATGTGATGTT 58.793 33.333 0.00 0.00 34.75 2.71
3694 4349 5.276461 GGCTTACCTTCCCCATAAAAATG 57.724 43.478 0.00 0.00 0.00 2.32
3714 4369 9.590451 TCAATCTTTTCATATCAAAATTCAGGC 57.410 29.630 0.00 0.00 0.00 4.85
3746 4401 5.882557 ACCAAGAAGTATGTTAGCAATCCAG 59.117 40.000 0.00 0.00 0.00 3.86
3750 4405 6.717289 TGGTACCAAGAAGTATGTTAGCAAT 58.283 36.000 13.60 0.00 0.00 3.56
3809 4464 9.962783 GTAGTTTCTTCAGTTCACTTCTAACTA 57.037 33.333 0.00 0.00 35.44 2.24
3834 4489 8.531982 TGAATGACTACTAAATCTAGCACTTGT 58.468 33.333 0.00 0.00 0.00 3.16
3835 4490 8.932945 TGAATGACTACTAAATCTAGCACTTG 57.067 34.615 0.00 0.00 0.00 3.16
3853 4508 4.816925 GGTGCTATTCTACCCTTGAATGAC 59.183 45.833 0.00 0.00 35.90 3.06
3865 4521 7.618019 ATTAAGGTCATCTGGTGCTATTCTA 57.382 36.000 0.00 0.00 0.00 2.10
3882 4538 6.888632 TCGTAGTTACTCTGGAGAATTAAGGT 59.111 38.462 4.49 0.00 0.00 3.50
3900 4556 7.491696 GGACAACTAAATCTAGCATTCGTAGTT 59.508 37.037 0.00 0.00 32.08 2.24
3901 4557 6.979238 GGACAACTAAATCTAGCATTCGTAGT 59.021 38.462 0.00 0.00 0.00 2.73
3902 4558 6.978659 TGGACAACTAAATCTAGCATTCGTAG 59.021 38.462 0.00 0.00 0.00 3.51
3903 4559 6.869695 TGGACAACTAAATCTAGCATTCGTA 58.130 36.000 0.00 0.00 0.00 3.43
3911 4575 7.121168 TGGCTTTGAATGGACAACTAAATCTAG 59.879 37.037 0.00 0.00 0.00 2.43
3933 4597 6.136857 TCTGGTAACTATATTCTGTCTGGCT 58.863 40.000 0.00 0.00 37.61 4.75
3946 4610 5.804639 TGTGAAATGTGCTCTGGTAACTAT 58.195 37.500 0.00 0.00 37.61 2.12
3950 4614 5.843673 TTTTGTGAAATGTGCTCTGGTAA 57.156 34.783 0.00 0.00 0.00 2.85
3976 4640 8.045176 ACAACTCAATTATCAAGTTAAGCCTC 57.955 34.615 0.00 0.00 32.20 4.70
4034 4698 1.466167 CAAAGACTTGGATCTGCACCG 59.534 52.381 0.00 0.00 0.00 4.94
4053 4717 7.592736 TCCTTCTACTAGGGTCTAAATCATCA 58.407 38.462 0.00 0.00 35.90 3.07
4277 4945 3.081804 CCATCCCGCTAACTTTCTTTGT 58.918 45.455 0.00 0.00 0.00 2.83
4282 4950 1.209747 ACCTCCATCCCGCTAACTTTC 59.790 52.381 0.00 0.00 0.00 2.62
4292 4960 4.855340 TGAAGTTTATGAACCTCCATCCC 58.145 43.478 0.00 0.00 36.39 3.85
4312 4980 5.175090 TGTTGTGTTTGCGATAACATTGA 57.825 34.783 6.13 0.00 39.93 2.57
4314 4982 5.527951 ACATGTTGTGTTTGCGATAACATT 58.472 33.333 0.00 0.00 39.25 2.71
4329 4997 2.151202 CTTGGGCGTCTAACATGTTGT 58.849 47.619 21.42 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.