Multiple sequence alignment - TraesCS5A01G145500

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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 TraesCS5A01G145500 chr5A 100.000 4894 0 0 1 4894 321721933 321717040 0.000000e+00 9038.0
1 TraesCS5A01G145500 chr5B 88.519 2613 149 42 1 2534 271299585 271302125 0.000000e+00 3024.0
2 TraesCS5A01G145500 chr5B 90.139 1440 76 35 2858 4258 271302426 271303838 0.000000e+00 1812.0
3 TraesCS5A01G145500 chr5B 88.542 288 23 6 2519 2803 271302143 271302423 1.690000e-89 340.0
4 TraesCS5A01G145500 chr5B 78.292 281 32 11 4336 4607 271303859 271304119 2.360000e-33 154.0
5 TraesCS5A01G145500 chr5B 94.872 39 2 0 537 575 237120079 237120041 1.470000e-05 62.1
6 TraesCS5A01G145500 chr5B 81.111 90 5 3 4808 4893 271304322 271304403 1.470000e-05 62.1
7 TraesCS5A01G145500 chr5D 91.326 1591 99 21 975 2532 233508479 233506895 0.000000e+00 2137.0
8 TraesCS5A01G145500 chr5D 93.439 1326 48 10 3088 4378 233506427 233505106 0.000000e+00 1930.0
9 TraesCS5A01G145500 chr5D 89.820 943 58 17 3 936 233509752 233508839 0.000000e+00 1175.0
10 TraesCS5A01G145500 chr5D 91.150 452 23 8 2519 2957 233506875 233506428 9.070000e-167 597.0
11 TraesCS5A01G145500 chr5D 84.097 371 37 13 999 1348 320921212 320920843 6.070000e-89 339.0
12 TraesCS5A01G145500 chr5D 82.749 371 42 12 999 1348 531913357 531913726 1.320000e-80 311.0
13 TraesCS5A01G145500 chr5D 97.101 138 4 0 4623 4760 233502845 233502708 2.950000e-57 233.0
14 TraesCS5A01G145500 chr5D 85.586 222 17 9 4394 4613 233505061 233504853 8.250000e-53 219.0
15 TraesCS5A01G145500 chr5D 89.683 126 5 1 4756 4881 233493165 233493048 2.360000e-33 154.0
16 TraesCS5A01G145500 chr5D 78.010 191 25 15 4633 4813 207577434 207577251 2.410000e-18 104.0
17 TraesCS5A01G145500 chr4A 85.753 365 37 7 999 1348 472918001 472918365 5.980000e-99 372.0
18 TraesCS5A01G145500 chr4B 85.205 365 39 7 999 1348 146498330 146497966 1.300000e-95 361.0
19 TraesCS5A01G145500 chr4B 76.111 180 32 9 4634 4806 95794457 95794632 3.140000e-12 84.2
20 TraesCS5A01G145500 chr4B 86.207 58 6 2 4633 4689 158978555 158978499 1.470000e-05 62.1
21 TraesCS5A01G145500 chr4D 85.014 367 36 10 999 1348 102168629 102168265 6.030000e-94 355.0
22 TraesCS5A01G145500 chr3A 81.671 371 46 13 999 1348 645742378 645742009 6.200000e-74 289.0
23 TraesCS5A01G145500 chr3A 82.595 316 35 9 1000 1295 260681283 260680968 1.350000e-65 261.0
24 TraesCS5A01G145500 chr3D 80.263 228 28 7 1137 1348 418847006 418847232 6.560000e-34 156.0
25 TraesCS5A01G145500 chr3D 79.755 163 22 9 4633 4786 302413518 302413358 1.860000e-19 108.0
26 TraesCS5A01G145500 chr3D 100.000 33 0 0 543 575 595760639 595760607 1.470000e-05 62.1
27 TraesCS5A01G145500 chr6D 77.778 189 29 10 4633 4813 123878114 123878297 2.410000e-18 104.0
28 TraesCS5A01G145500 chr3B 78.142 183 23 14 4633 4806 351417251 351417077 3.120000e-17 100.0
29 TraesCS5A01G145500 chr3B 97.222 36 1 0 537 572 691501970 691502005 1.470000e-05 62.1
30 TraesCS5A01G145500 chr3B 90.909 44 3 1 545 588 680344419 680344377 1.900000e-04 58.4
31 TraesCS5A01G145500 chr1B 76.842 190 30 12 4633 4813 311382668 311382484 1.450000e-15 95.3
32 TraesCS5A01G145500 chr7A 94.872 39 2 0 537 575 19069924 19069886 1.470000e-05 62.1
33 TraesCS5A01G145500 chr2D 97.222 36 1 0 537 572 285062943 285062978 1.470000e-05 62.1
34 TraesCS5A01G145500 chr7D 92.683 41 2 1 541 581 619038306 619038345 1.900000e-04 58.4


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 TraesCS5A01G145500 chr5A 321717040 321721933 4893 True 9038.00 9038 100.000000 1 4894 1 chr5A.!!$R1 4893
1 TraesCS5A01G145500 chr5B 271299585 271304403 4818 False 1078.42 3024 85.320600 1 4893 5 chr5B.!!$F1 4892
2 TraesCS5A01G145500 chr5D 233502708 233509752 7044 True 1048.50 2137 91.403667 3 4760 6 chr5D.!!$R4 4757

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
198 199 0.036952 CCAGTCGAGAGGTGCACATT 60.037 55.0 20.43 5.92 0.00 2.71 F
228 229 0.607217 TGCTGGAATCACACTGGCTG 60.607 55.0 0.00 0.00 0.00 4.85 F
1932 2300 0.881118 ACGCGCAATTCAGTTTGGAT 59.119 45.0 5.73 0.00 0.00 3.41 F
2144 2563 0.038159 CGTCCTTCACAGGTCAGACC 60.038 60.0 12.25 12.25 41.69 3.85 F
2362 2784 0.249911 CCCATGAGGTACCGCTTAGC 60.250 60.0 17.09 0.00 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1438 1778 0.463833 GGTAGCAGATTTCCGTGGGG 60.464 60.000 0.00 0.0 0.00 4.96 R
2012 2408 0.541392 AGTAATCAGGCGCATGGTCA 59.459 50.000 23.25 0.0 0.00 4.02 R
3199 3668 0.036732 AAGACCTTGGCAATCGCAGA 59.963 50.000 0.00 0.0 45.75 4.26 R
3265 3734 1.338020 CGCCAGGAAAAAGAGCTTGTT 59.662 47.619 0.00 0.0 0.00 2.83 R
4291 4811 0.796312 TTTGGAATGAGCGAGCGAAC 59.204 50.000 0.00 0.0 0.00 3.95 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
136 137 1.052124 TGGGAGTGTTCCGTCCACTT 61.052 55.000 0.00 0.00 45.04 3.16
144 145 1.531578 GTTCCGTCCACTTGAAGCTTC 59.468 52.381 19.89 19.89 0.00 3.86
170 171 3.635591 CTTTGAGTGGCCCCTAATTGAT 58.364 45.455 0.00 0.00 0.00 2.57
177 178 1.648720 CCCCTAATTGATGCGTGCG 59.351 57.895 0.00 0.00 0.00 5.34
188 189 4.400109 GCGTGCGTCCAGTCGAGA 62.400 66.667 0.00 0.00 0.00 4.04
189 190 2.202362 CGTGCGTCCAGTCGAGAG 60.202 66.667 0.00 0.00 0.00 3.20
190 191 2.179517 GTGCGTCCAGTCGAGAGG 59.820 66.667 0.00 0.00 0.00 3.69
191 192 2.282251 TGCGTCCAGTCGAGAGGT 60.282 61.111 3.23 0.00 0.00 3.85
192 193 2.179517 GCGTCCAGTCGAGAGGTG 59.820 66.667 3.23 0.00 0.00 4.00
193 194 2.179517 CGTCCAGTCGAGAGGTGC 59.820 66.667 3.23 0.00 0.00 5.01
194 195 2.626780 CGTCCAGTCGAGAGGTGCA 61.627 63.158 3.23 0.00 0.00 4.57
195 196 1.080434 GTCCAGTCGAGAGGTGCAC 60.080 63.158 8.80 8.80 0.00 4.57
196 197 1.530655 TCCAGTCGAGAGGTGCACA 60.531 57.895 20.43 0.00 0.00 4.57
197 198 0.900182 TCCAGTCGAGAGGTGCACAT 60.900 55.000 20.43 12.71 0.00 3.21
198 199 0.036952 CCAGTCGAGAGGTGCACATT 60.037 55.000 20.43 5.92 0.00 2.71
199 200 1.204704 CCAGTCGAGAGGTGCACATTA 59.795 52.381 20.43 0.00 0.00 1.90
228 229 0.607217 TGCTGGAATCACACTGGCTG 60.607 55.000 0.00 0.00 0.00 4.85
230 231 1.735386 CTGGAATCACACTGGCTGAG 58.265 55.000 0.00 0.00 0.00 3.35
233 234 1.277557 GGAATCACACTGGCTGAGAGT 59.722 52.381 0.00 0.00 0.00 3.24
247 248 3.873801 GCTGAGAGTTGGAGGCCAATTTA 60.874 47.826 5.01 0.00 45.80 1.40
289 292 3.116079 ACGACACCATCTTTAACCGTT 57.884 42.857 0.00 0.00 0.00 4.44
305 308 1.334329 CCGTTCTTTTGCCCGTTGTAC 60.334 52.381 0.00 0.00 0.00 2.90
312 315 2.172851 TTGCCCGTTGTACTTGGTAG 57.827 50.000 0.00 0.00 0.00 3.18
314 317 1.417145 TGCCCGTTGTACTTGGTAGTT 59.583 47.619 0.00 0.00 35.78 2.24
339 342 1.375908 GAATCCTCGTGTGCCAGCA 60.376 57.895 0.00 0.00 0.00 4.41
345 348 3.349006 CGTGTGCCAGCAGTCACC 61.349 66.667 7.54 0.00 32.51 4.02
357 360 1.000607 GCAGTCACCGTCAAGTGAGTA 60.001 52.381 1.92 0.00 46.35 2.59
403 406 1.131638 TGCCAGACCATACCATCTCC 58.868 55.000 0.00 0.00 0.00 3.71
502 505 1.274167 ACTCGTTATCTTTGTCCGGCA 59.726 47.619 0.00 0.00 0.00 5.69
515 518 0.974010 TCCGGCAAAGGGATAGTCGT 60.974 55.000 0.00 0.00 0.00 4.34
533 536 9.661187 GATAGTCGTTGAACTAAAATATCTCGA 57.339 33.333 0.00 0.00 35.47 4.04
572 575 7.788026 TCCCTTCGTAAAGAAATATAAGAGCA 58.212 34.615 0.00 0.00 38.57 4.26
584 587 9.080097 AGAAATATAAGAGCATTACGGAGTACT 57.920 33.333 0.00 0.00 45.76 2.73
660 667 6.947464 TCTAAAATCTTGAGAATCGGACCTT 58.053 36.000 0.00 0.00 38.61 3.50
726 741 3.225798 TTGCCAAGGCCAGCACAC 61.226 61.111 13.99 0.00 39.10 3.82
730 745 4.332637 CAAGGCCAGCACACACGC 62.333 66.667 5.01 0.00 0.00 5.34
800 815 3.585990 GCCCATCATTCGCCACCG 61.586 66.667 0.00 0.00 0.00 4.94
801 816 3.585990 CCCATCATTCGCCACCGC 61.586 66.667 0.00 0.00 0.00 5.68
802 817 3.585990 CCATCATTCGCCACCGCC 61.586 66.667 0.00 0.00 0.00 6.13
1209 1548 3.827898 GTCCGCCTCCTCTCCGTG 61.828 72.222 0.00 0.00 0.00 4.94
1411 1751 9.339850 TCTTCAGTATACTGTACTACCATCTTC 57.660 37.037 27.83 0.00 44.12 2.87
1436 1776 4.216257 TGCGTACCGATTCCTATAGTTACC 59.784 45.833 0.00 0.00 0.00 2.85
1438 1778 5.391416 GCGTACCGATTCCTATAGTTACCTC 60.391 48.000 0.00 0.00 0.00 3.85
1588 1931 6.860080 AGTAATTTGAAGCACTGATTGATGG 58.140 36.000 0.00 0.00 0.00 3.51
1602 1945 1.448540 GATGGTGCTGTGGAGGACG 60.449 63.158 0.00 0.00 41.37 4.79
1603 1946 2.859273 GATGGTGCTGTGGAGGACGG 62.859 65.000 0.00 0.00 41.37 4.79
1604 1947 3.311110 GGTGCTGTGGAGGACGGA 61.311 66.667 0.00 0.00 41.37 4.69
1605 1948 2.048127 GTGCTGTGGAGGACGGAC 60.048 66.667 0.00 0.00 30.02 4.79
1632 1979 3.301197 CGTACAAGAATCAGATCAACGCG 60.301 47.826 3.53 3.53 0.00 6.01
1687 2034 9.603298 GAAAGGTCTAATTTTTCGTAAATTCGT 57.397 29.630 12.10 1.97 32.64 3.85
1724 2071 5.798434 GCAACGACAAATTAGGAATGTAACC 59.202 40.000 0.00 0.00 0.00 2.85
1764 2111 2.685850 TGCTGGTGATGATCACTCAG 57.314 50.000 26.08 26.08 46.19 3.35
1823 2170 4.330944 TCCTAAAGTGAAAGAACGCTGA 57.669 40.909 0.00 0.00 0.00 4.26
1840 2194 2.861360 GCTGAGCTTGCTTTGGAAACAG 60.861 50.000 0.00 0.00 44.54 3.16
1864 2218 1.105457 CGCACCATCAATCCACCATT 58.895 50.000 0.00 0.00 0.00 3.16
1877 2239 5.659440 ATCCACCATTGTTGTTTCCATAC 57.341 39.130 0.00 0.00 0.00 2.39
1885 2247 6.202570 CCATTGTTGTTTCCATACAAACCTTG 59.797 38.462 0.00 0.00 39.54 3.61
1919 2287 3.550561 CAGTAAATTTTCTTCACGCGCA 58.449 40.909 5.73 0.00 0.00 6.09
1932 2300 0.881118 ACGCGCAATTCAGTTTGGAT 59.119 45.000 5.73 0.00 0.00 3.41
1977 2373 2.749076 CTGCATGGAATTCTCCGTTTCA 59.251 45.455 5.23 0.00 45.85 2.69
1985 2381 7.695480 TGGAATTCTCCGTTTCATATTTTGA 57.305 32.000 5.23 0.00 45.85 2.69
2006 2402 9.911788 TTTTGATTCTCTCCATTAGCTTCTATT 57.088 29.630 0.00 0.00 0.00 1.73
2007 2403 8.899427 TTGATTCTCTCCATTAGCTTCTATTG 57.101 34.615 0.00 0.00 0.00 1.90
2008 2404 6.933521 TGATTCTCTCCATTAGCTTCTATTGC 59.066 38.462 0.00 0.00 0.00 3.56
2011 2407 2.135139 TCCATTAGCTTCTATTGCGCG 58.865 47.619 0.00 0.00 35.28 6.86
2012 2408 1.867233 CCATTAGCTTCTATTGCGCGT 59.133 47.619 8.43 0.00 35.28 6.01
2013 2409 2.348872 CCATTAGCTTCTATTGCGCGTG 60.349 50.000 8.43 0.00 35.28 5.34
2014 2410 2.287393 TTAGCTTCTATTGCGCGTGA 57.713 45.000 8.43 0.00 35.28 4.35
2015 2411 1.556564 TAGCTTCTATTGCGCGTGAC 58.443 50.000 8.43 0.00 35.28 3.67
2016 2412 1.084370 AGCTTCTATTGCGCGTGACC 61.084 55.000 8.43 0.00 35.28 4.02
2017 2413 1.358725 GCTTCTATTGCGCGTGACCA 61.359 55.000 8.43 0.00 0.00 4.02
2018 2414 1.290203 CTTCTATTGCGCGTGACCAT 58.710 50.000 8.43 0.00 0.00 3.55
2019 2415 1.004610 CTTCTATTGCGCGTGACCATG 60.005 52.381 8.43 0.00 0.00 3.66
2020 2416 1.010797 CTATTGCGCGTGACCATGC 60.011 57.895 8.43 4.22 39.85 4.06
2034 2451 0.583438 CCATGCGCCTGATTACTTCG 59.417 55.000 14.72 0.00 0.00 3.79
2083 2502 3.470709 TGTCCTCTTGCAGAGTTTCTTG 58.529 45.455 10.86 0.00 40.72 3.02
2092 2511 5.284861 TGCAGAGTTTCTTGTACCAGTTA 57.715 39.130 0.00 0.00 0.00 2.24
2107 2526 2.414559 CCAGTTATGCAAAGGAACTGCG 60.415 50.000 20.33 13.60 45.66 5.18
2135 2554 2.359850 GCCATGGCGTCCTTCACA 60.360 61.111 23.48 0.00 0.00 3.58
2139 2558 1.021390 CATGGCGTCCTTCACAGGTC 61.021 60.000 0.00 0.00 41.69 3.85
2144 2563 0.038159 CGTCCTTCACAGGTCAGACC 60.038 60.000 12.25 12.25 41.69 3.85
2158 2577 2.354821 GTCAGACCTTTGTTGTGTGGTC 59.645 50.000 0.00 0.00 46.67 4.02
2169 2588 1.102154 TGTGTGGTCTTTGTTGCTGG 58.898 50.000 0.00 0.00 0.00 4.85
2191 2610 4.572389 GGAATTGTCAGCTCGATACAACAT 59.428 41.667 5.31 0.00 36.06 2.71
2194 2613 7.201609 GGAATTGTCAGCTCGATACAACATTTA 60.202 37.037 5.31 0.00 36.06 1.40
2217 2636 5.894807 ACATTTGCAGCTATGTGGTTAATC 58.105 37.500 11.50 0.00 33.90 1.75
2222 2641 5.940617 TGCAGCTATGTGGTTAATCCTATT 58.059 37.500 0.00 0.00 37.07 1.73
2296 2718 4.740902 AGAAAGGGGTACTGAAAATTGCT 58.259 39.130 0.00 0.00 0.00 3.91
2362 2784 0.249911 CCCATGAGGTACCGCTTAGC 60.250 60.000 17.09 0.00 0.00 3.09
2373 2795 2.294074 ACCGCTTAGCAACAAAGTTCA 58.706 42.857 4.70 0.00 0.00 3.18
2376 2798 4.083484 ACCGCTTAGCAACAAAGTTCATAC 60.083 41.667 4.70 0.00 0.00 2.39
2388 2810 9.658475 CAACAAAGTTCATACGATTTTACTGAA 57.342 29.630 0.00 0.00 0.00 3.02
2416 2838 6.183360 TGCTCTAGTAAGTTCCTCATCATGTC 60.183 42.308 0.00 0.00 0.00 3.06
2417 2839 6.378710 TCTAGTAAGTTCCTCATCATGTCG 57.621 41.667 0.00 0.00 0.00 4.35
2588 3042 4.591321 ACAATCCATGTACAACCTCCAT 57.409 40.909 0.00 0.00 41.63 3.41
2592 3046 4.131649 TCCATGTACAACCTCCATAACG 57.868 45.455 0.00 0.00 0.00 3.18
2631 3088 6.593770 AGATAAATCGTCACACTTGTGCAATA 59.406 34.615 4.38 0.00 45.25 1.90
2632 3089 5.431420 AAATCGTCACACTTGTGCAATAA 57.569 34.783 4.38 0.00 45.25 1.40
2633 3090 5.627499 AATCGTCACACTTGTGCAATAAT 57.373 34.783 4.38 0.00 45.25 1.28
2722 3179 8.201554 TCTTATGAAGCAGCACAATTTACTAG 57.798 34.615 0.00 0.00 0.00 2.57
2724 3181 8.560355 TTATGAAGCAGCACAATTTACTAGAA 57.440 30.769 0.00 0.00 0.00 2.10
2725 3182 6.486253 TGAAGCAGCACAATTTACTAGAAG 57.514 37.500 0.00 0.00 0.00 2.85
2726 3183 5.997746 TGAAGCAGCACAATTTACTAGAAGT 59.002 36.000 0.00 0.00 0.00 3.01
2727 3184 7.158697 TGAAGCAGCACAATTTACTAGAAGTA 58.841 34.615 0.00 0.00 0.00 2.24
2728 3185 6.969828 AGCAGCACAATTTACTAGAAGTAC 57.030 37.500 0.00 0.00 28.93 2.73
2729 3186 6.702329 AGCAGCACAATTTACTAGAAGTACT 58.298 36.000 0.00 0.00 28.93 2.73
2730 3187 6.814146 AGCAGCACAATTTACTAGAAGTACTC 59.186 38.462 0.00 0.00 28.93 2.59
2743 3201 8.570068 ACTAGAAGTACTCCAGTAAAAGAGAG 57.430 38.462 0.00 0.00 34.13 3.20
2748 3206 7.102847 AGTACTCCAGTAAAAGAGAGCATAC 57.897 40.000 0.00 0.00 34.13 2.39
2755 3213 8.038944 TCCAGTAAAAGAGAGCATACGTTTTAT 58.961 33.333 0.00 0.00 0.00 1.40
2819 3279 7.974675 TCTTATGAAGCAGTGCAATTTACTAC 58.025 34.615 19.20 0.00 0.00 2.73
2902 3370 3.071479 TGCAATCTACGTTCAACTTCCC 58.929 45.455 0.00 0.00 0.00 3.97
2903 3371 3.071479 GCAATCTACGTTCAACTTCCCA 58.929 45.455 0.00 0.00 0.00 4.37
2926 3395 7.596248 CCCAAGCAAAATACAATAGCATATGAC 59.404 37.037 6.97 0.00 0.00 3.06
3006 3475 9.715121 ACATCAAACAAAAGATTTAGCATTGAT 57.285 25.926 0.00 0.00 35.90 2.57
3009 3478 9.414295 TCAAACAAAAGATTTAGCATTGATCTG 57.586 29.630 0.00 0.00 30.91 2.90
3010 3479 9.199982 CAAACAAAAGATTTAGCATTGATCTGT 57.800 29.630 0.00 0.00 30.91 3.41
3013 3482 8.186821 ACAAAAGATTTAGCATTGATCTGTAGC 58.813 33.333 0.00 0.00 30.91 3.58
3014 3483 7.870509 AAAGATTTAGCATTGATCTGTAGCA 57.129 32.000 0.00 0.00 30.91 3.49
3015 3484 6.857777 AGATTTAGCATTGATCTGTAGCAC 57.142 37.500 0.00 0.00 0.00 4.40
3016 3485 6.590068 AGATTTAGCATTGATCTGTAGCACT 58.410 36.000 0.00 0.00 0.00 4.40
3017 3486 7.730084 AGATTTAGCATTGATCTGTAGCACTA 58.270 34.615 0.00 0.00 0.00 2.74
3018 3487 8.206867 AGATTTAGCATTGATCTGTAGCACTAA 58.793 33.333 0.00 0.00 0.00 2.24
3019 3488 8.915057 ATTTAGCATTGATCTGTAGCACTAAT 57.085 30.769 0.00 0.00 0.00 1.73
3020 3489 8.737168 TTTAGCATTGATCTGTAGCACTAATT 57.263 30.769 0.00 0.00 0.00 1.40
3021 3490 8.737168 TTAGCATTGATCTGTAGCACTAATTT 57.263 30.769 0.00 0.00 0.00 1.82
3022 3491 7.636150 AGCATTGATCTGTAGCACTAATTTT 57.364 32.000 0.00 0.00 0.00 1.82
3023 3492 8.737168 AGCATTGATCTGTAGCACTAATTTTA 57.263 30.769 0.00 0.00 0.00 1.52
3024 3493 8.834465 AGCATTGATCTGTAGCACTAATTTTAG 58.166 33.333 0.00 0.00 36.82 1.85
3025 3494 8.830580 GCATTGATCTGTAGCACTAATTTTAGA 58.169 33.333 4.40 0.00 34.84 2.10
3027 3496 8.948631 TTGATCTGTAGCACTAATTTTAGAGG 57.051 34.615 4.40 0.00 34.84 3.69
3028 3497 6.986817 TGATCTGTAGCACTAATTTTAGAGGC 59.013 38.462 4.40 7.30 36.00 4.70
3029 3498 5.671493 TCTGTAGCACTAATTTTAGAGGCC 58.329 41.667 0.00 0.00 36.21 5.19
3030 3499 5.425539 TCTGTAGCACTAATTTTAGAGGCCT 59.574 40.000 3.86 3.86 36.21 5.19
3046 3515 3.387962 AGGCCTCATCTTGTCAAGGATA 58.612 45.455 12.66 0.00 0.00 2.59
3047 3516 3.135530 AGGCCTCATCTTGTCAAGGATAC 59.864 47.826 12.66 0.00 0.00 2.24
3053 3522 6.261826 CCTCATCTTGTCAAGGATACCATTTC 59.738 42.308 12.66 0.00 37.17 2.17
3060 3529 7.452880 TGTCAAGGATACCATTTCAAAGAAG 57.547 36.000 0.00 0.00 37.17 2.85
3109 3578 8.587952 TGCTTTTGTTAGAAAAGAAATAAGCC 57.412 30.769 17.05 0.00 39.04 4.35
3199 3668 6.942532 TGCTTTCTTTGACTTGACACTATT 57.057 33.333 0.00 0.00 0.00 1.73
3209 3678 3.372206 ACTTGACACTATTCTGCGATTGC 59.628 43.478 0.00 0.00 43.20 3.56
3290 3759 1.609320 GCTCTTTTTCCTGGCGACTCT 60.609 52.381 0.00 0.00 0.00 3.24
3329 3798 8.177119 TGCTTCACATTTTCAGGTACTTTATT 57.823 30.769 0.00 0.00 34.60 1.40
3403 3890 4.634012 TGGGATGGTGTATTAGTATGCC 57.366 45.455 0.00 0.00 0.00 4.40
3417 3904 6.656632 TTAGTATGCCTGATCCTAGTGAAG 57.343 41.667 0.00 0.00 0.00 3.02
3534 4025 9.443283 GACAGTTTATTTCATTCTGTATGCATC 57.557 33.333 0.19 0.00 39.08 3.91
3552 4043 9.443283 GTATGCATCTAATCATTTGACTGAAAC 57.557 33.333 0.19 0.00 0.00 2.78
3633 4124 3.020274 TCTGAGAGACTGGCATGACTAC 58.980 50.000 0.00 0.00 0.00 2.73
3704 4195 2.164624 CTGAAGGACTCGACCTGTTAGG 59.835 54.545 0.00 0.00 40.49 2.69
3716 4207 5.104817 TCGACCTGTTAGGGGTAAATTAAGG 60.105 44.000 0.00 0.00 40.58 2.69
3726 4217 9.703677 TTAGGGGTAAATTAAGGGAAACATAAG 57.296 33.333 0.00 0.00 0.00 1.73
3775 4266 7.129457 TGAGGATGTTTGTATCTGAGCTAAT 57.871 36.000 0.00 0.00 0.00 1.73
3919 4410 0.109342 CTGCTGTCTTGGGAGTTGGT 59.891 55.000 0.00 0.00 0.00 3.67
4003 4494 6.374578 TCGATCTTGATTTATCAGCTACTCG 58.625 40.000 0.00 0.00 38.19 4.18
4079 4570 2.235402 GGATTCTGGTGGTCGGAAACTA 59.765 50.000 0.00 0.00 43.30 2.24
4092 4583 3.074412 CGGAAACTAAACTGCCACTCAT 58.926 45.455 0.00 0.00 0.00 2.90
4115 4621 8.324306 TCATGATATTCCCTGATGTTTCTATCC 58.676 37.037 0.00 0.00 0.00 2.59
4118 4624 1.416401 TCCCTGATGTTTCTATCCGGC 59.584 52.381 0.00 0.00 32.08 6.13
4216 4723 2.851263 TAACACACAGAGCGGGAAAT 57.149 45.000 0.00 0.00 0.00 2.17
4311 4831 1.398390 GTTCGCTCGCTCATTCCAAAT 59.602 47.619 0.00 0.00 0.00 2.32
4314 4834 2.487762 TCGCTCGCTCATTCCAAATTTT 59.512 40.909 0.00 0.00 0.00 1.82
4315 4835 2.848302 CGCTCGCTCATTCCAAATTTTC 59.152 45.455 0.00 0.00 0.00 2.29
4323 4843 6.626623 CGCTCATTCCAAATTTTCCAAGAGAT 60.627 38.462 9.62 0.00 0.00 2.75
4324 4844 6.534079 GCTCATTCCAAATTTTCCAAGAGATG 59.466 38.462 9.62 0.00 0.00 2.90
4325 4845 7.578189 GCTCATTCCAAATTTTCCAAGAGATGA 60.578 37.037 9.62 0.00 0.00 2.92
4326 4846 7.833786 TCATTCCAAATTTTCCAAGAGATGAG 58.166 34.615 0.00 0.00 0.00 2.90
4327 4847 5.649782 TCCAAATTTTCCAAGAGATGAGC 57.350 39.130 0.00 0.00 0.00 4.26
4328 4848 5.078949 TCCAAATTTTCCAAGAGATGAGCA 58.921 37.500 0.00 0.00 0.00 4.26
4329 4849 5.718130 TCCAAATTTTCCAAGAGATGAGCAT 59.282 36.000 0.00 0.00 0.00 3.79
4330 4850 6.040878 CCAAATTTTCCAAGAGATGAGCATC 58.959 40.000 2.27 2.27 38.09 3.91
4374 4895 8.472007 TTGTACCTTGTGATTTTGTAAGGATT 57.528 30.769 8.70 0.00 41.71 3.01
4378 4899 5.634859 CCTTGTGATTTTGTAAGGATTGTGC 59.365 40.000 0.00 0.00 41.71 4.57
4379 4900 5.132897 TGTGATTTTGTAAGGATTGTGCC 57.867 39.130 0.00 0.00 0.00 5.01
4380 4901 4.586421 TGTGATTTTGTAAGGATTGTGCCA 59.414 37.500 0.00 0.00 0.00 4.92
4381 4902 5.069648 TGTGATTTTGTAAGGATTGTGCCAA 59.930 36.000 0.00 0.00 0.00 4.52
4383 4904 7.039434 TGTGATTTTGTAAGGATTGTGCCAATA 60.039 33.333 1.06 0.00 0.00 1.90
4384 4905 7.981225 GTGATTTTGTAAGGATTGTGCCAATAT 59.019 33.333 1.06 0.00 0.00 1.28
4385 4906 7.980662 TGATTTTGTAAGGATTGTGCCAATATG 59.019 33.333 1.06 0.00 0.00 1.78
4387 4908 6.449635 TTGTAAGGATTGTGCCAATATGAC 57.550 37.500 1.06 0.00 0.00 3.06
4389 4910 6.186957 TGTAAGGATTGTGCCAATATGACTT 58.813 36.000 1.06 6.29 0.00 3.01
4390 4911 6.663093 TGTAAGGATTGTGCCAATATGACTTT 59.337 34.615 1.06 0.00 0.00 2.66
4391 4912 5.587388 AGGATTGTGCCAATATGACTTTG 57.413 39.130 1.06 0.00 0.00 2.77
4392 4913 4.403432 AGGATTGTGCCAATATGACTTTGG 59.597 41.667 1.06 0.00 45.30 3.28
4430 4980 3.248043 TGGCACAATCACTAGGCAC 57.752 52.632 0.00 0.00 31.92 5.01
4466 5016 3.306989 CCGAGCCAAGCCTTGATATCATA 60.307 47.826 5.89 0.00 0.00 2.15
4471 5021 4.747931 GCCAAGCCTTGATATCATACCACT 60.748 45.833 5.89 0.00 0.00 4.00
4472 5022 4.758674 CCAAGCCTTGATATCATACCACTG 59.241 45.833 5.89 0.88 0.00 3.66
4474 5024 6.464322 CCAAGCCTTGATATCATACCACTGTA 60.464 42.308 5.89 0.00 0.00 2.74
4475 5025 6.352016 AGCCTTGATATCATACCACTGTAG 57.648 41.667 6.17 0.00 0.00 2.74
4476 5026 5.841237 AGCCTTGATATCATACCACTGTAGT 59.159 40.000 6.17 0.00 0.00 2.73
4477 5027 6.015010 AGCCTTGATATCATACCACTGTAGTC 60.015 42.308 6.17 0.00 0.00 2.59
4478 5028 6.382608 CCTTGATATCATACCACTGTAGTCG 58.617 44.000 6.17 0.00 0.00 4.18
4479 5029 6.016192 CCTTGATATCATACCACTGTAGTCGT 60.016 42.308 6.17 0.00 0.00 4.34
4501 5059 2.717639 ATTGGTAAAGGAGATGCGCT 57.282 45.000 9.73 0.00 0.00 5.92
4505 5063 0.744414 GTAAAGGAGATGCGCTGCCA 60.744 55.000 9.73 0.00 35.18 4.92
4509 5067 2.042831 GGAGATGCGCTGCCAGTTT 61.043 57.895 9.73 0.00 0.00 2.66
4517 5075 1.145162 CGCTGCCAGTTTTTGCGTTT 61.145 50.000 0.00 0.00 41.45 3.60
4565 5123 1.479709 CCATAATTTGGCGAACCCCA 58.520 50.000 0.00 0.00 39.09 4.96
4567 5125 2.433970 CCATAATTTGGCGAACCCCAAT 59.566 45.455 0.00 0.00 43.91 3.16
4602 5184 3.400255 GGCCGTCCATAACCTATCTTTC 58.600 50.000 0.00 0.00 0.00 2.62
4605 5187 4.560919 GCCGTCCATAACCTATCTTTCGAT 60.561 45.833 0.00 0.00 0.00 3.59
4647 7227 4.516321 AGTGCCATTTCAAAAGCAAATTCC 59.484 37.500 0.02 0.00 36.91 3.01
4675 7255 1.751351 GCACAAATTTAGGGGGAGCTC 59.249 52.381 4.71 4.71 0.00 4.09
4760 7340 5.491070 AGCTATGTTGTCATCAAGTAGCAA 58.509 37.500 14.58 0.00 43.57 3.91
4761 7341 5.939883 AGCTATGTTGTCATCAAGTAGCAAA 59.060 36.000 14.58 0.00 43.57 3.68
4762 7342 6.430925 AGCTATGTTGTCATCAAGTAGCAAAA 59.569 34.615 14.58 0.00 43.57 2.44
4763 7343 7.040478 AGCTATGTTGTCATCAAGTAGCAAAAA 60.040 33.333 14.58 0.00 43.57 1.94
4764 7344 7.272084 GCTATGTTGTCATCAAGTAGCAAAAAG 59.728 37.037 9.95 0.00 42.30 2.27
4765 7345 5.830912 TGTTGTCATCAAGTAGCAAAAAGG 58.169 37.500 0.00 0.00 33.97 3.11
4766 7346 5.221224 TGTTGTCATCAAGTAGCAAAAAGGG 60.221 40.000 0.00 0.00 33.97 3.95
4767 7347 4.724399 TGTCATCAAGTAGCAAAAAGGGA 58.276 39.130 0.00 0.00 0.00 4.20
4768 7348 4.761739 TGTCATCAAGTAGCAAAAAGGGAG 59.238 41.667 0.00 0.00 0.00 4.30
4769 7349 5.003804 GTCATCAAGTAGCAAAAAGGGAGA 58.996 41.667 0.00 0.00 0.00 3.71
4770 7350 5.123027 GTCATCAAGTAGCAAAAAGGGAGAG 59.877 44.000 0.00 0.00 0.00 3.20
4790 7370 7.140048 GGAGAGATTCAAAATGCATCTTCATC 58.860 38.462 0.00 0.00 30.69 2.92
4791 7371 7.040473 AGAGATTCAAAATGCATCTTCATCC 57.960 36.000 0.00 0.00 30.69 3.51
4792 7372 6.834451 AGAGATTCAAAATGCATCTTCATCCT 59.166 34.615 0.00 0.00 30.69 3.24
4793 7373 7.013464 AGAGATTCAAAATGCATCTTCATCCTC 59.987 37.037 0.00 3.23 30.69 3.71
4794 7374 6.834451 AGATTCAAAATGCATCTTCATCCTCT 59.166 34.615 0.00 0.00 25.68 3.69
4795 7375 7.997223 AGATTCAAAATGCATCTTCATCCTCTA 59.003 33.333 0.00 0.00 25.68 2.43
4796 7376 7.563888 TTCAAAATGCATCTTCATCCTCTAG 57.436 36.000 0.00 0.00 0.00 2.43
4797 7377 6.060136 TCAAAATGCATCTTCATCCTCTAGG 58.940 40.000 0.00 0.00 0.00 3.02
4798 7378 5.643421 AAATGCATCTTCATCCTCTAGGT 57.357 39.130 0.00 0.00 36.34 3.08
4799 7379 4.620589 ATGCATCTTCATCCTCTAGGTG 57.379 45.455 0.00 0.00 36.34 4.00
4800 7380 2.702478 TGCATCTTCATCCTCTAGGTGG 59.298 50.000 0.00 0.00 36.34 4.61
4801 7381 2.968574 GCATCTTCATCCTCTAGGTGGA 59.031 50.000 7.64 7.64 38.06 4.02
4802 7382 3.582208 GCATCTTCATCCTCTAGGTGGAT 59.418 47.826 10.97 10.97 44.44 3.41
4803 7383 4.041444 GCATCTTCATCCTCTAGGTGGATT 59.959 45.833 13.26 0.24 41.94 3.01
4804 7384 5.455899 GCATCTTCATCCTCTAGGTGGATTT 60.456 44.000 13.26 0.00 41.94 2.17
4805 7385 6.599445 CATCTTCATCCTCTAGGTGGATTTT 58.401 40.000 13.26 0.00 41.94 1.82
4806 7386 6.642733 TCTTCATCCTCTAGGTGGATTTTT 57.357 37.500 13.26 0.00 41.94 1.94
4847 7427 8.852671 ATTTCAGATTATAACCCAAATTCCCA 57.147 30.769 0.00 0.00 0.00 4.37
4848 7428 8.671987 TTTCAGATTATAACCCAAATTCCCAA 57.328 30.769 0.00 0.00 0.00 4.12
4849 7429 8.671987 TTCAGATTATAACCCAAATTCCCAAA 57.328 30.769 0.00 0.00 0.00 3.28
4864 7444 0.040425 CCAAAAGACGCGACAAAGGG 60.040 55.000 15.93 3.87 0.00 3.95
4866 7446 1.069906 CAAAAGACGCGACAAAGGGAG 60.070 52.381 15.93 0.00 0.00 4.30
4868 7448 0.963962 AAGACGCGACAAAGGGAGTA 59.036 50.000 15.93 0.00 0.00 2.59
4873 7453 1.439679 GCGACAAAGGGAGTAGTTGG 58.560 55.000 0.00 0.00 0.00 3.77
4893 7477 6.265196 AGTTGGTGAAATAACTCTCATGCAAA 59.735 34.615 0.00 0.00 31.88 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 3.365265 GGGCCACTCAAAGCACGG 61.365 66.667 4.39 0.00 0.00 4.94
170 171 4.700365 CTCGACTGGACGCACGCA 62.700 66.667 0.00 0.00 0.00 5.24
177 178 1.080434 GTGCACCTCTCGACTGGAC 60.080 63.158 5.22 0.00 0.00 4.02
228 229 3.633986 CCATAAATTGGCCTCCAACTCTC 59.366 47.826 3.32 0.00 46.95 3.20
247 248 1.748950 TGCGTACATTGATGTGCCAT 58.251 45.000 6.87 0.00 41.89 4.40
261 262 2.157834 AGATGGTGTCGTTTTGCGTA 57.842 45.000 0.00 0.00 42.13 4.42
289 292 1.950909 CCAAGTACAACGGGCAAAAGA 59.049 47.619 0.00 0.00 0.00 2.52
305 308 5.464722 CGAGGATTCATGATCAACTACCAAG 59.535 44.000 0.00 0.00 36.43 3.61
312 315 3.242543 GCACACGAGGATTCATGATCAAC 60.243 47.826 0.00 0.00 36.43 3.18
314 317 2.554142 GCACACGAGGATTCATGATCA 58.446 47.619 0.00 0.00 36.43 2.92
339 342 2.553172 GACTACTCACTTGACGGTGACT 59.447 50.000 0.00 0.00 40.72 3.41
345 348 5.096169 CACATAAGGACTACTCACTTGACG 58.904 45.833 0.00 0.00 0.00 4.35
357 360 3.039011 AGTTATCGGCCACATAAGGACT 58.961 45.455 2.24 0.00 33.12 3.85
403 406 1.507141 AACTGGCGAAAGAGCGGTTG 61.507 55.000 0.00 0.00 38.18 3.77
502 505 9.901172 ATATTTTAGTTCAACGACTATCCCTTT 57.099 29.630 0.00 0.00 32.51 3.11
572 575 7.148306 CCATTGCTTTGTTTAGTACTCCGTAAT 60.148 37.037 0.00 0.00 0.00 1.89
576 579 4.142687 CCCATTGCTTTGTTTAGTACTCCG 60.143 45.833 0.00 0.00 0.00 4.63
577 580 5.007682 TCCCATTGCTTTGTTTAGTACTCC 58.992 41.667 0.00 0.00 0.00 3.85
584 587 3.886505 ACTTCGTCCCATTGCTTTGTTTA 59.113 39.130 0.00 0.00 0.00 2.01
634 641 6.819146 AGGTCCGATTCTCAAGATTTTAGAAC 59.181 38.462 0.00 0.00 32.38 3.01
741 756 2.109387 TGTAAAGTGCGGTGCGGT 59.891 55.556 0.00 0.00 0.00 5.68
785 800 3.585990 GGCGGTGGCGAATGATGG 61.586 66.667 0.00 0.00 41.24 3.51
800 815 1.226575 GGAATTGTTTAGCGGCGGC 60.227 57.895 9.78 8.43 40.37 6.53
801 816 1.061887 CGGAATTGTTTAGCGGCGG 59.938 57.895 9.78 0.00 0.00 6.13
802 817 1.582680 GCGGAATTGTTTAGCGGCG 60.583 57.895 0.51 0.51 0.00 6.46
953 973 0.250727 CTTGGGGTGTGGTGTGGTAG 60.251 60.000 0.00 0.00 0.00 3.18
1005 1344 3.428316 CCTTCTCCAGCTTCTCGTACTTC 60.428 52.174 0.00 0.00 0.00 3.01
1209 1548 2.360475 GGCTTGGTGACCTGCTCC 60.360 66.667 16.72 4.12 0.00 4.70
1324 1663 2.047213 TTGACGACCTGGGTGGGAAC 62.047 60.000 6.72 0.00 41.11 3.62
1326 1665 2.122769 TTGACGACCTGGGTGGGA 60.123 61.111 6.72 0.00 41.11 4.37
1332 1671 5.946972 AGATAGATATACCTTGACGACCTGG 59.053 44.000 0.00 0.00 0.00 4.45
1436 1776 0.830648 TAGCAGATTTCCGTGGGGAG 59.169 55.000 0.00 0.00 44.98 4.30
1438 1778 0.463833 GGTAGCAGATTTCCGTGGGG 60.464 60.000 0.00 0.00 0.00 4.96
1588 1931 2.048127 GTCCGTCCTCCACAGCAC 60.048 66.667 0.00 0.00 0.00 4.40
1602 1945 5.250235 TCTGATTCTTGTACGATCTGTCC 57.750 43.478 0.00 0.00 0.00 4.02
1603 1946 6.499172 TGATCTGATTCTTGTACGATCTGTC 58.501 40.000 0.00 4.36 0.00 3.51
1604 1947 6.456795 TGATCTGATTCTTGTACGATCTGT 57.543 37.500 0.00 0.00 0.00 3.41
1605 1948 6.075152 CGTTGATCTGATTCTTGTACGATCTG 60.075 42.308 0.00 3.27 0.00 2.90
1632 1979 1.065126 AGCATGAGGCCTTAGGTTGAC 60.065 52.381 6.77 0.00 46.50 3.18
1724 2071 4.142816 GCAAGGTACTGTAAATGCTGACAG 60.143 45.833 0.00 0.00 46.95 3.51
1823 2170 4.320494 CGTTATCTGTTTCCAAAGCAAGCT 60.320 41.667 0.00 0.00 0.00 3.74
1840 2194 2.290641 GGTGGATTGATGGTGCGTTATC 59.709 50.000 0.00 0.00 0.00 1.75
1864 2218 5.923733 ACAAGGTTTGTATGGAAACAACA 57.076 34.783 0.00 0.00 43.27 3.33
1877 2239 3.876914 TGCAGAGACAAGTACAAGGTTTG 59.123 43.478 0.00 0.00 0.00 2.93
1885 2247 8.089115 AGAAAATTTACTGCAGAGACAAGTAC 57.911 34.615 23.35 4.76 0.00 2.73
1896 2262 3.550561 CGCGTGAAGAAAATTTACTGCA 58.449 40.909 0.00 0.00 0.00 4.41
1897 2263 2.338520 GCGCGTGAAGAAAATTTACTGC 59.661 45.455 8.43 0.00 0.00 4.40
1919 2287 3.753272 CGACTGTGGATCCAAACTGAATT 59.247 43.478 18.20 0.00 0.00 2.17
1932 2300 0.888619 GATCCTGTGACGACTGTGGA 59.111 55.000 0.00 0.00 0.00 4.02
1985 2381 5.931146 CGCAATAGAAGCTAATGGAGAGAAT 59.069 40.000 0.00 0.00 0.00 2.40
2011 2407 0.657840 GTAATCAGGCGCATGGTCAC 59.342 55.000 23.25 7.73 0.00 3.67
2012 2408 0.541392 AGTAATCAGGCGCATGGTCA 59.459 50.000 23.25 0.00 0.00 4.02
2013 2409 1.599542 GAAGTAATCAGGCGCATGGTC 59.400 52.381 23.25 3.75 0.00 4.02
2014 2410 1.668419 GAAGTAATCAGGCGCATGGT 58.332 50.000 23.25 13.41 0.00 3.55
2015 2411 0.583438 CGAAGTAATCAGGCGCATGG 59.417 55.000 23.25 3.78 0.00 3.66
2016 2412 0.583438 CCGAAGTAATCAGGCGCATG 59.417 55.000 17.42 17.42 0.00 4.06
2017 2413 1.160329 GCCGAAGTAATCAGGCGCAT 61.160 55.000 10.83 0.00 37.75 4.73
2018 2414 1.813753 GCCGAAGTAATCAGGCGCA 60.814 57.895 10.83 0.00 37.75 6.09
2019 2415 1.160329 ATGCCGAAGTAATCAGGCGC 61.160 55.000 0.00 0.00 45.08 6.53
2020 2416 0.583438 CATGCCGAAGTAATCAGGCG 59.417 55.000 4.75 0.00 45.08 5.52
2021 2417 1.953559 TCATGCCGAAGTAATCAGGC 58.046 50.000 2.39 2.39 43.55 4.85
2022 2418 4.963276 TTTTCATGCCGAAGTAATCAGG 57.037 40.909 0.00 0.00 34.32 3.86
2034 2451 7.653311 AGAAAGTTACTTTGTCATTTTCATGCC 59.347 33.333 15.57 0.00 33.49 4.40
2083 2502 4.379499 GCAGTTCCTTTGCATAACTGGTAC 60.379 45.833 22.52 10.90 46.50 3.34
2092 2511 2.269978 ATGCGCAGTTCCTTTGCAT 58.730 47.368 18.32 0.00 41.59 3.96
2144 2563 3.367630 GCAACAAAGACCACACAACAAAG 59.632 43.478 0.00 0.00 0.00 2.77
2151 2570 1.388547 TCCAGCAACAAAGACCACAC 58.611 50.000 0.00 0.00 0.00 3.82
2152 2571 2.136298 TTCCAGCAACAAAGACCACA 57.864 45.000 0.00 0.00 0.00 4.17
2169 2588 5.725110 ATGTTGTATCGAGCTGACAATTC 57.275 39.130 0.00 0.00 35.65 2.17
2191 2610 5.720371 AACCACATAGCTGCAAATGTAAA 57.280 34.783 16.88 0.00 34.61 2.01
2194 2613 5.163519 GGATTAACCACATAGCTGCAAATGT 60.164 40.000 13.00 13.00 36.78 2.71
2217 2636 6.537355 TCCCTATGAAATCAAGCAGAATAGG 58.463 40.000 0.00 0.00 34.98 2.57
2222 2641 8.821686 TTTAAATCCCTATGAAATCAAGCAGA 57.178 30.769 0.00 0.00 0.00 4.26
2296 2718 1.134280 GCTCTGCTTAGCCCAAGATCA 60.134 52.381 0.29 0.00 36.22 2.92
2362 2784 9.658475 TTCAGTAAAATCGTATGAACTTTGTTG 57.342 29.630 5.90 4.87 0.00 3.33
2373 2795 8.198109 ACTAGAGCATGTTCAGTAAAATCGTAT 58.802 33.333 12.41 0.00 0.00 3.06
2376 2798 6.893958 ACTAGAGCATGTTCAGTAAAATCG 57.106 37.500 12.41 0.00 0.00 3.34
2388 2810 5.658634 TGATGAGGAACTTACTAGAGCATGT 59.341 40.000 0.00 0.00 41.55 3.21
2416 2838 5.676744 CACAATCTACAACACAAAACAGACG 59.323 40.000 0.00 0.00 0.00 4.18
2417 2839 6.687105 GTCACAATCTACAACACAAAACAGAC 59.313 38.462 0.00 0.00 0.00 3.51
2679 3136 9.970395 TTCATAAGATGCATGGAAATATCAAAC 57.030 29.630 2.46 0.00 0.00 2.93
2722 3179 6.026947 TGCTCTCTTTTACTGGAGTACTTC 57.973 41.667 0.00 0.00 0.00 3.01
2724 3181 6.183360 CGTATGCTCTCTTTTACTGGAGTACT 60.183 42.308 0.00 0.00 0.00 2.73
2725 3182 5.972382 CGTATGCTCTCTTTTACTGGAGTAC 59.028 44.000 0.00 0.00 0.00 2.73
2726 3183 5.651139 ACGTATGCTCTCTTTTACTGGAGTA 59.349 40.000 0.00 0.00 0.00 2.59
2727 3184 4.463186 ACGTATGCTCTCTTTTACTGGAGT 59.537 41.667 0.00 0.00 0.00 3.85
2728 3185 5.000012 ACGTATGCTCTCTTTTACTGGAG 58.000 43.478 0.00 0.00 0.00 3.86
2729 3186 5.401531 AACGTATGCTCTCTTTTACTGGA 57.598 39.130 0.00 0.00 0.00 3.86
2730 3187 6.481954 AAAACGTATGCTCTCTTTTACTGG 57.518 37.500 0.00 0.00 0.00 4.00
2743 3201 6.486248 TCTTGATGCAAGATAAAACGTATGC 58.514 36.000 5.81 0.00 44.27 3.14
2808 3268 5.164187 GCAAACGCTTTCTGTAGTAAATTGC 60.164 40.000 0.00 0.00 0.00 3.56
2819 3279 5.634896 AGATCAATTAGCAAACGCTTTCTG 58.365 37.500 0.00 0.00 41.09 3.02
2902 3370 9.740239 AAGTCATATGCTATTGTATTTTGCTTG 57.260 29.630 0.00 0.00 0.00 4.01
2903 3371 9.740239 CAAGTCATATGCTATTGTATTTTGCTT 57.260 29.630 0.00 0.00 0.00 3.91
2926 3395 3.253921 TGATTGTGATCAAGTGTGGCAAG 59.746 43.478 0.00 0.00 39.29 4.01
2995 3464 8.737168 AATTAGTGCTACAGATCAATGCTAAA 57.263 30.769 0.00 0.00 0.00 1.85
2996 3465 8.737168 AAATTAGTGCTACAGATCAATGCTAA 57.263 30.769 0.00 0.00 0.00 3.09
2998 3467 7.636150 AAAATTAGTGCTACAGATCAATGCT 57.364 32.000 0.00 0.00 0.00 3.79
3003 3472 6.986817 GCCTCTAAAATTAGTGCTACAGATCA 59.013 38.462 0.00 0.00 32.61 2.92
3004 3473 6.425417 GGCCTCTAAAATTAGTGCTACAGATC 59.575 42.308 0.00 0.00 33.40 2.75
3005 3474 6.100424 AGGCCTCTAAAATTAGTGCTACAGAT 59.900 38.462 0.00 0.00 33.40 2.90
3006 3475 5.425539 AGGCCTCTAAAATTAGTGCTACAGA 59.574 40.000 0.00 0.00 33.40 3.41
3007 3476 5.675538 AGGCCTCTAAAATTAGTGCTACAG 58.324 41.667 0.00 0.09 33.40 2.74
3008 3477 5.188948 TGAGGCCTCTAAAATTAGTGCTACA 59.811 40.000 32.28 4.46 33.40 2.74
3009 3478 5.671493 TGAGGCCTCTAAAATTAGTGCTAC 58.329 41.667 32.28 1.55 33.40 3.58
3010 3479 5.950544 TGAGGCCTCTAAAATTAGTGCTA 57.049 39.130 32.28 4.87 33.40 3.49
3011 3480 4.844349 TGAGGCCTCTAAAATTAGTGCT 57.156 40.909 32.28 0.00 33.40 4.40
3012 3481 5.372373 AGATGAGGCCTCTAAAATTAGTGC 58.628 41.667 32.28 6.36 32.61 4.40
3013 3482 6.825721 ACAAGATGAGGCCTCTAAAATTAGTG 59.174 38.462 32.28 18.47 32.61 2.74
3014 3483 6.963322 ACAAGATGAGGCCTCTAAAATTAGT 58.037 36.000 32.28 17.13 32.61 2.24
3015 3484 7.050377 TGACAAGATGAGGCCTCTAAAATTAG 58.950 38.462 32.28 16.55 0.00 1.73
3016 3485 6.957631 TGACAAGATGAGGCCTCTAAAATTA 58.042 36.000 32.28 11.82 0.00 1.40
3017 3486 5.819991 TGACAAGATGAGGCCTCTAAAATT 58.180 37.500 32.28 16.85 0.00 1.82
3018 3487 5.441718 TGACAAGATGAGGCCTCTAAAAT 57.558 39.130 32.28 18.19 0.00 1.82
3019 3488 4.908601 TGACAAGATGAGGCCTCTAAAA 57.091 40.909 32.28 13.81 0.00 1.52
3020 3489 4.323792 CCTTGACAAGATGAGGCCTCTAAA 60.324 45.833 32.28 14.20 0.00 1.85
3021 3490 3.198635 CCTTGACAAGATGAGGCCTCTAA 59.801 47.826 32.28 15.01 0.00 2.10
3022 3491 2.768527 CCTTGACAAGATGAGGCCTCTA 59.231 50.000 32.28 19.38 0.00 2.43
3023 3492 1.558756 CCTTGACAAGATGAGGCCTCT 59.441 52.381 32.28 18.41 0.00 3.69
3024 3493 1.556911 TCCTTGACAAGATGAGGCCTC 59.443 52.381 26.78 26.78 0.00 4.70
3025 3494 1.661463 TCCTTGACAAGATGAGGCCT 58.339 50.000 16.99 3.86 0.00 5.19
3026 3495 2.725221 ATCCTTGACAAGATGAGGCC 57.275 50.000 16.99 0.00 0.00 5.19
3027 3496 3.118261 TGGTATCCTTGACAAGATGAGGC 60.118 47.826 16.99 3.80 0.00 4.70
3028 3497 4.760530 TGGTATCCTTGACAAGATGAGG 57.239 45.455 16.99 0.00 0.00 3.86
3029 3498 6.825213 TGAAATGGTATCCTTGACAAGATGAG 59.175 38.462 16.99 0.00 0.00 2.90
3030 3499 6.720309 TGAAATGGTATCCTTGACAAGATGA 58.280 36.000 16.99 6.69 0.00 2.92
3046 3515 8.992073 GTTTATCAAATGCTTCTTTGAAATGGT 58.008 29.630 11.74 1.65 45.45 3.55
3047 3516 8.991026 TGTTTATCAAATGCTTCTTTGAAATGG 58.009 29.630 11.74 0.00 45.45 3.16
3060 3529 9.173939 GCATCTAGTACAATGTTTATCAAATGC 57.826 33.333 0.00 0.00 0.00 3.56
3071 3540 9.502091 TTCTAACAAAAGCATCTAGTACAATGT 57.498 29.630 0.00 0.00 0.00 2.71
3094 3563 6.239600 GGAAAACTGGGGCTTATTTCTTTTCT 60.240 38.462 0.00 0.00 32.14 2.52
3103 3572 2.110011 ACTGTGGAAAACTGGGGCTTAT 59.890 45.455 0.00 0.00 32.24 1.73
3109 3578 1.956477 CAAGGACTGTGGAAAACTGGG 59.044 52.381 0.00 0.00 32.24 4.45
3199 3668 0.036732 AAGACCTTGGCAATCGCAGA 59.963 50.000 0.00 0.00 45.75 4.26
3209 3678 6.155049 ACAATATCAAAATGGGAAGACCTTGG 59.845 38.462 0.00 0.00 41.11 3.61
3265 3734 1.338020 CGCCAGGAAAAAGAGCTTGTT 59.662 47.619 0.00 0.00 0.00 2.83
3351 3820 4.943705 ACCAGACAAAGTACTGCATATTGG 59.056 41.667 0.00 3.71 33.40 3.16
3403 3890 5.788450 ACAAGAACACTTCACTAGGATCAG 58.212 41.667 0.00 0.00 0.00 2.90
3417 3904 6.431234 AGGAATAATGGACAGAACAAGAACAC 59.569 38.462 0.00 0.00 0.00 3.32
3534 4025 6.506500 AGCAGGTTTCAGTCAAATGATTAG 57.493 37.500 0.00 0.00 0.00 1.73
3552 4043 3.491447 CCAACAACCTTTTCAGAAGCAGG 60.491 47.826 8.40 8.40 0.00 4.85
3704 4195 7.680350 GCGTCTTATGTTTCCCTTAATTTACCC 60.680 40.741 0.00 0.00 0.00 3.69
3716 4207 4.095610 CGAAATTGGCGTCTTATGTTTCC 58.904 43.478 0.00 0.00 0.00 3.13
3726 4217 2.671396 ACAGACATACGAAATTGGCGTC 59.329 45.455 9.53 0.00 42.62 5.19
3775 4266 3.807622 CAGTTCACCGAAGCAAGAAACTA 59.192 43.478 0.00 0.00 0.00 2.24
4003 4494 4.329462 TTGCCCACTCAATAACAAAACC 57.671 40.909 0.00 0.00 0.00 3.27
4079 4570 4.079558 AGGGAATATCATGAGTGGCAGTTT 60.080 41.667 0.09 0.00 0.00 2.66
4092 4583 6.295859 CCGGATAGAAACATCAGGGAATATCA 60.296 42.308 0.00 0.00 36.83 2.15
4115 4621 3.562973 AGATAAAACAGAGCATCATGCCG 59.437 43.478 5.84 0.00 46.52 5.69
4290 4810 1.019278 TTGGAATGAGCGAGCGAACC 61.019 55.000 0.00 0.00 0.00 3.62
4291 4811 0.796312 TTTGGAATGAGCGAGCGAAC 59.204 50.000 0.00 0.00 0.00 3.95
4294 4814 2.549633 AAATTTGGAATGAGCGAGCG 57.450 45.000 0.00 0.00 0.00 5.03
4303 4823 6.211986 TGCTCATCTCTTGGAAAATTTGGAAT 59.788 34.615 0.00 0.00 0.00 3.01
4311 4831 7.943079 TTAATGATGCTCATCTCTTGGAAAA 57.057 32.000 10.76 0.00 35.76 2.29
4314 4834 6.892485 TCTTTAATGATGCTCATCTCTTGGA 58.108 36.000 10.76 1.39 35.76 3.53
4315 4835 7.563888 TTCTTTAATGATGCTCATCTCTTGG 57.436 36.000 10.76 0.00 35.76 3.61
4323 4843 4.252878 TGTCGCTTCTTTAATGATGCTCA 58.747 39.130 20.10 16.70 35.71 4.26
4324 4844 4.864916 TGTCGCTTCTTTAATGATGCTC 57.135 40.909 20.10 15.12 35.71 4.26
4325 4845 4.274459 GGATGTCGCTTCTTTAATGATGCT 59.726 41.667 20.10 7.60 35.71 3.79
4326 4846 4.274459 AGGATGTCGCTTCTTTAATGATGC 59.726 41.667 15.36 15.36 34.88 3.91
4327 4847 5.998454 AGGATGTCGCTTCTTTAATGATG 57.002 39.130 0.00 0.00 0.00 3.07
4328 4848 5.882557 ACAAGGATGTCGCTTCTTTAATGAT 59.117 36.000 0.00 0.00 33.41 2.45
4329 4849 5.245531 ACAAGGATGTCGCTTCTTTAATGA 58.754 37.500 0.00 0.00 33.41 2.57
4330 4850 5.551760 ACAAGGATGTCGCTTCTTTAATG 57.448 39.130 0.00 0.00 33.41 1.90
4331 4851 5.585047 GGTACAAGGATGTCGCTTCTTTAAT 59.415 40.000 0.00 0.00 41.05 1.40
4332 4852 4.933400 GGTACAAGGATGTCGCTTCTTTAA 59.067 41.667 0.00 0.00 41.05 1.52
4333 4853 4.222145 AGGTACAAGGATGTCGCTTCTTTA 59.778 41.667 0.00 0.00 41.05 1.85
4379 4900 5.567138 GGTGAAGGACCAAAGTCATATTG 57.433 43.478 0.00 0.00 45.48 1.90
4391 4912 4.399303 CCAATATGACTTTGGTGAAGGACC 59.601 45.833 0.00 0.00 46.37 4.46
4392 4913 4.142381 GCCAATATGACTTTGGTGAAGGAC 60.142 45.833 4.53 0.00 44.52 3.85
4430 4980 0.861837 GCTCGGGCTCAATTACATCG 59.138 55.000 0.00 0.00 35.22 3.84
4466 5016 2.895404 ACCAATACACGACTACAGTGGT 59.105 45.455 0.00 0.00 43.41 4.16
4471 5021 5.711506 TCTCCTTTACCAATACACGACTACA 59.288 40.000 0.00 0.00 0.00 2.74
4472 5022 6.199937 TCTCCTTTACCAATACACGACTAC 57.800 41.667 0.00 0.00 0.00 2.73
4474 5024 5.661458 CATCTCCTTTACCAATACACGACT 58.339 41.667 0.00 0.00 0.00 4.18
4475 5025 4.270325 GCATCTCCTTTACCAATACACGAC 59.730 45.833 0.00 0.00 0.00 4.34
4476 5026 4.439057 GCATCTCCTTTACCAATACACGA 58.561 43.478 0.00 0.00 0.00 4.35
4477 5027 3.245284 CGCATCTCCTTTACCAATACACG 59.755 47.826 0.00 0.00 0.00 4.49
4478 5028 3.002348 GCGCATCTCCTTTACCAATACAC 59.998 47.826 0.30 0.00 0.00 2.90
4479 5029 3.118408 AGCGCATCTCCTTTACCAATACA 60.118 43.478 11.47 0.00 0.00 2.29
4501 5059 1.734465 CCAAAAACGCAAAAACTGGCA 59.266 42.857 0.00 0.00 0.00 4.92
4505 5063 3.682377 CCAAGTCCAAAAACGCAAAAACT 59.318 39.130 0.00 0.00 0.00 2.66
4509 5067 2.996621 CAACCAAGTCCAAAAACGCAAA 59.003 40.909 0.00 0.00 0.00 3.68
4514 5072 4.249661 TCTTTGCAACCAAGTCCAAAAAC 58.750 39.130 0.00 0.00 31.52 2.43
4517 5075 2.430332 CCTCTTTGCAACCAAGTCCAAA 59.570 45.455 0.00 0.00 31.52 3.28
4565 5123 1.539065 CGGCCGATAGACTTCAGCATT 60.539 52.381 24.07 0.00 39.76 3.56
4567 5125 1.320344 ACGGCCGATAGACTTCAGCA 61.320 55.000 35.90 0.00 39.76 4.41
4602 5184 7.855409 GCACTATGCTCTCTACTAATGATATCG 59.145 40.741 0.00 0.00 40.96 2.92
4605 5187 6.948309 TGGCACTATGCTCTCTACTAATGATA 59.052 38.462 0.13 0.00 44.28 2.15
4647 7227 6.133356 TCCCCCTAAATTTGTGCCTTATTAG 58.867 40.000 0.00 0.00 0.00 1.73
4718 7298 4.100707 GCTCAAAGCTTTGCATGTGATA 57.899 40.909 30.35 12.58 38.45 2.15
4760 7340 6.439692 AGATGCATTTTGAATCTCTCCCTTTT 59.560 34.615 0.00 0.00 38.36 2.27
4761 7341 5.956563 AGATGCATTTTGAATCTCTCCCTTT 59.043 36.000 0.00 0.00 38.36 3.11
4762 7342 5.516984 AGATGCATTTTGAATCTCTCCCTT 58.483 37.500 0.00 0.00 38.36 3.95
4763 7343 5.126699 AGATGCATTTTGAATCTCTCCCT 57.873 39.130 0.00 0.00 38.36 4.20
4764 7344 5.359009 TGAAGATGCATTTTGAATCTCTCCC 59.641 40.000 7.28 0.00 41.87 4.30
4765 7345 6.446781 TGAAGATGCATTTTGAATCTCTCC 57.553 37.500 7.28 0.00 41.87 3.71
4766 7346 7.013464 AGGATGAAGATGCATTTTGAATCTCTC 59.987 37.037 7.28 0.00 41.87 3.20
4767 7347 6.834451 AGGATGAAGATGCATTTTGAATCTCT 59.166 34.615 7.28 7.12 41.87 3.10
4768 7348 7.013464 AGAGGATGAAGATGCATTTTGAATCTC 59.987 37.037 7.28 9.92 41.87 2.75
4769 7349 6.834451 AGAGGATGAAGATGCATTTTGAATCT 59.166 34.615 7.28 2.37 44.56 2.40
4770 7350 7.040473 AGAGGATGAAGATGCATTTTGAATC 57.960 36.000 7.28 9.78 32.39 2.52
4842 7422 1.332375 CTTTGTCGCGTCTTTTGGGAA 59.668 47.619 5.77 0.00 0.00 3.97
4843 7423 0.941542 CTTTGTCGCGTCTTTTGGGA 59.058 50.000 5.77 0.00 0.00 4.37
4844 7424 0.040425 CCTTTGTCGCGTCTTTTGGG 60.040 55.000 5.77 0.00 0.00 4.12
4845 7425 0.040425 CCCTTTGTCGCGTCTTTTGG 60.040 55.000 5.77 2.91 0.00 3.28
4846 7426 0.941542 TCCCTTTGTCGCGTCTTTTG 59.058 50.000 5.77 0.00 0.00 2.44
4847 7427 1.226746 CTCCCTTTGTCGCGTCTTTT 58.773 50.000 5.77 0.00 0.00 2.27
4848 7428 0.106149 ACTCCCTTTGTCGCGTCTTT 59.894 50.000 5.77 0.00 0.00 2.52
4849 7429 0.963962 TACTCCCTTTGTCGCGTCTT 59.036 50.000 5.77 0.00 0.00 3.01
4864 7444 7.201565 GCATGAGAGTTATTTCACCAACTACTC 60.202 40.741 0.00 0.00 35.17 2.59
4866 7446 6.371548 TGCATGAGAGTTATTTCACCAACTAC 59.628 38.462 0.00 0.00 35.17 2.73
4868 7448 5.316167 TGCATGAGAGTTATTTCACCAACT 58.684 37.500 0.00 0.00 37.69 3.16


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

AutoCloner maintained by Alex Coulton.