Multiple sequence alignment - TraesCS6D01G261200

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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 TraesCS6D01G261200 chr6D 100.000 2543 0 0 1 2543 369500246 369502788 0.000000e+00 4697.0
1 TraesCS6D01G261200 chr6D 78.177 834 100 40 4 761 470887626 470886799 8.290000e-125 457.0
2 TraesCS6D01G261200 chr6D 78.671 286 32 13 273 534 461631734 461632014 2.020000e-36 163.0
3 TraesCS6D01G261200 chr6B 93.305 926 53 6 860 1783 555193981 555194899 0.000000e+00 1358.0
4 TraesCS6D01G261200 chr6B 76.769 650 81 29 173 761 195969705 195970345 1.480000e-77 300.0
5 TraesCS6D01G261200 chr6B 94.444 90 5 0 772 861 555193847 555193936 3.410000e-29 139.0
6 TraesCS6D01G261200 chr6B 77.619 210 25 11 353 541 200307825 200307617 9.620000e-20 108.0
7 TraesCS6D01G261200 chr6A 93.160 921 53 7 864 1783 510799195 510800106 0.000000e+00 1343.0
8 TraesCS6D01G261200 chr6A 96.731 520 16 1 1931 2449 5697149 5697668 0.000000e+00 865.0
9 TraesCS6D01G261200 chr6A 75.824 182 24 6 379 540 559810784 559810603 9.760000e-10 75.0
10 TraesCS6D01G261200 chr2B 97.313 521 13 1 1930 2449 682135893 682135373 0.000000e+00 883.0
11 TraesCS6D01G261200 chr2B 84.987 393 43 15 15 396 50710964 50710577 3.970000e-103 385.0
12 TraesCS6D01G261200 chr2B 81.567 434 58 15 1 419 97488594 97489020 3.130000e-89 339.0
13 TraesCS6D01G261200 chr3B 96.183 524 19 1 1927 2449 187444112 187444635 0.000000e+00 856.0
14 TraesCS6D01G261200 chr3B 83.908 87 12 1 467 551 728997180 728997094 5.830000e-12 82.4
15 TraesCS6D01G261200 chr5A 96.346 520 18 1 1931 2449 559742965 559743484 0.000000e+00 854.0
16 TraesCS6D01G261200 chr7A 95.977 522 19 2 1930 2449 619910121 619909600 0.000000e+00 846.0
17 TraesCS6D01G261200 chr2D 90.458 524 49 1 1927 2449 61789652 61790175 0.000000e+00 689.0
18 TraesCS6D01G261200 chr2D 80.258 775 91 29 29 760 4279596 4278841 6.230000e-146 527.0
19 TraesCS6D01G261200 chr2D 82.336 351 32 19 208 533 39420803 39420458 6.930000e-71 278.0
20 TraesCS6D01G261200 chr2D 76.078 510 67 25 306 761 640824617 640824109 5.510000e-52 215.0
21 TraesCS6D01G261200 chr3D 90.076 524 50 2 1927 2449 64072213 64072735 0.000000e+00 678.0
22 TraesCS6D01G261200 chr3D 80.367 545 51 19 275 768 104342883 104343422 1.860000e-96 363.0
23 TraesCS6D01G261200 chr7B 90.019 521 50 2 1930 2449 503479327 503478808 0.000000e+00 673.0
24 TraesCS6D01G261200 chr7B 78.191 807 94 36 12 761 10914169 10914950 8.350000e-120 440.0
25 TraesCS6D01G261200 chr7B 85.752 379 41 10 51 420 586655126 586654752 3.070000e-104 388.0
26 TraesCS6D01G261200 chr7B 83.465 127 17 2 1785 1907 578442833 578442959 5.750000e-22 115.0
27 TraesCS6D01G261200 chr1B 89.827 521 52 1 1930 2449 370725305 370725825 0.000000e+00 667.0
28 TraesCS6D01G261200 chr1B 79.958 474 71 19 1 461 569929513 569929051 6.780000e-86 327.0
29 TraesCS6D01G261200 chr1B 80.546 293 33 14 263 533 674872564 674872274 1.190000e-48 204.0
30 TraesCS6D01G261200 chr1B 80.620 129 22 2 1784 1910 277414950 277415077 2.080000e-16 97.1
31 TraesCS6D01G261200 chrUn 79.182 807 105 29 4 761 28721463 28722255 3.780000e-138 501.0
32 TraesCS6D01G261200 chr5D 80.163 615 67 26 171 761 367694654 367695237 2.350000e-110 409.0
33 TraesCS6D01G261200 chr5D 75.317 709 93 35 101 761 520583992 520584666 5.390000e-67 265.0
34 TraesCS6D01G261200 chr5B 80.987 547 66 23 12 524 562216747 562216205 1.420000e-107 399.0
35 TraesCS6D01G261200 chr5B 76.216 185 22 10 369 533 558613958 558613776 7.540000e-11 78.7
36 TraesCS6D01G261200 chr4D 77.932 648 82 28 171 761 404224803 404225446 5.210000e-92 348.0
37 TraesCS6D01G261200 chr4B 80.208 480 69 23 1 461 115076916 115076444 1.130000e-88 337.0
38 TraesCS6D01G261200 chr7D 75.039 641 63 33 171 761 589281984 589281391 9.220000e-50 207.0
39 TraesCS6D01G261200 chr7D 85.455 110 15 1 652 761 68769904 68769796 2.070000e-21 113.0
40 TraesCS6D01G261200 chr3A 79.016 305 42 12 250 533 623828762 623828459 3.340000e-44 189.0
41 TraesCS6D01G261200 chr3A 75.490 408 56 17 382 761 7484876 7484485 2.620000e-35 159.0
42 TraesCS6D01G261200 chr3A 85.135 148 20 2 171 318 19886888 19886743 1.580000e-32 150.0


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 TraesCS6D01G261200 chr6D 369500246 369502788 2542 False 4697.0 4697 100.0000 1 2543 1 chr6D.!!$F1 2542
1 TraesCS6D01G261200 chr6D 470886799 470887626 827 True 457.0 457 78.1770 4 761 1 chr6D.!!$R1 757
2 TraesCS6D01G261200 chr6B 555193847 555194899 1052 False 748.5 1358 93.8745 772 1783 2 chr6B.!!$F2 1011
3 TraesCS6D01G261200 chr6B 195969705 195970345 640 False 300.0 300 76.7690 173 761 1 chr6B.!!$F1 588
4 TraesCS6D01G261200 chr6A 510799195 510800106 911 False 1343.0 1343 93.1600 864 1783 1 chr6A.!!$F2 919
5 TraesCS6D01G261200 chr6A 5697149 5697668 519 False 865.0 865 96.7310 1931 2449 1 chr6A.!!$F1 518
6 TraesCS6D01G261200 chr2B 682135373 682135893 520 True 883.0 883 97.3130 1930 2449 1 chr2B.!!$R2 519
7 TraesCS6D01G261200 chr3B 187444112 187444635 523 False 856.0 856 96.1830 1927 2449 1 chr3B.!!$F1 522
8 TraesCS6D01G261200 chr5A 559742965 559743484 519 False 854.0 854 96.3460 1931 2449 1 chr5A.!!$F1 518
9 TraesCS6D01G261200 chr7A 619909600 619910121 521 True 846.0 846 95.9770 1930 2449 1 chr7A.!!$R1 519
10 TraesCS6D01G261200 chr2D 61789652 61790175 523 False 689.0 689 90.4580 1927 2449 1 chr2D.!!$F1 522
11 TraesCS6D01G261200 chr2D 4278841 4279596 755 True 527.0 527 80.2580 29 760 1 chr2D.!!$R1 731
12 TraesCS6D01G261200 chr2D 640824109 640824617 508 True 215.0 215 76.0780 306 761 1 chr2D.!!$R3 455
13 TraesCS6D01G261200 chr3D 64072213 64072735 522 False 678.0 678 90.0760 1927 2449 1 chr3D.!!$F1 522
14 TraesCS6D01G261200 chr3D 104342883 104343422 539 False 363.0 363 80.3670 275 768 1 chr3D.!!$F2 493
15 TraesCS6D01G261200 chr7B 503478808 503479327 519 True 673.0 673 90.0190 1930 2449 1 chr7B.!!$R1 519
16 TraesCS6D01G261200 chr7B 10914169 10914950 781 False 440.0 440 78.1910 12 761 1 chr7B.!!$F1 749
17 TraesCS6D01G261200 chr1B 370725305 370725825 520 False 667.0 667 89.8270 1930 2449 1 chr1B.!!$F2 519
18 TraesCS6D01G261200 chrUn 28721463 28722255 792 False 501.0 501 79.1820 4 761 1 chrUn.!!$F1 757
19 TraesCS6D01G261200 chr5D 367694654 367695237 583 False 409.0 409 80.1630 171 761 1 chr5D.!!$F1 590
20 TraesCS6D01G261200 chr5D 520583992 520584666 674 False 265.0 265 75.3170 101 761 1 chr5D.!!$F2 660
21 TraesCS6D01G261200 chr5B 562216205 562216747 542 True 399.0 399 80.9870 12 524 1 chr5B.!!$R2 512
22 TraesCS6D01G261200 chr4D 404224803 404225446 643 False 348.0 348 77.9320 171 761 1 chr4D.!!$F1 590
23 TraesCS6D01G261200 chr7D 589281391 589281984 593 True 207.0 207 75.0390 171 761 1 chr7D.!!$R2 590

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
135 137 0.100503 AACAAAACTGTGCCGCTCAC 59.899 50.0 0.0 0.0 45.82 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 2220 0.033504 AAATGAGCGTCTGTGTCCGT 59.966 50.0 0.0 0.0 0.0 4.69 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
39 40 5.503689 AAAACCAAACGAAAAACTGAACG 57.496 34.783 0.00 0.00 0.00 3.95
46 48 1.535462 CGAAAAACTGAACGGGAGCAT 59.465 47.619 0.00 0.00 0.00 3.79
117 119 2.035237 AACCGTGCCTCTCGTGGAAA 62.035 55.000 0.00 0.00 0.00 3.13
130 132 1.555477 GTGGAAACAAAACTGTGCCG 58.445 50.000 0.00 0.00 46.06 5.69
134 136 0.814457 AAACAAAACTGTGCCGCTCA 59.186 45.000 0.00 0.00 0.00 4.26
135 137 0.100503 AACAAAACTGTGCCGCTCAC 59.899 50.000 0.00 0.00 45.82 3.51
229 236 2.096713 CGTGCCTCTCGTGAAAGAAAAG 60.097 50.000 0.00 0.00 0.00 2.27
296 533 1.871080 CCTCTCGTGAAAGCACAACT 58.129 50.000 0.00 0.00 45.41 3.16
411 663 1.940613 GAAAGCACAACCGTGTCTCTT 59.059 47.619 0.00 0.00 45.50 2.85
504 780 3.750373 AAAGCACCGTGGCTGTCGT 62.750 57.895 0.00 0.00 45.07 4.34
648 1012 1.744374 TTAAAAAGAAACGCGTGCGG 58.256 45.000 14.98 0.68 44.69 5.69
722 1094 3.566261 CGCCAAGTGACGCTGATT 58.434 55.556 0.00 0.00 0.00 2.57
726 1098 1.001378 GCCAAGTGACGCTGATTGTTT 60.001 47.619 0.00 0.00 0.00 2.83
736 1108 1.888512 GCTGATTGTTTCAAGGCTCCA 59.111 47.619 0.00 0.00 32.78 3.86
761 1133 2.354821 GGAGCGCTGGTTAATTAGTTGG 59.645 50.000 18.48 0.00 0.00 3.77
762 1134 1.743394 AGCGCTGGTTAATTAGTTGGC 59.257 47.619 10.39 0.00 0.00 4.52
768 1140 4.402474 GCTGGTTAATTAGTTGGCCTCAAT 59.598 41.667 3.32 0.00 35.10 2.57
769 1141 5.679638 GCTGGTTAATTAGTTGGCCTCAATG 60.680 44.000 3.32 0.00 35.10 2.82
770 1142 5.575157 TGGTTAATTAGTTGGCCTCAATGA 58.425 37.500 3.32 0.00 35.10 2.57
781 1153 1.407979 GCCTCAATGATCAAAGCTGGG 59.592 52.381 0.00 0.00 0.00 4.45
797 1169 1.901833 CTGGGGCAAATGGTTTTAGCT 59.098 47.619 0.00 0.00 0.00 3.32
811 1183 2.524569 TTAGCTTTTTGCAGCCCAAC 57.475 45.000 0.00 0.00 45.94 3.77
840 1212 0.109723 ACCCTTTTTCTACCGCAGCA 59.890 50.000 0.00 0.00 0.00 4.41
841 1213 1.243902 CCCTTTTTCTACCGCAGCAA 58.756 50.000 0.00 0.00 0.00 3.91
909 1327 3.904717 AGATTCAGTCCGTCAGTCCTAT 58.095 45.455 0.00 0.00 0.00 2.57
948 1366 0.241213 CGTCCGAGCAGACAAGAAGA 59.759 55.000 2.99 0.00 36.52 2.87
949 1367 1.704070 GTCCGAGCAGACAAGAAGAC 58.296 55.000 0.00 0.00 36.73 3.01
974 1392 6.845302 TCTACGAACTTAATTAGTCGCTTCA 58.155 36.000 12.52 0.50 35.54 3.02
995 1413 5.171476 TCATTCGGAAACAAAAGCAACAAA 58.829 33.333 0.00 0.00 0.00 2.83
996 1414 4.912528 TTCGGAAACAAAAGCAACAAAC 57.087 36.364 0.00 0.00 0.00 2.93
1147 1565 0.456312 GGACTACGACTTCTGCGTGG 60.456 60.000 0.00 0.00 44.32 4.94
1218 1636 4.335647 AAGGTGGCAGCCCTCACG 62.336 66.667 13.95 0.00 34.93 4.35
1273 1691 3.580604 AAGGAGCTGCTGGCCAAGG 62.581 63.158 9.14 0.00 43.05 3.61
1551 1969 2.232452 CCTCATCCAGTGAAGAACGTCT 59.768 50.000 0.00 0.00 36.14 4.18
1561 1979 4.814771 AGTGAAGAACGTCTAAAACTTGGG 59.185 41.667 0.00 0.00 0.00 4.12
1682 2103 3.668447 ACTCGCATGTTTTGAGTCTCAT 58.332 40.909 2.68 0.00 38.55 2.90
1728 2149 6.538021 GCATCCTGAGCAATATCTATGTAAGG 59.462 42.308 0.00 0.00 0.00 2.69
1756 2177 3.670991 CCTCGTCTGAGAATATAAAGCGC 59.329 47.826 0.00 0.00 45.57 5.92
1764 2185 7.115095 GTCTGAGAATATAAAGCGCGTTAATCT 59.885 37.037 19.37 20.12 0.00 2.40
1774 2195 6.663944 AAGCGCGTTAATCTTCTAATCTTT 57.336 33.333 8.43 0.00 0.00 2.52
1801 2222 9.188588 TCTCAATACTTTTTCTAACACAGTACG 57.811 33.333 0.00 0.00 0.00 3.67
1802 2223 8.301730 TCAATACTTTTTCTAACACAGTACGG 57.698 34.615 0.00 0.00 0.00 4.02
1803 2224 8.143193 TCAATACTTTTTCTAACACAGTACGGA 58.857 33.333 0.00 0.00 0.00 4.69
1804 2225 7.880059 ATACTTTTTCTAACACAGTACGGAC 57.120 36.000 0.00 0.00 0.00 4.79
1805 2226 5.663456 ACTTTTTCTAACACAGTACGGACA 58.337 37.500 0.00 0.00 0.00 4.02
1806 2227 5.521372 ACTTTTTCTAACACAGTACGGACAC 59.479 40.000 0.00 0.00 0.00 3.67
1807 2228 4.652421 TTTCTAACACAGTACGGACACA 57.348 40.909 0.00 0.00 0.00 3.72
1808 2229 3.909776 TCTAACACAGTACGGACACAG 57.090 47.619 0.00 0.00 0.00 3.66
1809 2230 3.479489 TCTAACACAGTACGGACACAGA 58.521 45.455 0.00 0.00 0.00 3.41
1810 2231 2.503920 AACACAGTACGGACACAGAC 57.496 50.000 0.00 0.00 0.00 3.51
1811 2232 0.309922 ACACAGTACGGACACAGACG 59.690 55.000 0.00 0.00 0.00 4.18
1812 2233 1.002250 CACAGTACGGACACAGACGC 61.002 60.000 0.00 0.00 0.00 5.19
1813 2234 1.170919 ACAGTACGGACACAGACGCT 61.171 55.000 0.00 0.00 0.00 5.07
1814 2235 0.454620 CAGTACGGACACAGACGCTC 60.455 60.000 0.00 0.00 0.00 5.03
1815 2236 0.887836 AGTACGGACACAGACGCTCA 60.888 55.000 0.00 0.00 0.00 4.26
1816 2237 0.170561 GTACGGACACAGACGCTCAT 59.829 55.000 0.00 0.00 0.00 2.90
1817 2238 0.885879 TACGGACACAGACGCTCATT 59.114 50.000 0.00 0.00 0.00 2.57
1818 2239 0.033504 ACGGACACAGACGCTCATTT 59.966 50.000 0.00 0.00 0.00 2.32
1819 2240 1.271379 ACGGACACAGACGCTCATTTA 59.729 47.619 0.00 0.00 0.00 1.40
1820 2241 2.094182 ACGGACACAGACGCTCATTTAT 60.094 45.455 0.00 0.00 0.00 1.40
1821 2242 3.129813 ACGGACACAGACGCTCATTTATA 59.870 43.478 0.00 0.00 0.00 0.98
1822 2243 3.486108 CGGACACAGACGCTCATTTATAC 59.514 47.826 0.00 0.00 0.00 1.47
1823 2244 4.430007 GGACACAGACGCTCATTTATACA 58.570 43.478 0.00 0.00 0.00 2.29
1824 2245 4.267928 GGACACAGACGCTCATTTATACAC 59.732 45.833 0.00 0.00 0.00 2.90
1825 2246 4.816392 ACACAGACGCTCATTTATACACA 58.184 39.130 0.00 0.00 0.00 3.72
1826 2247 4.625742 ACACAGACGCTCATTTATACACAC 59.374 41.667 0.00 0.00 0.00 3.82
1827 2248 4.625311 CACAGACGCTCATTTATACACACA 59.375 41.667 0.00 0.00 0.00 3.72
1828 2249 5.291858 CACAGACGCTCATTTATACACACAT 59.708 40.000 0.00 0.00 0.00 3.21
1829 2250 6.475402 CACAGACGCTCATTTATACACACATA 59.525 38.462 0.00 0.00 0.00 2.29
1830 2251 6.475727 ACAGACGCTCATTTATACACACATAC 59.524 38.462 0.00 0.00 0.00 2.39
1831 2252 6.475402 CAGACGCTCATTTATACACACATACA 59.525 38.462 0.00 0.00 0.00 2.29
1832 2253 6.475727 AGACGCTCATTTATACACACATACAC 59.524 38.462 0.00 0.00 0.00 2.90
1833 2254 6.338146 ACGCTCATTTATACACACATACACT 58.662 36.000 0.00 0.00 0.00 3.55
1834 2255 6.475727 ACGCTCATTTATACACACATACACTC 59.524 38.462 0.00 0.00 0.00 3.51
1835 2256 6.475402 CGCTCATTTATACACACATACACTCA 59.525 38.462 0.00 0.00 0.00 3.41
1836 2257 7.169813 CGCTCATTTATACACACATACACTCAT 59.830 37.037 0.00 0.00 0.00 2.90
1837 2258 8.830580 GCTCATTTATACACACATACACTCATT 58.169 33.333 0.00 0.00 0.00 2.57
1839 2260 9.883142 TCATTTATACACACATACACTCATTCA 57.117 29.630 0.00 0.00 0.00 2.57
1846 2267 8.201554 ACACACATACACTCATTCATATGAAC 57.798 34.615 20.19 0.00 40.17 3.18
1847 2268 7.823799 ACACACATACACTCATTCATATGAACA 59.176 33.333 20.19 9.22 40.17 3.18
1848 2269 8.118607 CACACATACACTCATTCATATGAACAC 58.881 37.037 20.19 0.00 40.17 3.32
1849 2270 7.010460 ACACATACACTCATTCATATGAACACG 59.990 37.037 20.19 12.86 40.17 4.49
1850 2271 4.864916 ACACTCATTCATATGAACACGC 57.135 40.909 20.19 0.00 40.17 5.34
1851 2272 4.252878 ACACTCATTCATATGAACACGCA 58.747 39.130 20.19 0.00 40.17 5.24
1852 2273 4.877823 ACACTCATTCATATGAACACGCAT 59.122 37.500 20.19 0.64 40.17 4.73
1853 2274 5.202640 CACTCATTCATATGAACACGCATG 58.797 41.667 20.19 13.18 40.17 4.06
1854 2275 4.213596 TCATTCATATGAACACGCATGC 57.786 40.909 20.19 7.91 37.83 4.06
1855 2276 3.626670 TCATTCATATGAACACGCATGCA 59.373 39.130 20.19 0.00 37.83 3.96
1856 2277 3.403613 TTCATATGAACACGCATGCAC 57.596 42.857 19.57 3.84 0.00 4.57
1857 2278 2.354259 TCATATGAACACGCATGCACA 58.646 42.857 19.57 9.46 0.00 4.57
1858 2279 2.095692 TCATATGAACACGCATGCACAC 59.904 45.455 19.57 4.56 0.00 3.82
1859 2280 0.801872 TATGAACACGCATGCACACC 59.198 50.000 19.57 2.87 0.00 4.16
1860 2281 1.865788 ATGAACACGCATGCACACCC 61.866 55.000 19.57 3.99 0.00 4.61
1861 2282 2.203337 AACACGCATGCACACCCT 60.203 55.556 19.57 0.00 0.00 4.34
1862 2283 0.953471 GAACACGCATGCACACCCTA 60.953 55.000 19.57 0.00 0.00 3.53
1863 2284 1.234615 AACACGCATGCACACCCTAC 61.235 55.000 19.57 0.00 0.00 3.18
1864 2285 2.046314 ACGCATGCACACCCTACC 60.046 61.111 19.57 0.00 0.00 3.18
1865 2286 2.824041 CGCATGCACACCCTACCC 60.824 66.667 19.57 0.00 0.00 3.69
1866 2287 2.440247 GCATGCACACCCTACCCC 60.440 66.667 14.21 0.00 0.00 4.95
1867 2288 3.086143 CATGCACACCCTACCCCA 58.914 61.111 0.00 0.00 0.00 4.96
1868 2289 1.614711 CATGCACACCCTACCCCAT 59.385 57.895 0.00 0.00 0.00 4.00
1869 2290 0.752743 CATGCACACCCTACCCCATG 60.753 60.000 0.00 0.00 0.00 3.66
1870 2291 0.918799 ATGCACACCCTACCCCATGA 60.919 55.000 0.00 0.00 0.00 3.07
1871 2292 1.224592 GCACACCCTACCCCATGAG 59.775 63.158 0.00 0.00 0.00 2.90
1872 2293 1.224592 CACACCCTACCCCATGAGC 59.775 63.158 0.00 0.00 0.00 4.26
1873 2294 1.229820 ACACCCTACCCCATGAGCA 60.230 57.895 0.00 0.00 0.00 4.26
1874 2295 1.224592 CACCCTACCCCATGAGCAC 59.775 63.158 0.00 0.00 0.00 4.40
1875 2296 2.001269 ACCCTACCCCATGAGCACC 61.001 63.158 0.00 0.00 0.00 5.01
1876 2297 1.694169 CCCTACCCCATGAGCACCT 60.694 63.158 0.00 0.00 0.00 4.00
1877 2298 1.700042 CCCTACCCCATGAGCACCTC 61.700 65.000 0.00 0.00 0.00 3.85
1878 2299 1.700042 CCTACCCCATGAGCACCTCC 61.700 65.000 0.00 0.00 0.00 4.30
1879 2300 2.032860 CTACCCCATGAGCACCTCCG 62.033 65.000 0.00 0.00 0.00 4.63
1880 2301 2.523740 TACCCCATGAGCACCTCCGA 62.524 60.000 0.00 0.00 0.00 4.55
1881 2302 2.503061 CCCATGAGCACCTCCGAG 59.497 66.667 0.00 0.00 0.00 4.63
1882 2303 2.060383 CCCATGAGCACCTCCGAGA 61.060 63.158 0.00 0.00 0.00 4.04
1883 2304 1.440893 CCATGAGCACCTCCGAGAG 59.559 63.158 0.00 0.00 0.00 3.20
1884 2305 1.039785 CCATGAGCACCTCCGAGAGA 61.040 60.000 0.00 0.00 0.00 3.10
1885 2306 0.102120 CATGAGCACCTCCGAGAGAC 59.898 60.000 0.00 0.00 0.00 3.36
1886 2307 0.033601 ATGAGCACCTCCGAGAGACT 60.034 55.000 0.00 0.00 0.00 3.24
1887 2308 0.962855 TGAGCACCTCCGAGAGACTG 60.963 60.000 0.00 0.22 0.00 3.51
1888 2309 0.678366 GAGCACCTCCGAGAGACTGA 60.678 60.000 0.00 0.00 0.00 3.41
1889 2310 0.679640 AGCACCTCCGAGAGACTGAG 60.680 60.000 0.00 0.00 0.00 3.35
1890 2311 0.678366 GCACCTCCGAGAGACTGAGA 60.678 60.000 0.00 0.00 32.76 3.27
1891 2312 2.021723 GCACCTCCGAGAGACTGAGAT 61.022 57.143 0.00 0.00 32.76 2.75
1892 2313 1.675483 CACCTCCGAGAGACTGAGATG 59.325 57.143 0.00 0.00 32.76 2.90
1893 2314 0.667993 CCTCCGAGAGACTGAGATGC 59.332 60.000 0.00 0.00 32.76 3.91
1894 2315 0.667993 CTCCGAGAGACTGAGATGCC 59.332 60.000 0.00 0.00 32.76 4.40
1895 2316 0.034089 TCCGAGAGACTGAGATGCCA 60.034 55.000 0.00 0.00 0.00 4.92
1896 2317 1.039068 CCGAGAGACTGAGATGCCAT 58.961 55.000 0.00 0.00 0.00 4.40
1897 2318 2.158608 TCCGAGAGACTGAGATGCCATA 60.159 50.000 0.00 0.00 0.00 2.74
1898 2319 2.824936 CCGAGAGACTGAGATGCCATAT 59.175 50.000 0.00 0.00 0.00 1.78
1899 2320 3.119531 CCGAGAGACTGAGATGCCATATC 60.120 52.174 0.00 0.00 0.00 1.63
1900 2321 3.505293 CGAGAGACTGAGATGCCATATCA 59.495 47.826 1.56 1.56 0.00 2.15
1901 2322 4.158209 CGAGAGACTGAGATGCCATATCAT 59.842 45.833 1.94 0.00 29.05 2.45
1902 2323 5.653507 GAGAGACTGAGATGCCATATCATC 58.346 45.833 1.94 3.58 42.32 2.92
1976 2397 1.002868 CCTTCCTGGCAGTCCACAG 60.003 63.158 14.43 1.54 37.47 3.66
2162 2583 2.830923 CCATTGCCATTTACCACCTCAA 59.169 45.455 0.00 0.00 0.00 3.02
2221 2642 4.436998 GCCTGCGACGTGCCTACT 62.437 66.667 0.00 0.00 45.60 2.57
2321 2744 0.398318 GACTGGGAGTGCTCAACCTT 59.602 55.000 1.41 0.00 0.00 3.50
2449 2872 2.125912 CTTCGCGGCTGCTACACT 60.126 61.111 17.03 0.00 39.65 3.55
2450 2873 1.138883 CTTCGCGGCTGCTACACTA 59.861 57.895 17.03 0.00 39.65 2.74
2451 2874 0.867753 CTTCGCGGCTGCTACACTAG 60.868 60.000 17.03 0.00 39.65 2.57
2452 2875 1.592400 TTCGCGGCTGCTACACTAGT 61.592 55.000 17.03 0.00 39.65 2.57
2453 2876 1.153823 CGCGGCTGCTACACTAGTT 60.154 57.895 17.03 0.00 39.65 2.24
2454 2877 0.736325 CGCGGCTGCTACACTAGTTT 60.736 55.000 17.03 0.00 39.65 2.66
2455 2878 1.439679 GCGGCTGCTACACTAGTTTT 58.560 50.000 11.21 0.00 38.39 2.43
2456 2879 1.128692 GCGGCTGCTACACTAGTTTTG 59.871 52.381 11.21 0.00 38.39 2.44
2457 2880 1.732259 CGGCTGCTACACTAGTTTTGG 59.268 52.381 0.00 0.00 0.00 3.28
2458 2881 2.779506 GGCTGCTACACTAGTTTTGGT 58.220 47.619 0.00 0.00 0.00 3.67
2459 2882 2.484264 GGCTGCTACACTAGTTTTGGTG 59.516 50.000 0.00 0.00 41.19 4.17
2460 2883 2.484264 GCTGCTACACTAGTTTTGGTGG 59.516 50.000 0.00 0.00 39.86 4.61
2461 2884 3.740115 CTGCTACACTAGTTTTGGTGGT 58.260 45.455 0.00 0.00 39.86 4.16
2462 2885 3.472652 TGCTACACTAGTTTTGGTGGTG 58.527 45.455 0.00 0.00 39.86 4.17
2463 2886 3.118186 TGCTACACTAGTTTTGGTGGTGT 60.118 43.478 0.00 0.00 39.86 4.16
2464 2887 3.881089 GCTACACTAGTTTTGGTGGTGTT 59.119 43.478 0.00 0.00 39.86 3.32
2465 2888 4.337274 GCTACACTAGTTTTGGTGGTGTTT 59.663 41.667 0.00 0.00 39.86 2.83
2466 2889 4.976224 ACACTAGTTTTGGTGGTGTTTC 57.024 40.909 0.00 0.00 39.86 2.78
2467 2890 4.595986 ACACTAGTTTTGGTGGTGTTTCT 58.404 39.130 0.00 0.00 39.86 2.52
2468 2891 5.014202 ACACTAGTTTTGGTGGTGTTTCTT 58.986 37.500 0.00 0.00 39.86 2.52
2469 2892 5.124936 ACACTAGTTTTGGTGGTGTTTCTTC 59.875 40.000 0.00 0.00 39.86 2.87
2470 2893 3.775661 AGTTTTGGTGGTGTTTCTTCG 57.224 42.857 0.00 0.00 0.00 3.79
2471 2894 3.086282 AGTTTTGGTGGTGTTTCTTCGT 58.914 40.909 0.00 0.00 0.00 3.85
2472 2895 4.263435 AGTTTTGGTGGTGTTTCTTCGTA 58.737 39.130 0.00 0.00 0.00 3.43
2473 2896 4.885325 AGTTTTGGTGGTGTTTCTTCGTAT 59.115 37.500 0.00 0.00 0.00 3.06
2474 2897 5.008316 AGTTTTGGTGGTGTTTCTTCGTATC 59.992 40.000 0.00 0.00 0.00 2.24
2475 2898 3.755112 TGGTGGTGTTTCTTCGTATCA 57.245 42.857 0.00 0.00 0.00 2.15
2476 2899 4.280436 TGGTGGTGTTTCTTCGTATCAT 57.720 40.909 0.00 0.00 0.00 2.45
2477 2900 4.647611 TGGTGGTGTTTCTTCGTATCATT 58.352 39.130 0.00 0.00 0.00 2.57
2478 2901 5.795972 TGGTGGTGTTTCTTCGTATCATTA 58.204 37.500 0.00 0.00 0.00 1.90
2479 2902 6.231951 TGGTGGTGTTTCTTCGTATCATTAA 58.768 36.000 0.00 0.00 0.00 1.40
2480 2903 6.370442 TGGTGGTGTTTCTTCGTATCATTAAG 59.630 38.462 0.00 0.00 0.00 1.85
2481 2904 6.592607 GGTGGTGTTTCTTCGTATCATTAAGA 59.407 38.462 0.00 0.00 0.00 2.10
2482 2905 7.201530 GGTGGTGTTTCTTCGTATCATTAAGAG 60.202 40.741 0.00 0.00 31.30 2.85
2483 2906 6.816640 TGGTGTTTCTTCGTATCATTAAGAGG 59.183 38.462 0.00 0.00 31.30 3.69
2484 2907 6.817140 GGTGTTTCTTCGTATCATTAAGAGGT 59.183 38.462 0.00 0.00 31.30 3.85
2485 2908 7.201530 GGTGTTTCTTCGTATCATTAAGAGGTG 60.202 40.741 0.00 0.00 31.30 4.00
2486 2909 7.331193 GTGTTTCTTCGTATCATTAAGAGGTGT 59.669 37.037 0.00 0.00 31.30 4.16
2487 2910 7.330946 TGTTTCTTCGTATCATTAAGAGGTGTG 59.669 37.037 0.00 0.00 31.30 3.82
2488 2911 5.348986 TCTTCGTATCATTAAGAGGTGTGC 58.651 41.667 0.00 0.00 0.00 4.57
2489 2912 5.127194 TCTTCGTATCATTAAGAGGTGTGCT 59.873 40.000 0.00 0.00 0.00 4.40
2490 2913 5.339008 TCGTATCATTAAGAGGTGTGCTT 57.661 39.130 0.00 0.00 0.00 3.91
2491 2914 5.109210 TCGTATCATTAAGAGGTGTGCTTG 58.891 41.667 0.00 0.00 0.00 4.01
2492 2915 5.105513 TCGTATCATTAAGAGGTGTGCTTGA 60.106 40.000 0.00 0.00 0.00 3.02
2493 2916 5.580691 CGTATCATTAAGAGGTGTGCTTGAA 59.419 40.000 0.00 0.00 0.00 2.69
2494 2917 6.237942 CGTATCATTAAGAGGTGTGCTTGAAG 60.238 42.308 0.00 0.00 0.00 3.02
2495 2918 5.227569 TCATTAAGAGGTGTGCTTGAAGA 57.772 39.130 0.00 0.00 0.00 2.87
2496 2919 5.809001 TCATTAAGAGGTGTGCTTGAAGAT 58.191 37.500 0.00 0.00 0.00 2.40
2497 2920 5.645067 TCATTAAGAGGTGTGCTTGAAGATG 59.355 40.000 0.00 0.00 0.00 2.90
2498 2921 2.486472 AGAGGTGTGCTTGAAGATGG 57.514 50.000 0.00 0.00 0.00 3.51
2499 2922 1.701847 AGAGGTGTGCTTGAAGATGGT 59.298 47.619 0.00 0.00 0.00 3.55
2500 2923 1.808945 GAGGTGTGCTTGAAGATGGTG 59.191 52.381 0.00 0.00 0.00 4.17
2501 2924 1.143684 AGGTGTGCTTGAAGATGGTGT 59.856 47.619 0.00 0.00 0.00 4.16
2502 2925 1.267806 GGTGTGCTTGAAGATGGTGTG 59.732 52.381 0.00 0.00 0.00 3.82
2503 2926 1.949525 GTGTGCTTGAAGATGGTGTGT 59.050 47.619 0.00 0.00 0.00 3.72
2504 2927 2.031682 GTGTGCTTGAAGATGGTGTGTC 60.032 50.000 0.00 0.00 0.00 3.67
2505 2928 1.537202 GTGCTTGAAGATGGTGTGTCC 59.463 52.381 0.00 0.00 0.00 4.02
2506 2929 1.168714 GCTTGAAGATGGTGTGTCCC 58.831 55.000 0.00 0.00 34.77 4.46
2507 2930 1.826385 CTTGAAGATGGTGTGTCCCC 58.174 55.000 0.00 0.00 34.77 4.81
2508 2931 0.036164 TTGAAGATGGTGTGTCCCCG 59.964 55.000 0.00 0.00 34.77 5.73
2509 2932 1.125093 TGAAGATGGTGTGTCCCCGT 61.125 55.000 0.00 0.00 34.77 5.28
2510 2933 0.899720 GAAGATGGTGTGTCCCCGTA 59.100 55.000 0.00 0.00 34.77 4.02
2511 2934 0.611714 AAGATGGTGTGTCCCCGTAC 59.388 55.000 0.00 0.00 34.77 3.67
2512 2935 1.219935 GATGGTGTGTCCCCGTACC 59.780 63.158 0.00 0.00 34.77 3.34
2513 2936 1.229400 ATGGTGTGTCCCCGTACCT 60.229 57.895 0.00 0.00 34.32 3.08
2514 2937 1.550130 ATGGTGTGTCCCCGTACCTG 61.550 60.000 0.00 0.00 34.32 4.00
2515 2938 1.909781 GGTGTGTCCCCGTACCTGA 60.910 63.158 0.00 0.00 0.00 3.86
2516 2939 1.262640 GGTGTGTCCCCGTACCTGAT 61.263 60.000 0.00 0.00 0.00 2.90
2517 2940 0.611714 GTGTGTCCCCGTACCTGATT 59.388 55.000 0.00 0.00 0.00 2.57
2518 2941 0.899720 TGTGTCCCCGTACCTGATTC 59.100 55.000 0.00 0.00 0.00 2.52
2519 2942 1.192428 GTGTCCCCGTACCTGATTCT 58.808 55.000 0.00 0.00 0.00 2.40
2520 2943 1.136500 GTGTCCCCGTACCTGATTCTC 59.864 57.143 0.00 0.00 0.00 2.87
2521 2944 0.751452 GTCCCCGTACCTGATTCTCC 59.249 60.000 0.00 0.00 0.00 3.71
2522 2945 0.337082 TCCCCGTACCTGATTCTCCA 59.663 55.000 0.00 0.00 0.00 3.86
2523 2946 0.753262 CCCCGTACCTGATTCTCCAG 59.247 60.000 0.00 0.00 0.00 3.86
2530 2953 1.467920 CCTGATTCTCCAGGTTTGGC 58.532 55.000 0.00 0.00 46.62 4.52
2531 2954 1.005215 CCTGATTCTCCAGGTTTGGCT 59.995 52.381 0.00 0.00 46.62 4.75
2532 2955 2.556114 CCTGATTCTCCAGGTTTGGCTT 60.556 50.000 0.00 0.00 46.62 4.35
2533 2956 3.160269 CTGATTCTCCAGGTTTGGCTTT 58.840 45.455 0.00 0.00 44.63 3.51
2534 2957 3.575687 CTGATTCTCCAGGTTTGGCTTTT 59.424 43.478 0.00 0.00 44.63 2.27
2535 2958 3.966665 TGATTCTCCAGGTTTGGCTTTTT 59.033 39.130 0.00 0.00 44.63 1.94
2536 2959 4.039124 TGATTCTCCAGGTTTGGCTTTTTC 59.961 41.667 0.00 0.00 44.63 2.29
2537 2960 1.953686 TCTCCAGGTTTGGCTTTTTCG 59.046 47.619 0.00 0.00 44.63 3.46
2538 2961 1.681264 CTCCAGGTTTGGCTTTTTCGT 59.319 47.619 0.00 0.00 44.63 3.85
2539 2962 2.100749 CTCCAGGTTTGGCTTTTTCGTT 59.899 45.455 0.00 0.00 44.63 3.85
2540 2963 3.288964 TCCAGGTTTGGCTTTTTCGTTA 58.711 40.909 0.00 0.00 44.63 3.18
2541 2964 3.892588 TCCAGGTTTGGCTTTTTCGTTAT 59.107 39.130 0.00 0.00 44.63 1.89
2542 2965 4.022676 TCCAGGTTTGGCTTTTTCGTTATC 60.023 41.667 0.00 0.00 44.63 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 2.351738 CCATGCTCCCGTTCAGTTTTTC 60.352 50.000 0.00 0.00 0.00 2.29
34 35 0.178975 AAAACCCATGCTCCCGTTCA 60.179 50.000 0.00 0.00 0.00 3.18
63 65 1.675310 CACGGGCATGCCTCTTTCA 60.675 57.895 34.70 0.00 36.10 2.69
117 119 1.727467 GTGAGCGGCACAGTTTTGT 59.273 52.632 1.45 0.00 46.91 2.83
241 359 2.743126 TCGGAAACAGAAAACACACGTT 59.257 40.909 0.00 0.00 36.73 3.99
248 367 2.031944 GTGCCTCTCGGAAACAGAAAAC 60.032 50.000 0.00 0.00 0.00 2.43
296 533 4.742201 GCTTCCGCGAGAGGCACA 62.742 66.667 20.89 0.00 46.54 4.57
406 658 0.383949 GGCACGGTTTTGCAAAGAGA 59.616 50.000 12.41 0.00 44.94 3.10
411 663 0.526524 CGAAAGGCACGGTTTTGCAA 60.527 50.000 0.00 0.00 44.94 4.08
497 773 1.133407 TGGTTTTGTTTCCACGACAGC 59.867 47.619 0.00 0.00 0.00 4.40
504 780 2.962421 GGGAGTCATGGTTTTGTTTCCA 59.038 45.455 0.00 0.00 38.14 3.53
568 912 1.880027 CGGTCTTCCTGAACTTTTGGG 59.120 52.381 0.00 0.00 0.00 4.12
656 1028 2.283676 TGGACACTCCCTCCGACC 60.284 66.667 0.00 0.00 35.03 4.79
657 1029 1.304217 TCTGGACACTCCCTCCGAC 60.304 63.158 0.00 0.00 35.03 4.79
658 1030 1.000771 CTCTGGACACTCCCTCCGA 60.001 63.158 0.00 0.00 35.03 4.55
668 1040 2.335011 CGTGTCGCACTCTGGACA 59.665 61.111 8.07 0.00 40.63 4.02
722 1094 1.774254 TCCTTCTGGAGCCTTGAAACA 59.226 47.619 0.00 0.00 37.46 2.83
736 1108 2.789409 AATTAACCAGCGCTCCTTCT 57.211 45.000 7.13 0.00 0.00 2.85
748 1120 6.321181 TGATCATTGAGGCCAACTAATTAACC 59.679 38.462 5.01 0.00 34.72 2.85
761 1133 1.407979 CCCAGCTTTGATCATTGAGGC 59.592 52.381 0.00 0.00 0.00 4.70
762 1134 2.029623 CCCCAGCTTTGATCATTGAGG 58.970 52.381 0.00 0.00 0.00 3.86
768 1140 1.551430 CATTTGCCCCAGCTTTGATCA 59.449 47.619 0.00 0.00 40.80 2.92
769 1141 1.134610 CCATTTGCCCCAGCTTTGATC 60.135 52.381 0.00 0.00 40.80 2.92
770 1142 0.906775 CCATTTGCCCCAGCTTTGAT 59.093 50.000 0.00 0.00 40.80 2.57
781 1153 4.536065 GCAAAAAGCTAAAACCATTTGCC 58.464 39.130 9.26 0.00 44.03 4.52
797 1169 1.069978 GCTAAGGTTGGGCTGCAAAAA 59.930 47.619 0.50 0.00 0.00 1.94
811 1183 3.441500 AGAAAAAGGGTCCTGCTAAGG 57.558 47.619 0.00 0.00 46.06 2.69
909 1327 5.279506 GGACGGAATTGATATGAGCTAGGAA 60.280 44.000 0.00 0.00 0.00 3.36
948 1366 6.434018 AGCGACTAATTAAGTTCGTAGAGT 57.566 37.500 10.71 0.00 39.07 3.24
949 1367 6.965500 TGAAGCGACTAATTAAGTTCGTAGAG 59.035 38.462 10.71 0.00 39.07 2.43
974 1392 4.932200 TGTTTGTTGCTTTTGTTTCCGAAT 59.068 33.333 0.00 0.00 0.00 3.34
995 1413 1.473965 CCGTAGATGGCTTCATGCTGT 60.474 52.381 3.03 0.00 42.39 4.40
996 1414 1.224075 CCGTAGATGGCTTCATGCTG 58.776 55.000 3.03 0.00 42.39 4.41
1310 1728 2.125512 CGTACAGCTCCTGGCACC 60.126 66.667 0.00 0.00 44.79 5.01
1478 1896 2.352032 ACCGAGTAGGAGCTGTGCC 61.352 63.158 0.00 0.00 45.00 5.01
1551 1969 5.011943 ACACACGTAGTATCCCCAAGTTTTA 59.988 40.000 0.00 0.00 41.61 1.52
1561 1979 7.636359 CGTACTACTTTTACACACGTAGTATCC 59.364 40.741 10.27 0.85 43.34 2.59
1702 2123 5.494390 ACATAGATATTGCTCAGGATGCA 57.506 39.130 0.00 0.00 38.80 3.96
1728 2149 7.592164 GCTTTATATTCTCAGACGAGGAAGTAC 59.408 40.741 0.00 0.00 39.95 2.73
1783 2204 5.521010 TGTGTCCGTACTGTGTTAGAAAAAG 59.479 40.000 0.00 0.00 0.00 2.27
1784 2205 5.417811 TGTGTCCGTACTGTGTTAGAAAAA 58.582 37.500 0.00 0.00 0.00 1.94
1785 2206 5.008619 TGTGTCCGTACTGTGTTAGAAAA 57.991 39.130 0.00 0.00 0.00 2.29
1786 2207 4.338964 TCTGTGTCCGTACTGTGTTAGAAA 59.661 41.667 0.00 0.00 0.00 2.52
1787 2208 3.884693 TCTGTGTCCGTACTGTGTTAGAA 59.115 43.478 0.00 0.00 0.00 2.10
1788 2209 3.251729 GTCTGTGTCCGTACTGTGTTAGA 59.748 47.826 0.00 0.00 0.00 2.10
1789 2210 3.562505 GTCTGTGTCCGTACTGTGTTAG 58.437 50.000 0.00 0.00 0.00 2.34
1790 2211 2.031769 CGTCTGTGTCCGTACTGTGTTA 60.032 50.000 0.00 0.00 0.00 2.41
1791 2212 1.268896 CGTCTGTGTCCGTACTGTGTT 60.269 52.381 0.00 0.00 0.00 3.32
1792 2213 0.309922 CGTCTGTGTCCGTACTGTGT 59.690 55.000 0.00 0.00 0.00 3.72
1793 2214 1.002250 GCGTCTGTGTCCGTACTGTG 61.002 60.000 0.00 0.00 0.00 3.66
1794 2215 1.170919 AGCGTCTGTGTCCGTACTGT 61.171 55.000 0.00 0.00 0.00 3.55
1795 2216 0.454620 GAGCGTCTGTGTCCGTACTG 60.455 60.000 0.00 0.00 0.00 2.74
1796 2217 0.887836 TGAGCGTCTGTGTCCGTACT 60.888 55.000 0.00 0.00 0.00 2.73
1797 2218 0.170561 ATGAGCGTCTGTGTCCGTAC 59.829 55.000 0.00 0.00 0.00 3.67
1798 2219 0.885879 AATGAGCGTCTGTGTCCGTA 59.114 50.000 0.00 0.00 0.00 4.02
1799 2220 0.033504 AAATGAGCGTCTGTGTCCGT 59.966 50.000 0.00 0.00 0.00 4.69
1800 2221 1.990799 TAAATGAGCGTCTGTGTCCG 58.009 50.000 0.00 0.00 0.00 4.79
1801 2222 4.267928 GTGTATAAATGAGCGTCTGTGTCC 59.732 45.833 0.00 0.00 0.00 4.02
1802 2223 4.862574 TGTGTATAAATGAGCGTCTGTGTC 59.137 41.667 0.00 0.00 0.00 3.67
1803 2224 4.625742 GTGTGTATAAATGAGCGTCTGTGT 59.374 41.667 0.00 0.00 0.00 3.72
1804 2225 4.625311 TGTGTGTATAAATGAGCGTCTGTG 59.375 41.667 0.00 0.00 0.00 3.66
1805 2226 4.816392 TGTGTGTATAAATGAGCGTCTGT 58.184 39.130 0.00 0.00 0.00 3.41
1806 2227 5.973651 ATGTGTGTATAAATGAGCGTCTG 57.026 39.130 0.00 0.00 0.00 3.51
1807 2228 6.475727 GTGTATGTGTGTATAAATGAGCGTCT 59.524 38.462 0.00 0.00 0.00 4.18
1808 2229 6.475727 AGTGTATGTGTGTATAAATGAGCGTC 59.524 38.462 0.00 0.00 0.00 5.19
1809 2230 6.338146 AGTGTATGTGTGTATAAATGAGCGT 58.662 36.000 0.00 0.00 0.00 5.07
1810 2231 6.475402 TGAGTGTATGTGTGTATAAATGAGCG 59.525 38.462 0.00 0.00 0.00 5.03
1811 2232 7.770801 TGAGTGTATGTGTGTATAAATGAGC 57.229 36.000 0.00 0.00 0.00 4.26
1813 2234 9.883142 TGAATGAGTGTATGTGTGTATAAATGA 57.117 29.630 0.00 0.00 0.00 2.57
1820 2241 9.313118 GTTCATATGAATGAGTGTATGTGTGTA 57.687 33.333 20.65 0.00 42.97 2.90
1821 2242 7.823799 TGTTCATATGAATGAGTGTATGTGTGT 59.176 33.333 20.65 0.00 42.97 3.72
1822 2243 8.118607 GTGTTCATATGAATGAGTGTATGTGTG 58.881 37.037 20.65 0.00 42.97 3.82
1823 2244 7.010460 CGTGTTCATATGAATGAGTGTATGTGT 59.990 37.037 20.65 0.00 42.97 3.72
1824 2245 7.339953 CGTGTTCATATGAATGAGTGTATGTG 58.660 38.462 20.65 0.00 42.97 3.21
1825 2246 6.018751 GCGTGTTCATATGAATGAGTGTATGT 60.019 38.462 20.65 0.00 42.97 2.29
1826 2247 6.018832 TGCGTGTTCATATGAATGAGTGTATG 60.019 38.462 20.65 8.45 42.97 2.39
1827 2248 6.048509 TGCGTGTTCATATGAATGAGTGTAT 58.951 36.000 20.65 0.00 42.97 2.29
1828 2249 5.415221 TGCGTGTTCATATGAATGAGTGTA 58.585 37.500 20.65 7.03 42.97 2.90
1829 2250 4.252878 TGCGTGTTCATATGAATGAGTGT 58.747 39.130 20.65 0.00 42.97 3.55
1830 2251 4.863152 TGCGTGTTCATATGAATGAGTG 57.137 40.909 20.65 10.57 42.97 3.51
1831 2252 4.260907 GCATGCGTGTTCATATGAATGAGT 60.261 41.667 20.65 3.80 42.97 3.41
1832 2253 4.216731 GCATGCGTGTTCATATGAATGAG 58.783 43.478 20.65 14.80 42.97 2.90
1833 2254 3.626670 TGCATGCGTGTTCATATGAATGA 59.373 39.130 20.65 8.51 40.43 2.57
1834 2255 3.727227 GTGCATGCGTGTTCATATGAATG 59.273 43.478 20.65 14.27 36.33 2.67
1835 2256 3.377798 TGTGCATGCGTGTTCATATGAAT 59.622 39.130 20.65 1.34 36.33 2.57
1836 2257 2.746362 TGTGCATGCGTGTTCATATGAA 59.254 40.909 14.23 14.23 0.00 2.57
1837 2258 2.095692 GTGTGCATGCGTGTTCATATGA 59.904 45.455 14.09 0.00 0.00 2.15
1838 2259 2.443387 GTGTGCATGCGTGTTCATATG 58.557 47.619 14.09 0.00 0.00 1.78
1839 2260 1.401552 GGTGTGCATGCGTGTTCATAT 59.598 47.619 14.09 0.00 0.00 1.78
1840 2261 0.801872 GGTGTGCATGCGTGTTCATA 59.198 50.000 14.09 0.00 0.00 2.15
1841 2262 1.580942 GGTGTGCATGCGTGTTCAT 59.419 52.632 14.09 0.00 0.00 2.57
1842 2263 2.551006 GGGTGTGCATGCGTGTTCA 61.551 57.895 14.09 4.54 0.00 3.18
1843 2264 0.953471 TAGGGTGTGCATGCGTGTTC 60.953 55.000 14.09 2.61 0.00 3.18
1844 2265 1.072332 TAGGGTGTGCATGCGTGTT 59.928 52.632 14.09 0.00 0.00 3.32
1845 2266 1.671054 GTAGGGTGTGCATGCGTGT 60.671 57.895 14.09 0.00 0.00 4.49
1846 2267 2.398554 GGTAGGGTGTGCATGCGTG 61.399 63.158 14.09 0.09 0.00 5.34
1847 2268 2.046314 GGTAGGGTGTGCATGCGT 60.046 61.111 14.09 0.00 0.00 5.24
1848 2269 2.824041 GGGTAGGGTGTGCATGCG 60.824 66.667 14.09 0.00 0.00 4.73
1849 2270 2.440247 GGGGTAGGGTGTGCATGC 60.440 66.667 11.82 11.82 0.00 4.06
1850 2271 0.752743 CATGGGGTAGGGTGTGCATG 60.753 60.000 0.00 0.00 0.00 4.06
1851 2272 0.918799 TCATGGGGTAGGGTGTGCAT 60.919 55.000 0.00 0.00 0.00 3.96
1852 2273 1.540118 TCATGGGGTAGGGTGTGCA 60.540 57.895 0.00 0.00 0.00 4.57
1853 2274 1.224592 CTCATGGGGTAGGGTGTGC 59.775 63.158 0.00 0.00 0.00 4.57
1854 2275 1.224592 GCTCATGGGGTAGGGTGTG 59.775 63.158 0.00 0.00 0.00 3.82
1855 2276 1.229820 TGCTCATGGGGTAGGGTGT 60.230 57.895 0.00 0.00 0.00 4.16
1856 2277 1.224592 GTGCTCATGGGGTAGGGTG 59.775 63.158 0.00 0.00 0.00 4.61
1857 2278 2.001269 GGTGCTCATGGGGTAGGGT 61.001 63.158 0.00 0.00 0.00 4.34
1858 2279 1.694169 AGGTGCTCATGGGGTAGGG 60.694 63.158 0.00 0.00 0.00 3.53
1859 2280 1.700042 GGAGGTGCTCATGGGGTAGG 61.700 65.000 0.00 0.00 31.08 3.18
1860 2281 1.832912 GGAGGTGCTCATGGGGTAG 59.167 63.158 0.00 0.00 31.08 3.18
1861 2282 2.063979 CGGAGGTGCTCATGGGGTA 61.064 63.158 0.00 0.00 31.08 3.69
1862 2283 3.402681 CGGAGGTGCTCATGGGGT 61.403 66.667 0.00 0.00 31.08 4.95
1863 2284 3.083349 TCGGAGGTGCTCATGGGG 61.083 66.667 0.00 0.00 31.08 4.96
1864 2285 2.025767 CTCTCGGAGGTGCTCATGGG 62.026 65.000 4.96 0.00 31.08 4.00
1865 2286 1.039785 TCTCTCGGAGGTGCTCATGG 61.040 60.000 4.96 0.00 31.08 3.66
1866 2287 0.102120 GTCTCTCGGAGGTGCTCATG 59.898 60.000 4.96 0.00 31.08 3.07
1867 2288 0.033601 AGTCTCTCGGAGGTGCTCAT 60.034 55.000 4.96 0.00 31.08 2.90
1868 2289 0.962855 CAGTCTCTCGGAGGTGCTCA 60.963 60.000 4.96 0.00 31.08 4.26
1869 2290 0.678366 TCAGTCTCTCGGAGGTGCTC 60.678 60.000 4.96 0.00 0.00 4.26
1870 2291 0.679640 CTCAGTCTCTCGGAGGTGCT 60.680 60.000 4.96 0.00 35.32 4.40
1871 2292 0.678366 TCTCAGTCTCTCGGAGGTGC 60.678 60.000 4.96 0.00 38.55 5.01
1872 2293 1.675483 CATCTCAGTCTCTCGGAGGTG 59.325 57.143 4.96 0.00 41.43 4.00
1873 2294 2.021723 GCATCTCAGTCTCTCGGAGGT 61.022 57.143 4.96 0.00 38.55 3.85
1874 2295 0.667993 GCATCTCAGTCTCTCGGAGG 59.332 60.000 4.96 0.00 38.55 4.30
1875 2296 0.667993 GGCATCTCAGTCTCTCGGAG 59.332 60.000 0.00 0.00 39.19 4.63
1876 2297 0.034089 TGGCATCTCAGTCTCTCGGA 60.034 55.000 0.00 0.00 0.00 4.55
1877 2298 1.039068 ATGGCATCTCAGTCTCTCGG 58.961 55.000 0.00 0.00 0.00 4.63
1878 2299 3.505293 TGATATGGCATCTCAGTCTCTCG 59.495 47.826 11.12 0.00 0.00 4.04
1879 2300 5.653507 GATGATATGGCATCTCAGTCTCTC 58.346 45.833 18.67 9.01 41.09 3.20
1880 2301 5.664294 GATGATATGGCATCTCAGTCTCT 57.336 43.478 18.67 4.07 41.09 3.10
1909 2330 0.107643 TCAAGGTCGATGTTGCCACA 59.892 50.000 0.00 0.00 37.31 4.17
1910 2331 0.517316 GTCAAGGTCGATGTTGCCAC 59.483 55.000 5.13 0.00 0.00 5.01
1911 2332 0.107643 TGTCAAGGTCGATGTTGCCA 59.892 50.000 5.13 0.00 0.00 4.92
1912 2333 1.069227 GTTGTCAAGGTCGATGTTGCC 60.069 52.381 5.13 0.00 0.00 4.52
1913 2334 1.601903 TGTTGTCAAGGTCGATGTTGC 59.398 47.619 5.13 2.49 0.00 4.17
1914 2335 3.423515 CGATGTTGTCAAGGTCGATGTTG 60.424 47.826 12.02 3.85 34.46 3.33
1915 2336 2.736721 CGATGTTGTCAAGGTCGATGTT 59.263 45.455 12.02 0.00 34.46 2.71
1916 2337 2.029380 TCGATGTTGTCAAGGTCGATGT 60.029 45.455 14.78 0.00 36.52 3.06
1917 2338 2.345641 GTCGATGTTGTCAAGGTCGATG 59.654 50.000 19.30 0.00 42.37 3.84
1918 2339 2.607187 GTCGATGTTGTCAAGGTCGAT 58.393 47.619 19.30 0.00 42.37 3.59
1919 2340 1.336517 GGTCGATGTTGTCAAGGTCGA 60.337 52.381 14.78 14.78 38.79 4.20
1920 2341 1.068474 GGTCGATGTTGTCAAGGTCG 58.932 55.000 11.43 11.43 0.00 4.79
1921 2342 2.457366 AGGTCGATGTTGTCAAGGTC 57.543 50.000 0.00 0.00 0.00 3.85
1922 2343 2.104111 TCAAGGTCGATGTTGTCAAGGT 59.896 45.455 8.94 0.00 0.00 3.50
1923 2344 2.480419 GTCAAGGTCGATGTTGTCAAGG 59.520 50.000 8.94 0.00 0.00 3.61
1924 2345 3.130633 TGTCAAGGTCGATGTTGTCAAG 58.869 45.455 8.94 0.00 0.00 3.02
1925 2346 3.186702 TGTCAAGGTCGATGTTGTCAA 57.813 42.857 8.94 0.00 0.00 3.18
1928 2349 2.912771 TGTTGTCAAGGTCGATGTTGT 58.087 42.857 8.94 0.00 0.00 3.32
1973 2394 0.981183 TCGCATGGGGAAAGTACTGT 59.019 50.000 10.21 0.00 0.00 3.55
1974 2395 2.332063 ATCGCATGGGGAAAGTACTG 57.668 50.000 10.21 0.00 0.00 2.74
1976 2397 4.273148 AGATATCGCATGGGGAAAGTAC 57.727 45.455 10.21 0.00 0.00 2.73
2162 2583 2.035632 CAACCGGAAGATCTAGAGGCT 58.964 52.381 9.46 0.00 0.00 4.58
2221 2642 0.251386 TTATCACAGCCCGCCCAAAA 60.251 50.000 0.00 0.00 0.00 2.44
2321 2744 1.139853 AGGGCGGTTGCAAATTTTTGA 59.860 42.857 0.00 0.00 45.35 2.69
2449 2872 4.263435 ACGAAGAAACACCACCAAAACTA 58.737 39.130 0.00 0.00 0.00 2.24
2450 2873 3.086282 ACGAAGAAACACCACCAAAACT 58.914 40.909 0.00 0.00 0.00 2.66
2451 2874 3.497297 ACGAAGAAACACCACCAAAAC 57.503 42.857 0.00 0.00 0.00 2.43
2452 2875 4.882427 TGATACGAAGAAACACCACCAAAA 59.118 37.500 0.00 0.00 0.00 2.44
2453 2876 4.452825 TGATACGAAGAAACACCACCAAA 58.547 39.130 0.00 0.00 0.00 3.28
2454 2877 4.074627 TGATACGAAGAAACACCACCAA 57.925 40.909 0.00 0.00 0.00 3.67
2455 2878 3.755112 TGATACGAAGAAACACCACCA 57.245 42.857 0.00 0.00 0.00 4.17
2456 2879 6.592607 TCTTAATGATACGAAGAAACACCACC 59.407 38.462 0.00 0.00 0.00 4.61
2457 2880 7.201530 CCTCTTAATGATACGAAGAAACACCAC 60.202 40.741 0.00 0.00 0.00 4.16
2458 2881 6.816640 CCTCTTAATGATACGAAGAAACACCA 59.183 38.462 0.00 0.00 0.00 4.17
2459 2882 6.817140 ACCTCTTAATGATACGAAGAAACACC 59.183 38.462 0.00 0.00 0.00 4.16
2460 2883 7.331193 ACACCTCTTAATGATACGAAGAAACAC 59.669 37.037 0.00 0.00 0.00 3.32
2461 2884 7.330946 CACACCTCTTAATGATACGAAGAAACA 59.669 37.037 0.00 0.00 0.00 2.83
2462 2885 7.674240 GCACACCTCTTAATGATACGAAGAAAC 60.674 40.741 0.00 0.00 0.00 2.78
2463 2886 6.312918 GCACACCTCTTAATGATACGAAGAAA 59.687 38.462 0.00 0.00 0.00 2.52
2464 2887 5.810587 GCACACCTCTTAATGATACGAAGAA 59.189 40.000 0.00 0.00 0.00 2.52
2465 2888 5.127194 AGCACACCTCTTAATGATACGAAGA 59.873 40.000 0.00 0.00 0.00 2.87
2466 2889 5.352284 AGCACACCTCTTAATGATACGAAG 58.648 41.667 0.00 0.00 0.00 3.79
2467 2890 5.339008 AGCACACCTCTTAATGATACGAA 57.661 39.130 0.00 0.00 0.00 3.85
2468 2891 5.105513 TCAAGCACACCTCTTAATGATACGA 60.106 40.000 0.00 0.00 0.00 3.43
2469 2892 5.109210 TCAAGCACACCTCTTAATGATACG 58.891 41.667 0.00 0.00 0.00 3.06
2470 2893 6.818644 TCTTCAAGCACACCTCTTAATGATAC 59.181 38.462 0.00 0.00 0.00 2.24
2471 2894 6.946340 TCTTCAAGCACACCTCTTAATGATA 58.054 36.000 0.00 0.00 0.00 2.15
2472 2895 5.809001 TCTTCAAGCACACCTCTTAATGAT 58.191 37.500 0.00 0.00 0.00 2.45
2473 2896 5.227569 TCTTCAAGCACACCTCTTAATGA 57.772 39.130 0.00 0.00 0.00 2.57
2474 2897 5.163683 CCATCTTCAAGCACACCTCTTAATG 60.164 44.000 0.00 0.00 0.00 1.90
2475 2898 4.946157 CCATCTTCAAGCACACCTCTTAAT 59.054 41.667 0.00 0.00 0.00 1.40
2476 2899 4.202461 ACCATCTTCAAGCACACCTCTTAA 60.202 41.667 0.00 0.00 0.00 1.85
2477 2900 3.327757 ACCATCTTCAAGCACACCTCTTA 59.672 43.478 0.00 0.00 0.00 2.10
2478 2901 2.107204 ACCATCTTCAAGCACACCTCTT 59.893 45.455 0.00 0.00 0.00 2.85
2479 2902 1.701847 ACCATCTTCAAGCACACCTCT 59.298 47.619 0.00 0.00 0.00 3.69
2480 2903 1.808945 CACCATCTTCAAGCACACCTC 59.191 52.381 0.00 0.00 0.00 3.85
2481 2904 1.143684 ACACCATCTTCAAGCACACCT 59.856 47.619 0.00 0.00 0.00 4.00
2482 2905 1.267806 CACACCATCTTCAAGCACACC 59.732 52.381 0.00 0.00 0.00 4.16
2483 2906 1.949525 ACACACCATCTTCAAGCACAC 59.050 47.619 0.00 0.00 0.00 3.82
2484 2907 2.221169 GACACACCATCTTCAAGCACA 58.779 47.619 0.00 0.00 0.00 4.57
2485 2908 1.537202 GGACACACCATCTTCAAGCAC 59.463 52.381 0.00 0.00 38.79 4.40
2486 2909 1.545428 GGGACACACCATCTTCAAGCA 60.545 52.381 0.00 0.00 41.20 3.91
2487 2910 1.168714 GGGACACACCATCTTCAAGC 58.831 55.000 0.00 0.00 41.20 4.01
2488 2911 1.826385 GGGGACACACCATCTTCAAG 58.174 55.000 0.00 0.00 41.20 3.02
2489 2912 0.036164 CGGGGACACACCATCTTCAA 59.964 55.000 0.00 0.00 41.20 2.69
2490 2913 1.125093 ACGGGGACACACCATCTTCA 61.125 55.000 0.00 0.00 41.20 3.02
2491 2914 0.899720 TACGGGGACACACCATCTTC 59.100 55.000 0.00 0.00 41.20 2.87
2492 2915 0.611714 GTACGGGGACACACCATCTT 59.388 55.000 0.00 0.00 41.20 2.40
2493 2916 1.262640 GGTACGGGGACACACCATCT 61.263 60.000 0.00 0.00 41.20 2.90
2494 2917 1.219935 GGTACGGGGACACACCATC 59.780 63.158 0.00 0.00 41.20 3.51
2495 2918 1.229400 AGGTACGGGGACACACCAT 60.229 57.895 0.00 0.00 41.20 3.55
2496 2919 2.202053 AGGTACGGGGACACACCA 59.798 61.111 0.00 0.00 41.20 4.17
2497 2920 1.262640 ATCAGGTACGGGGACACACC 61.263 60.000 0.00 0.00 34.74 4.16
2498 2921 0.611714 AATCAGGTACGGGGACACAC 59.388 55.000 0.00 0.00 0.00 3.82
2499 2922 0.899720 GAATCAGGTACGGGGACACA 59.100 55.000 0.00 0.00 0.00 3.72
2500 2923 1.136500 GAGAATCAGGTACGGGGACAC 59.864 57.143 0.00 0.00 33.17 3.67
2501 2924 1.481871 GAGAATCAGGTACGGGGACA 58.518 55.000 0.00 0.00 33.17 4.02
2502 2925 0.751452 GGAGAATCAGGTACGGGGAC 59.249 60.000 0.00 0.00 36.25 4.46
2503 2926 0.337082 TGGAGAATCAGGTACGGGGA 59.663 55.000 0.00 0.00 36.25 4.81
2504 2927 0.753262 CTGGAGAATCAGGTACGGGG 59.247 60.000 0.00 0.00 36.25 5.73
2505 2928 0.753262 CCTGGAGAATCAGGTACGGG 59.247 60.000 2.93 0.00 46.89 5.28
2512 2935 2.503895 AGCCAAACCTGGAGAATCAG 57.496 50.000 0.00 0.00 46.92 2.90
2513 2936 2.978156 AAGCCAAACCTGGAGAATCA 57.022 45.000 0.00 0.00 46.92 2.57
2514 2937 4.560128 GAAAAAGCCAAACCTGGAGAATC 58.440 43.478 0.00 0.00 46.92 2.52
2515 2938 3.005791 CGAAAAAGCCAAACCTGGAGAAT 59.994 43.478 0.00 0.00 46.92 2.40
2516 2939 2.360801 CGAAAAAGCCAAACCTGGAGAA 59.639 45.455 0.00 0.00 46.92 2.87
2517 2940 1.953686 CGAAAAAGCCAAACCTGGAGA 59.046 47.619 0.00 0.00 46.92 3.71
2518 2941 1.681264 ACGAAAAAGCCAAACCTGGAG 59.319 47.619 0.00 0.00 46.92 3.86
2519 2942 1.770294 ACGAAAAAGCCAAACCTGGA 58.230 45.000 0.00 0.00 46.92 3.86
2520 2943 2.595124 AACGAAAAAGCCAAACCTGG 57.405 45.000 0.00 0.00 46.65 4.45


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

AutoCloner maintained by Alex Coulton.