Multiple sequence alignment - TraesCS7D01G437200

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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 TraesCS7D01G437200 chr7D 100.000 2543 0 0 1 2543 556447533 556450075 0.000000e+00 4697.0
1 TraesCS7D01G437200 chr7D 83.938 193 23 4 521 711 412475089 412475275 7.230000e-41 178.0
2 TraesCS7D01G437200 chr7D 100.000 31 0 0 1743 1773 560910801 560910771 9.830000e-05 58.4
3 TraesCS7D01G437200 chr7B 92.017 1190 60 12 2 1176 603991556 603992725 0.000000e+00 1639.0
4 TraesCS7D01G437200 chr7B 89.462 873 64 9 34 897 603623850 603624703 0.000000e+00 1077.0
5 TraesCS7D01G437200 chr7B 93.935 709 24 6 894 1601 603663491 603664181 0.000000e+00 1053.0
6 TraesCS7D01G437200 chr7B 94.412 519 23 3 1108 1623 603992702 603993217 0.000000e+00 793.0
7 TraesCS7D01G437200 chr7B 78.076 634 93 24 884 1483 603835261 603835882 2.410000e-95 359.0
8 TraesCS7D01G437200 chr7B 82.933 416 49 9 830 1233 603944114 603944519 3.110000e-94 355.0
9 TraesCS7D01G437200 chr7B 79.104 536 64 27 1736 2249 603993248 603993757 2.440000e-85 326.0
10 TraesCS7D01G437200 chr7A 87.482 1374 100 28 686 2025 642159503 642160838 0.000000e+00 1519.0
11 TraesCS7D01G437200 chr7A 93.119 218 15 0 2014 2231 642165692 642165909 1.140000e-83 320.0
12 TraesCS7D01G437200 chr7A 90.476 63 6 0 1684 1746 24956747 24956809 1.620000e-12 84.2
13 TraesCS7D01G437200 chr6D 98.299 294 5 0 2249 2542 410911020 410910727 1.350000e-142 516.0
14 TraesCS7D01G437200 chr6D 97.966 295 6 0 2248 2542 277579525 277579231 1.740000e-141 512.0
15 TraesCS7D01G437200 chr6D 97.973 296 5 1 2248 2543 380557762 380557468 1.740000e-141 512.0
16 TraesCS7D01G437200 chr3D 97.980 297 6 0 2247 2543 558572926 558573222 1.350000e-142 516.0
17 TraesCS7D01G437200 chr3D 97.973 296 6 0 2248 2543 531076035 531075740 4.850000e-142 514.0
18 TraesCS7D01G437200 chr3D 97.973 296 6 0 2248 2543 570314737 570314442 4.850000e-142 514.0
19 TraesCS7D01G437200 chr3D 80.430 465 70 10 1 451 288543798 288544255 4.050000e-88 335.0
20 TraesCS7D01G437200 chr3D 100.000 31 0 0 1740 1770 5616231 5616201 9.830000e-05 58.4
21 TraesCS7D01G437200 chr4D 97.966 295 6 0 2248 2542 371784895 371784601 1.740000e-141 512.0
22 TraesCS7D01G437200 chr1D 97.966 295 6 0 2248 2542 386936133 386935839 1.740000e-141 512.0
23 TraesCS7D01G437200 chr1D 96.875 32 0 1 1743 1774 484410843 484410873 5.000000e-03 52.8
24 TraesCS7D01G437200 chr3B 93.884 327 16 3 2219 2542 307011308 307011633 8.180000e-135 490.0
25 TraesCS7D01G437200 chr3B 80.622 547 74 14 1 524 825577748 825577211 6.590000e-106 394.0
26 TraesCS7D01G437200 chr3B 80.183 545 80 16 1 524 24918311 24918848 1.430000e-102 383.0
27 TraesCS7D01G437200 chr3B 79.450 545 82 12 1 522 381461516 381462053 2.410000e-95 359.0
28 TraesCS7D01G437200 chr3B 84.896 192 22 3 521 711 519864503 519864688 1.200000e-43 187.0
29 TraesCS7D01G437200 chr3B 97.500 40 0 1 1697 1736 125790441 125790403 1.630000e-07 67.6
30 TraesCS7D01G437200 chr3B 88.889 54 4 2 1683 1735 71406290 71406238 5.870000e-07 65.8
31 TraesCS7D01G437200 chr1B 80.586 546 77 12 1 523 12732157 12731618 6.590000e-106 394.0
32 TraesCS7D01G437200 chr2B 77.713 691 103 29 40 711 154498122 154498780 2.390000e-100 375.0
33 TraesCS7D01G437200 chr2B 78.650 548 87 12 1 524 765261260 765260719 1.130000e-88 337.0
34 TraesCS7D01G437200 chr2B 76.338 355 56 13 190 524 601391493 601391839 5.630000e-37 165.0
35 TraesCS7D01G437200 chr2B 82.474 194 24 6 521 711 154597049 154596863 7.280000e-36 161.0
36 TraesCS7D01G437200 chr2B 76.471 272 51 7 190 451 740751185 740750917 4.410000e-28 135.0
37 TraesCS7D01G437200 chr2B 95.652 46 1 1 1695 1739 373758798 373758753 3.510000e-09 73.1
38 TraesCS7D01G437200 chr2B 97.500 40 0 1 1697 1736 103476471 103476509 1.630000e-07 67.6
39 TraesCS7D01G437200 chr2B 88.462 52 6 0 400 451 64184174 64184123 2.110000e-06 63.9
40 TraesCS7D01G437200 chr6B 79.008 524 73 19 1 501 56969460 56969969 8.780000e-85 324.0
41 TraesCS7D01G437200 chr2A 77.798 554 89 18 1 524 459548715 459549264 6.830000e-81 311.0
42 TraesCS7D01G437200 chr2A 82.990 194 23 6 521 711 515503593 515503779 1.560000e-37 167.0
43 TraesCS7D01G437200 chr2A 91.489 47 4 0 1684 1730 735010394 735010440 5.870000e-07 65.8
44 TraesCS7D01G437200 chr2D 78.090 356 51 16 190 524 110022461 110022112 1.540000e-47 200.0
45 TraesCS7D01G437200 chr2D 91.837 49 2 1 1737 1783 427150436 427150388 1.630000e-07 67.6
46 TraesCS7D01G437200 chr4A 80.153 262 39 8 199 451 722279175 722278918 1.550000e-42 183.0
47 TraesCS7D01G437200 chr4A 93.182 44 2 1 1691 1734 6279548 6279506 2.110000e-06 63.9
48 TraesCS7D01G437200 chr6A 82.039 206 24 9 521 722 158307194 158307390 2.020000e-36 163.0
49 TraesCS7D01G437200 chr3A 82.383 193 26 5 521 711 9623503 9623689 7.280000e-36 161.0
50 TraesCS7D01G437200 chr3A 88.462 52 6 0 1684 1735 724384238 724384289 2.110000e-06 63.9
51 TraesCS7D01G437200 chr3A 87.273 55 4 2 1740 1792 578876343 578876290 2.730000e-05 60.2
52 TraesCS7D01G437200 chr5D 79.293 198 23 7 316 503 457333930 457333741 3.440000e-24 122.0
53 TraesCS7D01G437200 chr5D 94.595 37 2 0 1739 1775 560262634 560262670 9.830000e-05 58.4
54 TraesCS7D01G437200 chr5A 76.498 217 37 12 320 524 683271370 683271156 3.460000e-19 106.0
55 TraesCS7D01G437200 chr5A 100.000 29 0 0 1743 1771 190875807 190875835 1.000000e-03 54.7


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 TraesCS7D01G437200 chr7D 556447533 556450075 2542 False 4697.000000 4697 100.000 1 2543 1 chr7D.!!$F2 2542
1 TraesCS7D01G437200 chr7B 603623850 603624703 853 False 1077.000000 1077 89.462 34 897 1 chr7B.!!$F1 863
2 TraesCS7D01G437200 chr7B 603663491 603664181 690 False 1053.000000 1053 93.935 894 1601 1 chr7B.!!$F2 707
3 TraesCS7D01G437200 chr7B 603991556 603993757 2201 False 919.333333 1639 88.511 2 2249 3 chr7B.!!$F5 2247
4 TraesCS7D01G437200 chr7B 603835261 603835882 621 False 359.000000 359 78.076 884 1483 1 chr7B.!!$F3 599
5 TraesCS7D01G437200 chr7A 642159503 642160838 1335 False 1519.000000 1519 87.482 686 2025 1 chr7A.!!$F2 1339
6 TraesCS7D01G437200 chr3B 825577211 825577748 537 True 394.000000 394 80.622 1 524 1 chr3B.!!$R3 523
7 TraesCS7D01G437200 chr3B 24918311 24918848 537 False 383.000000 383 80.183 1 524 1 chr3B.!!$F1 523
8 TraesCS7D01G437200 chr3B 381461516 381462053 537 False 359.000000 359 79.450 1 522 1 chr3B.!!$F3 521
9 TraesCS7D01G437200 chr1B 12731618 12732157 539 True 394.000000 394 80.586 1 523 1 chr1B.!!$R1 522
10 TraesCS7D01G437200 chr2B 154498122 154498780 658 False 375.000000 375 77.713 40 711 1 chr2B.!!$F2 671
11 TraesCS7D01G437200 chr2B 765260719 765261260 541 True 337.000000 337 78.650 1 524 1 chr2B.!!$R5 523
12 TraesCS7D01G437200 chr6B 56969460 56969969 509 False 324.000000 324 79.008 1 501 1 chr6B.!!$F1 500
13 TraesCS7D01G437200 chr2A 459548715 459549264 549 False 311.000000 311 77.798 1 524 1 chr2A.!!$F1 523

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
446 477 0.32336 GTGCAGGGGTGCCAAATCTA 60.323 55.0 0.0 0.0 0.0 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2263 0.033504 GCCACTCCAACTCAACGAGA 59.966 55.0 0.0 0.0 33.32 4.04 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
157 161 4.853743 GCACCGAATGAAAATTCTTCAGAC 59.146 41.667 8.38 5.23 0.00 3.51
324 349 1.271597 GCTTGGAAGGTGAGTGGATGT 60.272 52.381 0.00 0.00 0.00 3.06
335 360 4.565652 GGTGAGTGGATGTAGATTGTGGTT 60.566 45.833 0.00 0.00 0.00 3.67
350 375 2.477176 GGTTTGCATCGGCGGCATA 61.477 57.895 11.46 4.56 45.35 3.14
356 381 1.514678 GCATCGGCGGCATATGGAAA 61.515 55.000 18.95 0.00 0.00 3.13
446 477 0.323360 GTGCAGGGGTGCCAAATCTA 60.323 55.000 0.00 0.00 0.00 1.98
492 533 2.147150 TGATTCGTTCAACGGCAATGA 58.853 42.857 10.69 0.00 42.81 2.57
554 596 6.409524 TTTGATGTCAAGCTCAAAGGATTT 57.590 33.333 0.00 0.00 36.67 2.17
593 635 9.191995 GTTTGTATTTTTACTTCTTGGATGGTG 57.808 33.333 0.00 0.00 0.00 4.17
596 638 8.919145 TGTATTTTTACTTCTTGGATGGTGTTT 58.081 29.630 0.00 0.00 0.00 2.83
617 659 2.074547 TGTGTGTAAAGGCTAGCGTC 57.925 50.000 10.89 0.00 0.00 5.19
659 701 7.760794 CAGTTTTACAAGGTCGGTATGTACATA 59.239 37.037 11.62 11.62 29.78 2.29
712 755 7.921786 TGAGACAGTATTACCATGAAAAAGG 57.078 36.000 0.00 0.00 0.00 3.11
713 756 7.685481 TGAGACAGTATTACCATGAAAAAGGA 58.315 34.615 0.00 0.00 0.00 3.36
714 757 8.160765 TGAGACAGTATTACCATGAAAAAGGAA 58.839 33.333 0.00 0.00 0.00 3.36
731 774 9.673454 GAAAAAGGAAAAATACATAACACGAGT 57.327 29.630 0.00 0.00 0.00 4.18
872 915 5.619625 TCTACGCATATCTCAGTGATGAG 57.380 43.478 0.00 0.00 36.65 2.90
1601 1761 4.634883 ACTATCCGGCTATACATGTACTCG 59.365 45.833 7.96 9.41 0.00 4.18
1603 1763 2.810274 TCCGGCTATACATGTACTCGAC 59.190 50.000 7.96 0.68 0.00 4.20
1611 1771 1.068055 ACATGTACTCGACGGTCAACC 60.068 52.381 9.10 0.00 0.00 3.77
1625 1785 1.003866 GTCAACCGTGTCTGCTTGTTC 60.004 52.381 0.00 0.00 0.00 3.18
1631 1791 2.058798 CGTGTCTGCTTGTTCACGTAT 58.941 47.619 8.11 0.00 45.26 3.06
1639 1799 3.370672 TGCTTGTTCACGTATGTATGCAG 59.629 43.478 0.00 0.00 0.00 4.41
1641 1801 2.276201 TGTTCACGTATGTATGCAGGC 58.724 47.619 0.00 0.00 0.00 4.85
1648 1808 3.260632 ACGTATGTATGCAGGCATCCATA 59.739 43.478 13.46 13.46 35.23 2.74
1649 1809 4.080919 ACGTATGTATGCAGGCATCCATAT 60.081 41.667 18.45 7.03 37.49 1.78
1651 1811 3.793819 TGTATGCAGGCATCCATATGT 57.206 42.857 10.48 0.00 37.82 2.29
1652 1812 4.906747 TGTATGCAGGCATCCATATGTA 57.093 40.909 10.48 0.00 37.82 2.29
1653 1813 4.578871 TGTATGCAGGCATCCATATGTAC 58.421 43.478 10.48 1.54 37.82 2.90
1654 1814 4.286808 TGTATGCAGGCATCCATATGTACT 59.713 41.667 10.48 0.00 37.82 2.73
1655 1815 3.407424 TGCAGGCATCCATATGTACTC 57.593 47.619 1.24 0.00 35.38 2.59
1658 1818 3.244700 GCAGGCATCCATATGTACTCCTT 60.245 47.826 1.24 0.00 35.38 3.36
1660 1820 3.584848 AGGCATCCATATGTACTCCTTCC 59.415 47.826 1.24 0.00 35.38 3.46
1661 1821 3.589988 GCATCCATATGTACTCCTTCCG 58.410 50.000 1.24 0.00 35.38 4.30
1664 1824 4.931661 TCCATATGTACTCCTTCCGTTC 57.068 45.455 1.24 0.00 0.00 3.95
1665 1825 4.543689 TCCATATGTACTCCTTCCGTTCT 58.456 43.478 1.24 0.00 0.00 3.01
1666 1826 4.960469 TCCATATGTACTCCTTCCGTTCTT 59.040 41.667 1.24 0.00 0.00 2.52
1667 1827 5.424252 TCCATATGTACTCCTTCCGTTCTTT 59.576 40.000 1.24 0.00 0.00 2.52
1668 1828 6.070424 TCCATATGTACTCCTTCCGTTCTTTT 60.070 38.462 1.24 0.00 0.00 2.27
1669 1829 6.598064 CCATATGTACTCCTTCCGTTCTTTTT 59.402 38.462 1.24 0.00 0.00 1.94
1693 1853 2.930826 TTGAAAGAGCCTTCCGTTCT 57.069 45.000 0.00 0.00 0.00 3.01
1705 1865 6.514063 AGCCTTCCGTTCTATATTACTTGTC 58.486 40.000 0.00 0.00 0.00 3.18
1920 2080 6.191657 ACTTATGATGAATCTGGCCATACA 57.808 37.500 5.51 4.73 0.00 2.29
1941 2101 0.725117 GCGAATCGGACAAACGGAAT 59.275 50.000 4.35 0.00 0.00 3.01
1947 2107 1.066716 TCGGACAAACGGAATCGGAAT 60.067 47.619 0.00 0.00 41.39 3.01
1971 2131 1.751927 GGCCTCCCATGTTGCTCTG 60.752 63.158 0.00 0.00 0.00 3.35
1975 2135 2.360350 CCCATGTTGCTCTGCCGT 60.360 61.111 0.00 0.00 0.00 5.68
2037 2197 3.878667 CCTCCATCCCCTTCCCGC 61.879 72.222 0.00 0.00 0.00 6.13
2038 2198 2.770048 CTCCATCCCCTTCCCGCT 60.770 66.667 0.00 0.00 0.00 5.52
2039 2199 3.089874 TCCATCCCCTTCCCGCTG 61.090 66.667 0.00 0.00 0.00 5.18
2040 2200 4.883354 CCATCCCCTTCCCGCTGC 62.883 72.222 0.00 0.00 0.00 5.25
2041 2201 4.883354 CATCCCCTTCCCGCTGCC 62.883 72.222 0.00 0.00 0.00 4.85
2077 2237 1.004200 AAAGCCCACCCGACGTTAG 60.004 57.895 0.00 0.00 0.00 2.34
2078 2238 3.600898 AAGCCCACCCGACGTTAGC 62.601 63.158 0.00 0.00 0.00 3.09
2085 2245 4.728102 CCGACGTTAGCGGTGGCA 62.728 66.667 3.45 0.00 43.66 4.92
2086 2246 3.475774 CGACGTTAGCGGTGGCAC 61.476 66.667 9.70 9.70 43.41 5.01
2090 2252 3.116531 GTTAGCGGTGGCACGGAC 61.117 66.667 26.86 17.66 43.41 4.79
2098 2260 2.847234 TGGCACGGACCAGTTCCT 60.847 61.111 6.68 0.00 43.25 3.36
2101 2263 2.584391 GCACGGACCAGTTCCTCCT 61.584 63.158 0.00 0.00 43.25 3.69
2102 2264 1.592223 CACGGACCAGTTCCTCCTC 59.408 63.158 0.00 0.00 43.25 3.71
2104 2266 0.612453 ACGGACCAGTTCCTCCTCTC 60.612 60.000 0.00 0.00 43.25 3.20
2106 2268 0.612453 GGACCAGTTCCTCCTCTCGT 60.612 60.000 0.00 0.00 41.95 4.18
2109 2271 1.257743 CCAGTTCCTCCTCTCGTTGA 58.742 55.000 0.00 0.00 0.00 3.18
2117 2279 1.889829 CTCCTCTCGTTGAGTTGGAGT 59.110 52.381 20.01 0.00 41.44 3.85
2118 2280 1.613925 TCCTCTCGTTGAGTTGGAGTG 59.386 52.381 7.25 0.00 41.11 3.51
2121 2283 0.249868 CTCGTTGAGTTGGAGTGGCA 60.250 55.000 0.00 0.00 0.00 4.92
2122 2284 0.396435 TCGTTGAGTTGGAGTGGCAT 59.604 50.000 0.00 0.00 0.00 4.40
2127 2307 3.070576 GTTGGAGTGGCATGGGGC 61.071 66.667 0.00 0.00 43.74 5.80
2154 2334 3.740397 GCAGCCAAGATGCACGCA 61.740 61.111 0.00 0.00 44.90 5.24
2157 2337 3.058160 GCCAAGATGCACGCACCT 61.058 61.111 0.00 0.00 0.00 4.00
2225 2405 3.482722 CTGCATTAGCTTGGTCTGTTG 57.517 47.619 0.00 0.00 42.74 3.33
2226 2406 2.161855 TGCATTAGCTTGGTCTGTTGG 58.838 47.619 0.00 0.00 42.74 3.77
2233 2413 2.771328 CTTGGTCTGTTGGGGCCCTC 62.771 65.000 25.93 17.17 0.00 4.30
2235 2415 4.410400 GTCTGTTGGGGCCCTCCG 62.410 72.222 25.93 13.18 36.01 4.63
2236 2416 4.974438 TCTGTTGGGGCCCTCCGT 62.974 66.667 25.93 0.00 36.01 4.69
2249 2429 3.144120 CTCCGTCCCGATCTGGCTG 62.144 68.421 0.00 0.00 35.87 4.85
2250 2430 3.147595 CCGTCCCGATCTGGCTGA 61.148 66.667 0.00 0.00 35.87 4.26
2251 2431 2.721167 CCGTCCCGATCTGGCTGAA 61.721 63.158 0.00 0.00 35.87 3.02
2252 2432 1.227089 CGTCCCGATCTGGCTGAAG 60.227 63.158 0.00 0.00 35.87 3.02
2253 2433 1.144936 GTCCCGATCTGGCTGAAGG 59.855 63.158 10.78 10.78 35.87 3.46
2254 2434 1.001631 TCCCGATCTGGCTGAAGGA 59.998 57.895 16.81 12.00 35.87 3.36
2255 2435 0.617535 TCCCGATCTGGCTGAAGGAA 60.618 55.000 16.81 0.00 35.87 3.36
2256 2436 0.253044 CCCGATCTGGCTGAAGGAAA 59.747 55.000 16.81 0.00 35.87 3.13
2257 2437 1.133976 CCCGATCTGGCTGAAGGAAAT 60.134 52.381 16.81 0.00 35.87 2.17
2258 2438 2.648059 CCGATCTGGCTGAAGGAAATT 58.352 47.619 11.90 0.00 0.00 1.82
2259 2439 3.019564 CCGATCTGGCTGAAGGAAATTT 58.980 45.455 11.90 0.00 0.00 1.82
2260 2440 3.181493 CCGATCTGGCTGAAGGAAATTTG 60.181 47.826 11.90 0.00 0.00 2.32
2261 2441 3.733077 CGATCTGGCTGAAGGAAATTTGC 60.733 47.826 0.68 0.68 0.00 3.68
2262 2442 1.895131 TCTGGCTGAAGGAAATTTGCC 59.105 47.619 6.02 7.02 39.68 4.52
2263 2443 0.975887 TGGCTGAAGGAAATTTGCCC 59.024 50.000 6.02 0.71 38.97 5.36
2264 2444 1.269958 GGCTGAAGGAAATTTGCCCT 58.730 50.000 6.02 0.00 35.82 5.19
2265 2445 2.225242 TGGCTGAAGGAAATTTGCCCTA 60.225 45.455 6.02 0.00 38.97 3.53
2266 2446 2.428530 GGCTGAAGGAAATTTGCCCTAG 59.571 50.000 6.02 3.56 35.82 3.02
2267 2447 3.356290 GCTGAAGGAAATTTGCCCTAGA 58.644 45.455 6.02 0.00 31.36 2.43
2268 2448 3.379688 GCTGAAGGAAATTTGCCCTAGAG 59.620 47.826 6.02 3.57 31.36 2.43
2269 2449 3.950395 CTGAAGGAAATTTGCCCTAGAGG 59.050 47.826 6.02 0.00 39.47 3.69
2344 2524 8.902540 ATTCATGCTAGAATTGTATTAACCGA 57.097 30.769 0.00 0.00 34.70 4.69
2345 2525 8.725405 TTCATGCTAGAATTGTATTAACCGAA 57.275 30.769 0.00 0.00 0.00 4.30
2346 2526 8.725405 TCATGCTAGAATTGTATTAACCGAAA 57.275 30.769 0.00 0.00 0.00 3.46
2347 2527 9.168451 TCATGCTAGAATTGTATTAACCGAAAA 57.832 29.630 0.00 0.00 0.00 2.29
2348 2528 9.221775 CATGCTAGAATTGTATTAACCGAAAAC 57.778 33.333 0.00 0.00 0.00 2.43
2349 2529 8.325421 TGCTAGAATTGTATTAACCGAAAACA 57.675 30.769 0.00 0.00 0.00 2.83
2350 2530 8.952278 TGCTAGAATTGTATTAACCGAAAACAT 58.048 29.630 0.00 0.00 0.00 2.71
2362 2542 9.781834 ATTAACCGAAAACATAATACATGTGTG 57.218 29.630 9.11 4.81 31.80 3.82
2363 2543 7.441890 AACCGAAAACATAATACATGTGTGA 57.558 32.000 9.11 0.00 31.80 3.58
2364 2544 7.441890 ACCGAAAACATAATACATGTGTGAA 57.558 32.000 9.11 0.00 31.80 3.18
2365 2545 8.050778 ACCGAAAACATAATACATGTGTGAAT 57.949 30.769 9.11 0.00 31.80 2.57
2366 2546 9.168451 ACCGAAAACATAATACATGTGTGAATA 57.832 29.630 9.11 0.00 31.80 1.75
2367 2547 9.433317 CCGAAAACATAATACATGTGTGAATAC 57.567 33.333 9.11 0.00 31.80 1.89
2368 2548 9.980780 CGAAAACATAATACATGTGTGAATACA 57.019 29.630 9.11 0.00 34.63 2.29
2378 2558 7.977789 ACATGTGTGAATACATAGACAAACA 57.022 32.000 0.00 0.00 39.17 2.83
2379 2559 8.565896 ACATGTGTGAATACATAGACAAACAT 57.434 30.769 0.00 0.00 40.42 2.71
2380 2560 9.665719 ACATGTGTGAATACATAGACAAACATA 57.334 29.630 0.00 0.00 38.58 2.29
2382 2562 9.890629 ATGTGTGAATACATAGACAAACATAGT 57.109 29.630 0.00 0.00 38.77 2.12
2383 2563 9.150348 TGTGTGAATACATAGACAAACATAGTG 57.850 33.333 0.00 0.00 39.39 2.74
2384 2564 9.151471 GTGTGAATACATAGACAAACATAGTGT 57.849 33.333 0.00 0.00 39.39 3.55
2385 2565 9.366216 TGTGAATACATAGACAAACATAGTGTC 57.634 33.333 0.00 0.00 44.75 3.67
2386 2566 9.366216 GTGAATACATAGACAAACATAGTGTCA 57.634 33.333 7.26 0.00 46.44 3.58
2387 2567 9.366216 TGAATACATAGACAAACATAGTGTCAC 57.634 33.333 7.26 0.00 46.44 3.67
2388 2568 9.587772 GAATACATAGACAAACATAGTGTCACT 57.412 33.333 10.99 10.99 46.44 3.41
2391 2571 8.123639 ACATAGACAAACATAGTGTCACTAGT 57.876 34.615 17.43 12.40 46.44 2.57
2392 2572 9.239551 ACATAGACAAACATAGTGTCACTAGTA 57.760 33.333 17.43 0.00 46.44 1.82
2395 2575 7.036220 AGACAAACATAGTGTCACTAGTATGC 58.964 38.462 17.43 9.88 46.44 3.14
2396 2576 6.106673 ACAAACATAGTGTCACTAGTATGCC 58.893 40.000 17.43 0.00 37.44 4.40
2397 2577 6.070767 ACAAACATAGTGTCACTAGTATGCCT 60.071 38.462 17.43 2.21 37.44 4.75
2398 2578 5.776173 ACATAGTGTCACTAGTATGCCTC 57.224 43.478 17.43 0.00 37.44 4.70
2399 2579 5.450453 ACATAGTGTCACTAGTATGCCTCT 58.550 41.667 17.43 0.00 37.44 3.69
2400 2580 6.602278 ACATAGTGTCACTAGTATGCCTCTA 58.398 40.000 17.43 0.00 37.44 2.43
2401 2581 6.487331 ACATAGTGTCACTAGTATGCCTCTAC 59.513 42.308 17.43 0.00 37.44 2.59
2402 2582 5.118729 AGTGTCACTAGTATGCCTCTACT 57.881 43.478 2.87 0.00 36.04 2.57
2403 2583 5.511363 AGTGTCACTAGTATGCCTCTACTT 58.489 41.667 2.87 0.00 33.96 2.24
2404 2584 5.358442 AGTGTCACTAGTATGCCTCTACTTG 59.642 44.000 2.87 0.00 33.96 3.16
2405 2585 5.357314 GTGTCACTAGTATGCCTCTACTTGA 59.643 44.000 0.00 0.18 33.96 3.02
2406 2586 5.357314 TGTCACTAGTATGCCTCTACTTGAC 59.643 44.000 0.00 11.98 38.64 3.18
2407 2587 5.591067 GTCACTAGTATGCCTCTACTTGACT 59.409 44.000 0.00 0.00 36.95 3.41
2408 2588 6.766944 GTCACTAGTATGCCTCTACTTGACTA 59.233 42.308 0.00 0.00 36.95 2.59
2409 2589 6.993308 TCACTAGTATGCCTCTACTTGACTAG 59.007 42.308 0.00 0.00 40.35 2.57
2410 2590 5.766174 ACTAGTATGCCTCTACTTGACTAGC 59.234 44.000 0.00 0.00 38.86 3.42
2411 2591 4.798882 AGTATGCCTCTACTTGACTAGCT 58.201 43.478 0.00 0.00 0.00 3.32
2412 2592 4.825085 AGTATGCCTCTACTTGACTAGCTC 59.175 45.833 0.00 0.00 0.00 4.09
2413 2593 2.017782 TGCCTCTACTTGACTAGCTCG 58.982 52.381 0.00 0.00 0.00 5.03
2414 2594 2.018515 GCCTCTACTTGACTAGCTCGT 58.981 52.381 0.00 0.00 0.00 4.18
2415 2595 2.424246 GCCTCTACTTGACTAGCTCGTT 59.576 50.000 0.00 0.00 0.00 3.85
2416 2596 3.626670 GCCTCTACTTGACTAGCTCGTTA 59.373 47.826 0.00 0.00 0.00 3.18
2417 2597 4.096081 GCCTCTACTTGACTAGCTCGTTAA 59.904 45.833 0.00 0.00 0.00 2.01
2418 2598 5.221087 GCCTCTACTTGACTAGCTCGTTAAT 60.221 44.000 0.00 0.00 0.00 1.40
2419 2599 6.432107 CCTCTACTTGACTAGCTCGTTAATC 58.568 44.000 0.00 0.00 0.00 1.75
2420 2600 6.038382 CCTCTACTTGACTAGCTCGTTAATCA 59.962 42.308 0.00 0.00 0.00 2.57
2421 2601 7.387119 TCTACTTGACTAGCTCGTTAATCAA 57.613 36.000 0.00 0.00 0.00 2.57
2422 2602 7.823665 TCTACTTGACTAGCTCGTTAATCAAA 58.176 34.615 0.00 0.00 0.00 2.69
2423 2603 6.952935 ACTTGACTAGCTCGTTAATCAAAG 57.047 37.500 0.00 0.00 0.00 2.77
2424 2604 6.688578 ACTTGACTAGCTCGTTAATCAAAGA 58.311 36.000 0.00 0.00 0.00 2.52
2425 2605 7.324178 ACTTGACTAGCTCGTTAATCAAAGAT 58.676 34.615 0.00 0.00 0.00 2.40
2426 2606 7.276658 ACTTGACTAGCTCGTTAATCAAAGATG 59.723 37.037 0.00 0.00 0.00 2.90
2427 2607 6.042777 TGACTAGCTCGTTAATCAAAGATGG 58.957 40.000 0.00 0.00 0.00 3.51
2428 2608 5.978814 ACTAGCTCGTTAATCAAAGATGGT 58.021 37.500 0.00 0.00 0.00 3.55
2429 2609 6.407202 ACTAGCTCGTTAATCAAAGATGGTT 58.593 36.000 0.00 0.00 33.49 3.67
2430 2610 7.553334 ACTAGCTCGTTAATCAAAGATGGTTA 58.447 34.615 0.00 0.00 30.84 2.85
2431 2611 8.038944 ACTAGCTCGTTAATCAAAGATGGTTAA 58.961 33.333 0.00 0.00 39.28 2.01
2432 2612 7.308782 AGCTCGTTAATCAAAGATGGTTAAG 57.691 36.000 0.00 0.00 41.55 1.85
2433 2613 6.879458 AGCTCGTTAATCAAAGATGGTTAAGT 59.121 34.615 0.00 0.00 41.55 2.24
2434 2614 7.390718 AGCTCGTTAATCAAAGATGGTTAAGTT 59.609 33.333 0.00 0.00 41.55 2.66
2435 2615 8.021396 GCTCGTTAATCAAAGATGGTTAAGTTT 58.979 33.333 0.00 0.00 41.55 2.66
2436 2616 9.543018 CTCGTTAATCAAAGATGGTTAAGTTTC 57.457 33.333 0.00 0.00 41.55 2.78
2437 2617 8.508875 TCGTTAATCAAAGATGGTTAAGTTTCC 58.491 33.333 0.00 0.00 41.55 3.13
2438 2618 8.512138 CGTTAATCAAAGATGGTTAAGTTTCCT 58.488 33.333 0.00 0.00 41.55 3.36
2441 2621 7.631717 ATCAAAGATGGTTAAGTTTCCTAGC 57.368 36.000 0.00 0.00 0.00 3.42
2442 2622 5.944007 TCAAAGATGGTTAAGTTTCCTAGCC 59.056 40.000 0.00 0.00 0.00 3.93
2443 2623 5.514500 AAGATGGTTAAGTTTCCTAGCCA 57.486 39.130 0.00 0.00 0.00 4.75
2444 2624 5.717119 AGATGGTTAAGTTTCCTAGCCAT 57.283 39.130 0.00 0.00 37.88 4.40
2445 2625 5.440610 AGATGGTTAAGTTTCCTAGCCATG 58.559 41.667 3.32 0.00 35.64 3.66
2446 2626 3.963129 TGGTTAAGTTTCCTAGCCATGG 58.037 45.455 7.63 7.63 0.00 3.66
2447 2627 3.589735 TGGTTAAGTTTCCTAGCCATGGA 59.410 43.478 18.40 0.00 0.00 3.41
2448 2628 3.945921 GGTTAAGTTTCCTAGCCATGGAC 59.054 47.826 18.40 7.03 32.65 4.02
2449 2629 4.566907 GGTTAAGTTTCCTAGCCATGGACA 60.567 45.833 18.40 0.00 32.65 4.02
2450 2630 5.193679 GTTAAGTTTCCTAGCCATGGACAT 58.806 41.667 18.40 2.45 32.65 3.06
2451 2631 3.287867 AGTTTCCTAGCCATGGACATG 57.712 47.619 18.40 5.33 38.51 3.21
2452 2632 2.846206 AGTTTCCTAGCCATGGACATGA 59.154 45.455 18.40 2.89 41.20 3.07
2453 2633 3.118112 AGTTTCCTAGCCATGGACATGAG 60.118 47.826 18.40 3.89 41.20 2.90
2454 2634 2.180946 TCCTAGCCATGGACATGAGT 57.819 50.000 18.40 3.22 41.20 3.41
2455 2635 2.481441 TCCTAGCCATGGACATGAGTT 58.519 47.619 18.40 4.97 41.20 3.01
2456 2636 2.171237 TCCTAGCCATGGACATGAGTTG 59.829 50.000 18.40 0.00 41.20 3.16
2457 2637 2.092753 CCTAGCCATGGACATGAGTTGT 60.093 50.000 18.40 0.00 41.20 3.32
2471 2651 6.611381 ACATGAGTTGTCATTTGATTAACGG 58.389 36.000 0.00 0.00 40.84 4.44
2472 2652 5.621197 TGAGTTGTCATTTGATTAACGGG 57.379 39.130 0.00 0.00 32.73 5.28
2473 2653 5.309638 TGAGTTGTCATTTGATTAACGGGA 58.690 37.500 0.00 0.00 32.73 5.14
2474 2654 5.943416 TGAGTTGTCATTTGATTAACGGGAT 59.057 36.000 0.00 0.00 32.73 3.85
2475 2655 6.093495 TGAGTTGTCATTTGATTAACGGGATC 59.907 38.462 0.00 0.00 32.73 3.36
2476 2656 5.943416 AGTTGTCATTTGATTAACGGGATCA 59.057 36.000 0.00 0.00 32.73 2.92
2477 2657 5.811399 TGTCATTTGATTAACGGGATCAC 57.189 39.130 0.00 0.00 33.51 3.06
2478 2658 5.249420 TGTCATTTGATTAACGGGATCACA 58.751 37.500 0.00 0.00 33.51 3.58
2479 2659 5.885352 TGTCATTTGATTAACGGGATCACAT 59.115 36.000 0.00 0.00 33.51 3.21
2480 2660 6.038161 TGTCATTTGATTAACGGGATCACATC 59.962 38.462 0.00 0.00 33.51 3.06
2481 2661 6.038161 GTCATTTGATTAACGGGATCACATCA 59.962 38.462 0.00 0.00 33.51 3.07
2482 2662 6.772233 TCATTTGATTAACGGGATCACATCAT 59.228 34.615 0.00 0.00 33.51 2.45
2483 2663 7.285172 TCATTTGATTAACGGGATCACATCATT 59.715 33.333 0.00 0.00 33.51 2.57
2484 2664 8.567104 CATTTGATTAACGGGATCACATCATTA 58.433 33.333 0.00 0.00 33.51 1.90
2485 2665 7.728847 TTGATTAACGGGATCACATCATTAG 57.271 36.000 0.00 0.00 33.51 1.73
2486 2666 7.061566 TGATTAACGGGATCACATCATTAGA 57.938 36.000 0.00 0.00 0.00 2.10
2487 2667 7.505258 TGATTAACGGGATCACATCATTAGAA 58.495 34.615 0.00 0.00 0.00 2.10
2488 2668 7.657354 TGATTAACGGGATCACATCATTAGAAG 59.343 37.037 0.00 0.00 0.00 2.85
2489 2669 5.614324 AACGGGATCACATCATTAGAAGA 57.386 39.130 0.00 0.00 0.00 2.87
2490 2670 5.614324 ACGGGATCACATCATTAGAAGAA 57.386 39.130 0.00 0.00 0.00 2.52
2491 2671 6.179906 ACGGGATCACATCATTAGAAGAAT 57.820 37.500 0.00 0.00 0.00 2.40
2492 2672 5.994054 ACGGGATCACATCATTAGAAGAATG 59.006 40.000 0.00 0.00 0.00 2.67
2493 2673 6.183361 ACGGGATCACATCATTAGAAGAATGA 60.183 38.462 0.00 2.66 40.50 2.57
2494 2674 6.877855 CGGGATCACATCATTAGAAGAATGAT 59.122 38.462 6.90 6.90 45.40 2.45
2509 2689 8.273780 AGAAGAATGATGTGATTTACTTGACC 57.726 34.615 0.00 0.00 0.00 4.02
2510 2690 7.337942 AGAAGAATGATGTGATTTACTTGACCC 59.662 37.037 0.00 0.00 0.00 4.46
2511 2691 6.484288 AGAATGATGTGATTTACTTGACCCA 58.516 36.000 0.00 0.00 0.00 4.51
2512 2692 7.121382 AGAATGATGTGATTTACTTGACCCAT 58.879 34.615 0.00 0.00 0.00 4.00
2513 2693 7.616935 AGAATGATGTGATTTACTTGACCCATT 59.383 33.333 0.00 0.00 0.00 3.16
2514 2694 6.757897 TGATGTGATTTACTTGACCCATTC 57.242 37.500 0.00 0.00 0.00 2.67
2515 2695 5.652014 TGATGTGATTTACTTGACCCATTCC 59.348 40.000 0.00 0.00 0.00 3.01
2516 2696 4.006989 TGTGATTTACTTGACCCATTCCG 58.993 43.478 0.00 0.00 0.00 4.30
2517 2697 4.007659 GTGATTTACTTGACCCATTCCGT 58.992 43.478 0.00 0.00 0.00 4.69
2518 2698 4.457949 GTGATTTACTTGACCCATTCCGTT 59.542 41.667 0.00 0.00 0.00 4.44
2519 2699 5.644636 GTGATTTACTTGACCCATTCCGTTA 59.355 40.000 0.00 0.00 0.00 3.18
2520 2700 5.878116 TGATTTACTTGACCCATTCCGTTAG 59.122 40.000 0.00 0.00 0.00 2.34
2521 2701 2.109425 ACTTGACCCATTCCGTTAGC 57.891 50.000 0.00 0.00 0.00 3.09
2522 2702 1.628846 ACTTGACCCATTCCGTTAGCT 59.371 47.619 0.00 0.00 0.00 3.32
2523 2703 2.039879 ACTTGACCCATTCCGTTAGCTT 59.960 45.455 0.00 0.00 0.00 3.74
2524 2704 3.262405 ACTTGACCCATTCCGTTAGCTTA 59.738 43.478 0.00 0.00 0.00 3.09
2525 2705 3.536956 TGACCCATTCCGTTAGCTTAG 57.463 47.619 0.00 0.00 0.00 2.18
2526 2706 2.210961 GACCCATTCCGTTAGCTTAGC 58.789 52.381 0.00 0.00 0.00 3.09
2527 2707 1.557832 ACCCATTCCGTTAGCTTAGCA 59.442 47.619 7.07 0.00 0.00 3.49
2528 2708 1.940613 CCCATTCCGTTAGCTTAGCAC 59.059 52.381 7.07 0.00 0.00 4.40
2529 2709 2.420129 CCCATTCCGTTAGCTTAGCACT 60.420 50.000 7.07 0.00 0.00 4.40
2530 2710 3.270877 CCATTCCGTTAGCTTAGCACTT 58.729 45.455 7.07 0.00 0.00 3.16
2531 2711 3.063997 CCATTCCGTTAGCTTAGCACTTG 59.936 47.826 7.07 0.00 0.00 3.16
2532 2712 3.671008 TTCCGTTAGCTTAGCACTTGA 57.329 42.857 7.07 0.00 0.00 3.02
2533 2713 3.887621 TCCGTTAGCTTAGCACTTGAT 57.112 42.857 7.07 0.00 0.00 2.57
2534 2714 3.782046 TCCGTTAGCTTAGCACTTGATC 58.218 45.455 7.07 0.00 0.00 2.92
2535 2715 2.535984 CCGTTAGCTTAGCACTTGATCG 59.464 50.000 7.07 1.46 0.00 3.69
2536 2716 3.179830 CGTTAGCTTAGCACTTGATCGT 58.820 45.455 7.07 0.00 0.00 3.73
2537 2717 3.612860 CGTTAGCTTAGCACTTGATCGTT 59.387 43.478 7.07 0.00 0.00 3.85
2538 2718 4.091509 CGTTAGCTTAGCACTTGATCGTTT 59.908 41.667 7.07 0.00 0.00 3.60
2539 2719 5.287752 CGTTAGCTTAGCACTTGATCGTTTA 59.712 40.000 7.07 0.00 0.00 2.01
2540 2720 6.506513 CGTTAGCTTAGCACTTGATCGTTTAG 60.507 42.308 7.07 0.00 0.00 1.85
2541 2721 4.822026 AGCTTAGCACTTGATCGTTTAGT 58.178 39.130 7.07 0.00 0.00 2.24
2542 2722 5.238583 AGCTTAGCACTTGATCGTTTAGTT 58.761 37.500 7.07 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.367648 TGACCCCCACACCACTGT 60.368 61.111 0.00 0.00 0.00 3.55
68 70 9.475620 AAAACCTAAGCTACTAATGCCTAAAAT 57.524 29.630 0.00 0.00 0.00 1.82
157 161 2.356818 GATCGCCTCGTCAGGAAGGG 62.357 65.000 0.00 0.00 43.65 3.95
181 192 1.304879 TTTCCAAATCCAGCCCCCG 60.305 57.895 0.00 0.00 0.00 5.73
239 257 3.566261 GACACATGTCCGCCACAG 58.434 61.111 0.00 0.00 38.85 3.66
310 328 4.323792 CCACAATCTACATCCACTCACCTT 60.324 45.833 0.00 0.00 0.00 3.50
324 349 1.742831 GCCGATGCAAACCACAATCTA 59.257 47.619 0.00 0.00 37.47 1.98
335 360 2.260154 CCATATGCCGCCGATGCAA 61.260 57.895 0.00 0.00 42.92 4.08
350 375 2.754552 CACACGATCCACCATTTTCCAT 59.245 45.455 0.00 0.00 0.00 3.41
356 381 0.677731 CCAGCACACGATCCACCATT 60.678 55.000 0.00 0.00 0.00 3.16
446 477 3.148084 CAACACCCCGGACACTCT 58.852 61.111 0.73 0.00 0.00 3.24
554 596 9.505995 GTAAAAATACAAACAAGAAGACCGAAA 57.494 29.630 0.00 0.00 0.00 3.46
588 630 4.161377 AGCCTTTACACACAAAAACACCAT 59.839 37.500 0.00 0.00 0.00 3.55
593 635 3.972502 CGCTAGCCTTTACACACAAAAAC 59.027 43.478 9.66 0.00 0.00 2.43
596 638 2.803956 GACGCTAGCCTTTACACACAAA 59.196 45.455 9.66 0.00 0.00 2.83
642 684 6.290294 ACAAACTATGTACATACCGACCTT 57.710 37.500 11.62 0.00 41.63 3.50
711 754 9.148104 ACTTAGACTCGTGTTATGTATTTTTCC 57.852 33.333 0.00 0.00 0.00 3.13
719 762 6.091437 GCTGTAACTTAGACTCGTGTTATGT 58.909 40.000 0.00 0.00 0.00 2.29
723 766 3.305881 GGGCTGTAACTTAGACTCGTGTT 60.306 47.826 0.00 0.00 0.00 3.32
731 774 6.808321 ATTCATAGTGGGCTGTAACTTAGA 57.192 37.500 0.00 0.00 0.00 2.10
741 784 1.424638 ACGGCTATTCATAGTGGGCT 58.575 50.000 0.00 0.00 32.96 5.19
872 915 0.461961 CACCCAGCTCTAGGTGCTAC 59.538 60.000 12.81 0.00 46.55 3.58
1012 1064 2.461695 CTTCAGAGTAAGAGGGCCTGA 58.538 52.381 12.95 0.00 32.67 3.86
1548 1708 2.890945 TCAGCACTCAACACTAGCTACA 59.109 45.455 0.00 0.00 33.59 2.74
1625 1785 1.800586 GGATGCCTGCATACATACGTG 59.199 52.381 9.47 0.00 37.24 4.49
1639 1799 3.617531 CGGAAGGAGTACATATGGATGCC 60.618 52.174 7.80 4.34 36.43 4.40
1641 1801 4.873746 ACGGAAGGAGTACATATGGATG 57.126 45.455 7.80 0.00 39.16 3.51
1671 1831 3.951680 AGAACGGAAGGCTCTTTCAAAAA 59.048 39.130 0.00 0.00 0.00 1.94
1672 1832 3.551846 AGAACGGAAGGCTCTTTCAAAA 58.448 40.909 0.00 0.00 0.00 2.44
1673 1833 3.208747 AGAACGGAAGGCTCTTTCAAA 57.791 42.857 0.00 0.00 0.00 2.69
1674 1834 2.930826 AGAACGGAAGGCTCTTTCAA 57.069 45.000 0.00 0.00 0.00 2.69
1675 1835 5.871396 ATATAGAACGGAAGGCTCTTTCA 57.129 39.130 0.00 0.00 0.00 2.69
1676 1836 7.435305 AGTAATATAGAACGGAAGGCTCTTTC 58.565 38.462 0.00 0.00 0.00 2.62
1677 1837 7.362802 AGTAATATAGAACGGAAGGCTCTTT 57.637 36.000 0.00 0.00 0.00 2.52
1678 1838 6.980416 AGTAATATAGAACGGAAGGCTCTT 57.020 37.500 0.00 0.00 0.00 2.85
1679 1839 6.324254 ACAAGTAATATAGAACGGAAGGCTCT 59.676 38.462 0.00 0.00 0.00 4.09
1680 1840 6.514063 ACAAGTAATATAGAACGGAAGGCTC 58.486 40.000 0.00 0.00 0.00 4.70
1681 1841 6.324254 AGACAAGTAATATAGAACGGAAGGCT 59.676 38.462 0.00 0.00 0.00 4.58
1682 1842 6.514063 AGACAAGTAATATAGAACGGAAGGC 58.486 40.000 0.00 0.00 0.00 4.35
1920 2080 0.390603 TCCGTTTGTCCGATTCGCAT 60.391 50.000 0.00 0.00 0.00 4.73
1941 2101 1.831286 GGAGGCCCTCGTATTCCGA 60.831 63.158 4.29 0.00 45.00 4.55
1947 2107 1.306654 AACATGGGAGGCCCTCGTA 60.307 57.895 4.29 0.00 45.70 3.43
1971 2131 1.167155 TCTCCTAGATCGCTCACGGC 61.167 60.000 0.00 0.00 40.63 5.68
1975 2135 2.952978 GGTTTCTCTCCTAGATCGCTCA 59.047 50.000 0.00 0.00 33.05 4.26
1984 2144 2.105766 GCGGGTAAGGTTTCTCTCCTA 58.894 52.381 0.00 0.00 34.56 2.94
2043 2203 1.926511 CTTTGCCCGGTGATGCTCAC 61.927 60.000 0.00 7.52 46.23 3.51
2044 2204 1.675310 CTTTGCCCGGTGATGCTCA 60.675 57.895 0.00 0.00 0.00 4.26
2045 2205 3.056313 GCTTTGCCCGGTGATGCTC 62.056 63.158 0.00 0.00 0.00 4.26
2073 2233 3.116531 GTCCGTGCCACCGCTAAC 61.117 66.667 0.00 0.00 35.36 2.34
2078 2238 4.619227 AACTGGTCCGTGCCACCG 62.619 66.667 0.00 0.00 36.61 4.94
2079 2239 2.668550 GAACTGGTCCGTGCCACC 60.669 66.667 0.00 0.00 34.36 4.61
2090 2252 1.203523 CTCAACGAGAGGAGGAACTGG 59.796 57.143 0.00 0.00 40.84 4.00
2101 2263 0.033504 GCCACTCCAACTCAACGAGA 59.966 55.000 0.00 0.00 33.32 4.04
2102 2264 0.249868 TGCCACTCCAACTCAACGAG 60.250 55.000 0.00 0.00 35.52 4.18
2104 2266 0.518636 CATGCCACTCCAACTCAACG 59.481 55.000 0.00 0.00 0.00 4.10
2106 2268 0.251297 CCCATGCCACTCCAACTCAA 60.251 55.000 0.00 0.00 0.00 3.02
2109 2271 2.765969 CCCCATGCCACTCCAACT 59.234 61.111 0.00 0.00 0.00 3.16
2132 2312 4.487412 GCATCTTGGCTGCCGTGC 62.487 66.667 14.98 16.72 33.44 5.34
2137 2317 3.740397 TGCGTGCATCTTGGCTGC 61.740 61.111 0.00 0.00 40.10 5.25
2154 2334 3.362399 CTCACGCCTCATCGCAGGT 62.362 63.158 0.00 0.00 35.72 4.00
2157 2337 3.706563 GAGCTCACGCCTCATCGCA 62.707 63.158 9.40 0.00 36.60 5.10
2211 2391 1.378762 GCCCCAACAGACCAAGCTA 59.621 57.895 0.00 0.00 0.00 3.32
2219 2399 4.974438 ACGGAGGGCCCCAACAGA 62.974 66.667 21.43 0.00 0.00 3.41
2235 2415 1.144936 CCTTCAGCCAGATCGGGAC 59.855 63.158 16.86 7.12 34.06 4.46
2236 2416 0.617535 TTCCTTCAGCCAGATCGGGA 60.618 55.000 16.86 0.00 34.06 5.14
2260 2440 8.637196 AATAACTTTATTATTGCCTCTAGGGC 57.363 34.615 13.60 13.60 44.71 5.19
2318 2498 9.990360 TCGGTTAATACAATTCTAGCATGAATA 57.010 29.630 0.00 0.00 35.82 1.75
2319 2499 8.902540 TCGGTTAATACAATTCTAGCATGAAT 57.097 30.769 0.00 0.00 38.19 2.57
2320 2500 8.725405 TTCGGTTAATACAATTCTAGCATGAA 57.275 30.769 0.00 0.00 0.00 2.57
2321 2501 8.725405 TTTCGGTTAATACAATTCTAGCATGA 57.275 30.769 0.00 0.00 0.00 3.07
2322 2502 9.221775 GTTTTCGGTTAATACAATTCTAGCATG 57.778 33.333 0.00 0.00 0.00 4.06
2323 2503 8.952278 TGTTTTCGGTTAATACAATTCTAGCAT 58.048 29.630 0.00 0.00 0.00 3.79
2324 2504 8.325421 TGTTTTCGGTTAATACAATTCTAGCA 57.675 30.769 0.00 0.00 0.00 3.49
2336 2516 9.781834 CACACATGTATTATGTTTTCGGTTAAT 57.218 29.630 0.00 0.00 0.00 1.40
2337 2517 9.000486 TCACACATGTATTATGTTTTCGGTTAA 58.000 29.630 0.00 0.00 0.00 2.01
2338 2518 8.549338 TCACACATGTATTATGTTTTCGGTTA 57.451 30.769 0.00 0.00 0.00 2.85
2339 2519 7.441890 TCACACATGTATTATGTTTTCGGTT 57.558 32.000 0.00 0.00 0.00 4.44
2340 2520 7.441890 TTCACACATGTATTATGTTTTCGGT 57.558 32.000 0.00 0.00 0.00 4.69
2341 2521 9.433317 GTATTCACACATGTATTATGTTTTCGG 57.567 33.333 0.00 0.00 0.00 4.30
2342 2522 9.980780 TGTATTCACACATGTATTATGTTTTCG 57.019 29.630 0.00 0.00 0.00 3.46
2352 2532 9.665719 TGTTTGTCTATGTATTCACACATGTAT 57.334 29.630 0.00 0.00 39.46 2.29
2353 2533 9.665719 ATGTTTGTCTATGTATTCACACATGTA 57.334 29.630 0.00 0.00 39.46 2.29
2354 2534 7.977789 TGTTTGTCTATGTATTCACACATGT 57.022 32.000 0.00 0.00 39.46 3.21
2356 2536 9.890629 ACTATGTTTGTCTATGTATTCACACAT 57.109 29.630 0.00 0.00 41.88 3.21
2357 2537 9.150348 CACTATGTTTGTCTATGTATTCACACA 57.850 33.333 0.00 0.00 37.54 3.72
2358 2538 9.151471 ACACTATGTTTGTCTATGTATTCACAC 57.849 33.333 0.00 0.00 37.54 3.82
2359 2539 9.366216 GACACTATGTTTGTCTATGTATTCACA 57.634 33.333 0.00 0.00 40.30 3.58
2360 2540 9.366216 TGACACTATGTTTGTCTATGTATTCAC 57.634 33.333 4.27 0.00 43.30 3.18
2361 2541 9.366216 GTGACACTATGTTTGTCTATGTATTCA 57.634 33.333 0.00 0.00 43.30 2.57
2362 2542 9.587772 AGTGACACTATGTTTGTCTATGTATTC 57.412 33.333 6.24 0.00 43.30 1.75
2365 2545 9.239551 ACTAGTGACACTATGTTTGTCTATGTA 57.760 33.333 15.58 0.00 43.30 2.29
2366 2546 8.123639 ACTAGTGACACTATGTTTGTCTATGT 57.876 34.615 15.58 3.27 43.30 2.29
2369 2549 8.188799 GCATACTAGTGACACTATGTTTGTCTA 58.811 37.037 15.58 1.91 43.30 2.59
2370 2550 7.036220 GCATACTAGTGACACTATGTTTGTCT 58.964 38.462 15.58 0.71 43.30 3.41
2371 2551 6.255887 GGCATACTAGTGACACTATGTTTGTC 59.744 42.308 15.58 16.05 43.22 3.18
2372 2552 6.070767 AGGCATACTAGTGACACTATGTTTGT 60.071 38.462 15.58 11.73 29.08 2.83
2373 2553 6.341316 AGGCATACTAGTGACACTATGTTTG 58.659 40.000 15.58 18.04 29.08 2.93
2374 2554 6.381420 AGAGGCATACTAGTGACACTATGTTT 59.619 38.462 15.58 8.50 29.08 2.83
2375 2555 5.894393 AGAGGCATACTAGTGACACTATGTT 59.106 40.000 15.58 6.32 29.08 2.71
2376 2556 5.450453 AGAGGCATACTAGTGACACTATGT 58.550 41.667 15.58 16.25 29.08 2.29
2377 2557 6.712998 AGTAGAGGCATACTAGTGACACTATG 59.287 42.308 15.58 13.06 33.76 2.23
2378 2558 6.843752 AGTAGAGGCATACTAGTGACACTAT 58.156 40.000 15.58 8.80 33.76 2.12
2379 2559 6.249911 AGTAGAGGCATACTAGTGACACTA 57.750 41.667 14.53 14.53 34.21 2.74
2380 2560 5.118729 AGTAGAGGCATACTAGTGACACT 57.881 43.478 13.68 13.68 34.21 3.55
2381 2561 5.357314 TCAAGTAGAGGCATACTAGTGACAC 59.643 44.000 5.39 0.00 34.90 3.67
2382 2562 5.357314 GTCAAGTAGAGGCATACTAGTGACA 59.643 44.000 19.41 0.00 40.28 3.58
2383 2563 5.591067 AGTCAAGTAGAGGCATACTAGTGAC 59.409 44.000 17.97 17.97 40.57 3.67
2384 2564 5.756918 AGTCAAGTAGAGGCATACTAGTGA 58.243 41.667 5.39 2.59 34.90 3.41
2385 2565 6.293735 GCTAGTCAAGTAGAGGCATACTAGTG 60.294 46.154 5.39 0.00 38.02 2.74
2386 2566 5.766174 GCTAGTCAAGTAGAGGCATACTAGT 59.234 44.000 0.00 0.00 38.02 2.57
2387 2567 6.001460 AGCTAGTCAAGTAGAGGCATACTAG 58.999 44.000 0.00 0.00 38.50 2.57
2388 2568 5.942961 AGCTAGTCAAGTAGAGGCATACTA 58.057 41.667 3.23 0.00 34.90 1.82
2389 2569 4.798882 AGCTAGTCAAGTAGAGGCATACT 58.201 43.478 0.00 0.00 37.61 2.12
2390 2570 4.319911 CGAGCTAGTCAAGTAGAGGCATAC 60.320 50.000 0.00 0.00 0.00 2.39
2391 2571 3.815962 CGAGCTAGTCAAGTAGAGGCATA 59.184 47.826 0.00 0.00 0.00 3.14
2392 2572 2.621055 CGAGCTAGTCAAGTAGAGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
2393 2573 2.017782 CGAGCTAGTCAAGTAGAGGCA 58.982 52.381 0.00 0.00 0.00 4.75
2394 2574 2.018515 ACGAGCTAGTCAAGTAGAGGC 58.981 52.381 0.00 0.00 0.00 4.70
2395 2575 5.814764 TTAACGAGCTAGTCAAGTAGAGG 57.185 43.478 0.00 0.00 0.00 3.69
2396 2576 7.017498 TGATTAACGAGCTAGTCAAGTAGAG 57.983 40.000 0.00 0.00 0.00 2.43
2397 2577 6.997239 TGATTAACGAGCTAGTCAAGTAGA 57.003 37.500 0.00 0.00 0.00 2.59
2398 2578 7.968956 TCTTTGATTAACGAGCTAGTCAAGTAG 59.031 37.037 0.00 0.00 31.56 2.57
2399 2579 7.823665 TCTTTGATTAACGAGCTAGTCAAGTA 58.176 34.615 0.00 0.00 31.56 2.24
2400 2580 6.688578 TCTTTGATTAACGAGCTAGTCAAGT 58.311 36.000 0.00 0.00 31.56 3.16
2401 2581 7.254252 CCATCTTTGATTAACGAGCTAGTCAAG 60.254 40.741 0.00 0.00 31.56 3.02
2402 2582 6.535150 CCATCTTTGATTAACGAGCTAGTCAA 59.465 38.462 0.00 0.00 0.00 3.18
2403 2583 6.042777 CCATCTTTGATTAACGAGCTAGTCA 58.957 40.000 0.00 0.00 0.00 3.41
2404 2584 6.043411 ACCATCTTTGATTAACGAGCTAGTC 58.957 40.000 0.00 0.00 0.00 2.59
2405 2585 5.978814 ACCATCTTTGATTAACGAGCTAGT 58.021 37.500 0.00 0.00 0.00 2.57
2406 2586 6.910536 AACCATCTTTGATTAACGAGCTAG 57.089 37.500 0.00 0.00 0.00 3.42
2407 2587 8.038944 ACTTAACCATCTTTGATTAACGAGCTA 58.961 33.333 0.00 0.00 0.00 3.32
2408 2588 6.879458 ACTTAACCATCTTTGATTAACGAGCT 59.121 34.615 0.00 0.00 0.00 4.09
2409 2589 7.073342 ACTTAACCATCTTTGATTAACGAGC 57.927 36.000 0.00 0.00 0.00 5.03
2410 2590 9.543018 GAAACTTAACCATCTTTGATTAACGAG 57.457 33.333 0.00 0.00 0.00 4.18
2411 2591 8.508875 GGAAACTTAACCATCTTTGATTAACGA 58.491 33.333 0.00 0.00 0.00 3.85
2412 2592 8.512138 AGGAAACTTAACCATCTTTGATTAACG 58.488 33.333 0.00 0.00 37.44 3.18
2415 2595 9.174166 GCTAGGAAACTTAACCATCTTTGATTA 57.826 33.333 0.00 0.00 43.67 1.75
2416 2596 7.122799 GGCTAGGAAACTTAACCATCTTTGATT 59.877 37.037 0.00 0.00 43.67 2.57
2417 2597 6.603599 GGCTAGGAAACTTAACCATCTTTGAT 59.396 38.462 0.00 0.00 43.67 2.57
2418 2598 5.944007 GGCTAGGAAACTTAACCATCTTTGA 59.056 40.000 0.00 0.00 43.67 2.69
2419 2599 5.710099 TGGCTAGGAAACTTAACCATCTTTG 59.290 40.000 0.00 0.00 43.67 2.77
2420 2600 5.887754 TGGCTAGGAAACTTAACCATCTTT 58.112 37.500 0.00 0.00 43.67 2.52
2421 2601 5.514500 TGGCTAGGAAACTTAACCATCTT 57.486 39.130 0.00 0.00 43.67 2.40
2422 2602 5.440610 CATGGCTAGGAAACTTAACCATCT 58.559 41.667 0.00 0.00 41.51 2.90
2423 2603 4.580580 CCATGGCTAGGAAACTTAACCATC 59.419 45.833 0.00 0.00 41.51 3.51
2424 2604 4.229582 TCCATGGCTAGGAAACTTAACCAT 59.770 41.667 6.96 0.00 43.13 3.55
2425 2605 3.589735 TCCATGGCTAGGAAACTTAACCA 59.410 43.478 6.96 0.00 43.67 3.67
2426 2606 3.945921 GTCCATGGCTAGGAAACTTAACC 59.054 47.826 6.96 0.00 43.67 2.85
2427 2607 4.585879 TGTCCATGGCTAGGAAACTTAAC 58.414 43.478 6.96 0.00 43.67 2.01
2428 2608 4.919774 TGTCCATGGCTAGGAAACTTAA 57.080 40.909 6.96 0.00 43.67 1.85
2429 2609 4.473196 TCATGTCCATGGCTAGGAAACTTA 59.527 41.667 6.96 0.00 39.56 2.24
2430 2610 3.266772 TCATGTCCATGGCTAGGAAACTT 59.733 43.478 6.96 0.00 39.56 2.66
2431 2611 2.846206 TCATGTCCATGGCTAGGAAACT 59.154 45.455 6.96 0.00 40.99 2.66
2432 2612 3.209410 CTCATGTCCATGGCTAGGAAAC 58.791 50.000 6.96 0.00 39.24 2.78
2433 2613 2.846206 ACTCATGTCCATGGCTAGGAAA 59.154 45.455 6.96 0.00 39.24 3.13
2434 2614 2.481441 ACTCATGTCCATGGCTAGGAA 58.519 47.619 6.96 0.00 39.24 3.36
2435 2615 2.171237 CAACTCATGTCCATGGCTAGGA 59.829 50.000 6.96 4.55 39.24 2.94
2436 2616 2.092753 ACAACTCATGTCCATGGCTAGG 60.093 50.000 6.96 0.00 37.96 3.02
2437 2617 3.272574 ACAACTCATGTCCATGGCTAG 57.727 47.619 6.96 2.08 37.96 3.42
2448 2628 6.029607 CCCGTTAATCAAATGACAACTCATG 58.970 40.000 7.65 0.00 37.20 3.07
2449 2629 5.943416 TCCCGTTAATCAAATGACAACTCAT 59.057 36.000 7.65 0.00 38.94 2.90
2450 2630 5.309638 TCCCGTTAATCAAATGACAACTCA 58.690 37.500 7.65 0.00 0.00 3.41
2451 2631 5.873179 TCCCGTTAATCAAATGACAACTC 57.127 39.130 7.65 0.00 0.00 3.01
2452 2632 5.943416 TGATCCCGTTAATCAAATGACAACT 59.057 36.000 0.00 0.00 30.37 3.16
2453 2633 6.027749 GTGATCCCGTTAATCAAATGACAAC 58.972 40.000 0.00 0.00 35.04 3.32
2454 2634 5.707764 TGTGATCCCGTTAATCAAATGACAA 59.292 36.000 0.00 0.00 35.04 3.18
2455 2635 5.249420 TGTGATCCCGTTAATCAAATGACA 58.751 37.500 0.00 0.00 35.04 3.58
2456 2636 5.811399 TGTGATCCCGTTAATCAAATGAC 57.189 39.130 0.00 0.00 35.04 3.06
2457 2637 6.118852 TGATGTGATCCCGTTAATCAAATGA 58.881 36.000 0.00 0.00 32.39 2.57
2458 2638 6.375945 TGATGTGATCCCGTTAATCAAATG 57.624 37.500 0.00 0.00 32.39 2.32
2459 2639 7.587037 AATGATGTGATCCCGTTAATCAAAT 57.413 32.000 0.00 0.00 34.46 2.32
2460 2640 7.990314 TCTAATGATGTGATCCCGTTAATCAAA 59.010 33.333 0.00 0.00 35.04 2.69
2461 2641 7.505258 TCTAATGATGTGATCCCGTTAATCAA 58.495 34.615 0.00 0.00 35.04 2.57
2462 2642 7.061566 TCTAATGATGTGATCCCGTTAATCA 57.938 36.000 0.00 0.00 0.00 2.57
2463 2643 7.872993 TCTTCTAATGATGTGATCCCGTTAATC 59.127 37.037 0.00 0.00 0.00 1.75
2464 2644 7.735917 TCTTCTAATGATGTGATCCCGTTAAT 58.264 34.615 0.00 0.00 0.00 1.40
2465 2645 7.119709 TCTTCTAATGATGTGATCCCGTTAA 57.880 36.000 0.00 0.00 0.00 2.01
2466 2646 6.724893 TCTTCTAATGATGTGATCCCGTTA 57.275 37.500 0.00 0.00 0.00 3.18
2467 2647 5.614324 TCTTCTAATGATGTGATCCCGTT 57.386 39.130 0.00 0.00 0.00 4.44
2468 2648 5.614324 TTCTTCTAATGATGTGATCCCGT 57.386 39.130 0.00 0.00 0.00 5.28
2469 2649 6.226052 TCATTCTTCTAATGATGTGATCCCG 58.774 40.000 0.00 0.00 32.21 5.14
2483 2663 9.383519 GGTCAAGTAAATCACATCATTCTTCTA 57.616 33.333 0.00 0.00 0.00 2.10
2484 2664 7.337942 GGGTCAAGTAAATCACATCATTCTTCT 59.662 37.037 0.00 0.00 0.00 2.85
2485 2665 7.121168 TGGGTCAAGTAAATCACATCATTCTTC 59.879 37.037 0.00 0.00 0.00 2.87
2486 2666 6.947733 TGGGTCAAGTAAATCACATCATTCTT 59.052 34.615 0.00 0.00 0.00 2.52
2487 2667 6.484288 TGGGTCAAGTAAATCACATCATTCT 58.516 36.000 0.00 0.00 0.00 2.40
2488 2668 6.757897 TGGGTCAAGTAAATCACATCATTC 57.242 37.500 0.00 0.00 0.00 2.67
2489 2669 7.147846 GGAATGGGTCAAGTAAATCACATCATT 60.148 37.037 0.00 0.00 0.00 2.57
2490 2670 6.322201 GGAATGGGTCAAGTAAATCACATCAT 59.678 38.462 0.00 0.00 0.00 2.45
2491 2671 5.652014 GGAATGGGTCAAGTAAATCACATCA 59.348 40.000 0.00 0.00 0.00 3.07
2492 2672 5.220854 CGGAATGGGTCAAGTAAATCACATC 60.221 44.000 0.00 0.00 0.00 3.06
2493 2673 4.640201 CGGAATGGGTCAAGTAAATCACAT 59.360 41.667 0.00 0.00 0.00 3.21
2494 2674 4.006989 CGGAATGGGTCAAGTAAATCACA 58.993 43.478 0.00 0.00 0.00 3.58
2495 2675 4.007659 ACGGAATGGGTCAAGTAAATCAC 58.992 43.478 0.00 0.00 0.00 3.06
2496 2676 4.295141 ACGGAATGGGTCAAGTAAATCA 57.705 40.909 0.00 0.00 0.00 2.57
2497 2677 5.220796 GCTAACGGAATGGGTCAAGTAAATC 60.221 44.000 0.00 0.00 0.00 2.17
2498 2678 4.638865 GCTAACGGAATGGGTCAAGTAAAT 59.361 41.667 0.00 0.00 0.00 1.40
2499 2679 4.004982 GCTAACGGAATGGGTCAAGTAAA 58.995 43.478 0.00 0.00 0.00 2.01
2500 2680 3.262405 AGCTAACGGAATGGGTCAAGTAA 59.738 43.478 0.00 0.00 0.00 2.24
2501 2681 2.835764 AGCTAACGGAATGGGTCAAGTA 59.164 45.455 0.00 0.00 0.00 2.24
2502 2682 1.628846 AGCTAACGGAATGGGTCAAGT 59.371 47.619 0.00 0.00 0.00 3.16
2503 2683 2.403252 AGCTAACGGAATGGGTCAAG 57.597 50.000 0.00 0.00 0.00 3.02
2504 2684 2.871096 AAGCTAACGGAATGGGTCAA 57.129 45.000 0.00 0.00 0.00 3.18
2505 2685 2.419574 GCTAAGCTAACGGAATGGGTCA 60.420 50.000 0.00 0.00 0.00 4.02
2506 2686 2.210961 GCTAAGCTAACGGAATGGGTC 58.789 52.381 0.00 0.00 0.00 4.46
2507 2687 1.557832 TGCTAAGCTAACGGAATGGGT 59.442 47.619 0.00 0.00 0.00 4.51
2508 2688 1.940613 GTGCTAAGCTAACGGAATGGG 59.059 52.381 0.00 0.00 0.00 4.00
2509 2689 2.906354 AGTGCTAAGCTAACGGAATGG 58.094 47.619 0.00 0.00 0.00 3.16
2510 2690 3.932710 TCAAGTGCTAAGCTAACGGAATG 59.067 43.478 0.00 0.00 0.00 2.67
2511 2691 4.202245 TCAAGTGCTAAGCTAACGGAAT 57.798 40.909 0.00 0.00 0.00 3.01
2512 2692 3.671008 TCAAGTGCTAAGCTAACGGAA 57.329 42.857 0.00 0.00 0.00 4.30
2513 2693 3.733988 CGATCAAGTGCTAAGCTAACGGA 60.734 47.826 0.00 0.00 0.00 4.69
2514 2694 2.535984 CGATCAAGTGCTAAGCTAACGG 59.464 50.000 0.00 0.00 0.00 4.44
2515 2695 3.179830 ACGATCAAGTGCTAAGCTAACG 58.820 45.455 0.00 0.00 0.00 3.18
2516 2696 5.532025 AAACGATCAAGTGCTAAGCTAAC 57.468 39.130 0.00 0.00 0.00 2.34
2517 2697 6.395629 ACTAAACGATCAAGTGCTAAGCTAA 58.604 36.000 0.00 0.00 0.00 3.09
2518 2698 5.962433 ACTAAACGATCAAGTGCTAAGCTA 58.038 37.500 0.00 0.00 0.00 3.32
2519 2699 4.822026 ACTAAACGATCAAGTGCTAAGCT 58.178 39.130 0.00 0.00 0.00 3.74
2520 2700 5.532025 AACTAAACGATCAAGTGCTAAGC 57.468 39.130 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.