Multiple sequence alignment - TraesCS3A01G054300

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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 TraesCS3A01G054300 chr3A 100.000 2543 0 0 1 2543 31789678 31787136 0.000000e+00 4697.0
1 TraesCS3A01G054300 chr3A 93.333 180 11 1 656 834 31788858 31788679 5.390000e-67 265.0
2 TraesCS3A01G054300 chr3A 93.333 180 11 1 821 1000 31789023 31788845 5.390000e-67 265.0
3 TraesCS3A01G054300 chr3A 94.969 159 8 0 2376 2534 518731285 518731127 1.510000e-62 250.0
4 TraesCS3A01G054300 chr3A 92.000 175 13 1 1757 1931 31932008 31931835 7.030000e-61 244.0
5 TraesCS3A01G054300 chr3A 88.462 52 4 2 1930 1979 95471745 95471694 7.600000e-06 62.1
6 TraesCS3A01G054300 chr3A 96.875 32 1 0 1935 1966 557408356 557408387 1.000000e-03 54.7
7 TraesCS3A01G054300 chr3B 94.699 1377 71 2 989 2364 39141578 39140203 0.000000e+00 2137.0
8 TraesCS3A01G054300 chr3B 92.710 823 48 5 3 823 39142420 39141608 0.000000e+00 1177.0
9 TraesCS3A01G054300 chr3B 80.103 774 137 9 821 1577 40848103 40847330 6.140000e-156 560.0
10 TraesCS3A01G054300 chr3B 94.643 168 9 0 821 988 39141775 39141608 6.980000e-66 261.0
11 TraesCS3A01G054300 chr3B 90.000 50 3 2 1932 1979 633537609 633537560 2.110000e-06 63.9
12 TraesCS3A01G054300 chr3D 80.230 784 137 10 821 1587 23145234 23144452 7.890000e-160 573.0
13 TraesCS3A01G054300 chr3D 95.035 141 7 0 2376 2516 399521216 399521076 3.290000e-54 222.0
14 TraesCS3A01G054300 chr7B 81.046 459 50 23 2090 2534 63632425 63631990 5.240000e-87 331.0
15 TraesCS3A01G054300 chr7B 83.673 196 18 8 2089 2272 63627440 63627247 3.360000e-39 172.0
16 TraesCS3A01G054300 chr7A 85.526 304 21 13 2089 2392 539653896 539653616 1.910000e-76 296.0
17 TraesCS3A01G054300 chr1D 91.975 162 9 3 2373 2534 484578380 484578537 9.160000e-55 224.0
18 TraesCS3A01G054300 chr2B 89.937 159 16 0 2376 2534 42729002 42728844 3.320000e-49 206.0
19 TraesCS3A01G054300 chr2B 89.937 159 16 0 2376 2534 42867438 42867280 3.320000e-49 206.0
20 TraesCS3A01G054300 chr2B 91.156 147 13 0 2388 2534 42697150 42697004 1.540000e-47 200.0
21 TraesCS3A01G054300 chr2B 91.156 147 13 0 2388 2534 42767093 42766947 1.540000e-47 200.0
22 TraesCS3A01G054300 chr1B 88.889 162 14 3 2373 2534 674841413 674841570 2.000000e-46 196.0
23 TraesCS3A01G054300 chr1B 94.737 38 2 0 1936 1973 91558067 91558030 2.730000e-05 60.2
24 TraesCS3A01G054300 chr7D 79.245 318 28 22 2089 2392 109016790 109016497 1.200000e-43 187.0
25 TraesCS3A01G054300 chr5D 95.082 61 3 0 2098 2158 24048555 24048495 2.080000e-16 97.1
26 TraesCS3A01G054300 chr6B 97.222 36 1 0 1930 1965 941781 941746 7.600000e-06 62.1
27 TraesCS3A01G054300 chr6B 100.000 31 0 0 1936 1966 11584440 11584470 9.830000e-05 58.4
28 TraesCS3A01G054300 chr6B 92.500 40 2 1 1930 1968 650601513 650601474 3.530000e-04 56.5
29 TraesCS3A01G054300 chr2D 100.000 28 0 0 1936 1963 648157402 648157429 5.000000e-03 52.8


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 TraesCS3A01G054300 chr3A 31787136 31789678 2542 True 1742.333333 4697 95.555333 1 2543 3 chr3A.!!$R4 2542
1 TraesCS3A01G054300 chr3B 39140203 39142420 2217 True 1191.666667 2137 94.017333 3 2364 3 chr3B.!!$R3 2361
2 TraesCS3A01G054300 chr3B 40847330 40848103 773 True 560.000000 560 80.103000 821 1577 1 chr3B.!!$R1 756
3 TraesCS3A01G054300 chr3D 23144452 23145234 782 True 573.000000 573 80.230000 821 1587 1 chr3D.!!$R1 766

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
49 50 0.318955 AAATGAGCCACTTGCAACGC 60.319 50.0 0.00 0.0 44.83 4.84 F
829 832 0.607620 GCATGCACCCCAAAAGCTAA 59.392 50.0 14.21 0.0 0.00 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1151 1183 0.112995 ATGGGAGCTTTGTGGCTTGA 59.887 50.0 0.00 0.0 43.20 3.02 R
2511 2544 0.032540 GGTTGCAAGCAAGGAGTTGG 59.967 55.0 23.18 0.0 36.52 3.77 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
28 29 1.809619 TGATAACAGAGGCGCGCAC 60.810 57.895 34.42 25.00 0.00 5.34
29 30 1.809619 GATAACAGAGGCGCGCACA 60.810 57.895 34.42 10.37 0.00 4.57
30 31 1.358725 GATAACAGAGGCGCGCACAA 61.359 55.000 34.42 10.68 0.00 3.33
48 49 1.788308 CAAAATGAGCCACTTGCAACG 59.212 47.619 0.00 0.00 44.83 4.10
49 50 0.318955 AAATGAGCCACTTGCAACGC 60.319 50.000 0.00 0.00 44.83 4.84
133 134 1.799157 AATTGCTAGGTGGTGGCCCA 61.799 55.000 0.00 0.00 38.87 5.36
163 164 1.743623 CATACGCGTGCAAGGGGAA 60.744 57.895 24.59 8.77 38.11 3.97
341 344 3.747529 GGGGCTGATTTGTGTCATTTTTG 59.252 43.478 0.00 0.00 0.00 2.44
432 435 5.724328 TGTTCATTTGCAAAACTGGTTGTA 58.276 33.333 17.19 0.00 0.00 2.41
443 446 5.418310 AAACTGGTTGTACGTTGATTCAG 57.582 39.130 0.00 0.00 0.00 3.02
462 465 4.023980 TCAGTAGATGAATTCACGGGAGT 58.976 43.478 11.07 0.00 38.39 3.85
479 482 4.681781 CGGGAGTTAGAGCACTCATTTGAT 60.682 45.833 4.51 0.00 44.53 2.57
480 483 4.813697 GGGAGTTAGAGCACTCATTTGATC 59.186 45.833 4.51 0.00 44.53 2.92
481 484 5.423015 GGAGTTAGAGCACTCATTTGATCA 58.577 41.667 4.51 0.00 44.53 2.92
482 485 6.054295 GGAGTTAGAGCACTCATTTGATCAT 58.946 40.000 0.00 0.00 44.53 2.45
489 492 6.602009 AGAGCACTCATTTGATCATTCATTCA 59.398 34.615 0.00 0.00 34.19 2.57
510 513 8.723311 CATTCATTCATTTATTTGGTTTGCTGT 58.277 29.630 0.00 0.00 0.00 4.40
512 515 9.770097 TTCATTCATTTATTTGGTTTGCTGTTA 57.230 25.926 0.00 0.00 0.00 2.41
515 518 8.586570 TTCATTTATTTGGTTTGCTGTTACAG 57.413 30.769 8.18 8.18 34.12 2.74
660 663 5.947228 TTCACTAGCTGGATTCACAAAAG 57.053 39.130 3.17 0.00 0.00 2.27
666 669 5.990120 AGCTGGATTCACAAAAGCTAAAT 57.010 34.783 0.00 0.00 42.25 1.40
667 670 6.350629 AGCTGGATTCACAAAAGCTAAATT 57.649 33.333 0.00 0.00 42.25 1.82
775 778 6.762661 GGAGATCTGAGAAGGATTTTCTCTTG 59.237 42.308 15.53 9.86 43.91 3.02
782 785 2.648838 AGGATTTTCTCTTGGAGGGGT 58.351 47.619 0.00 0.00 0.00 4.95
783 786 2.310052 AGGATTTTCTCTTGGAGGGGTG 59.690 50.000 0.00 0.00 0.00 4.61
784 787 2.041755 GGATTTTCTCTTGGAGGGGTGT 59.958 50.000 0.00 0.00 0.00 4.16
785 788 2.951229 TTTTCTCTTGGAGGGGTGTC 57.049 50.000 0.00 0.00 0.00 3.67
786 789 2.118403 TTTCTCTTGGAGGGGTGTCT 57.882 50.000 0.00 0.00 0.00 3.41
787 790 3.269592 TTTCTCTTGGAGGGGTGTCTA 57.730 47.619 0.00 0.00 0.00 2.59
788 791 3.491766 TTCTCTTGGAGGGGTGTCTAT 57.508 47.619 0.00 0.00 0.00 1.98
789 792 4.620086 TTCTCTTGGAGGGGTGTCTATA 57.380 45.455 0.00 0.00 0.00 1.31
790 793 4.834406 TCTCTTGGAGGGGTGTCTATAT 57.166 45.455 0.00 0.00 0.00 0.86
791 794 5.942977 TCTCTTGGAGGGGTGTCTATATA 57.057 43.478 0.00 0.00 0.00 0.86
792 795 6.485388 TCTCTTGGAGGGGTGTCTATATAT 57.515 41.667 0.00 0.00 0.00 0.86
793 796 7.599353 TCTCTTGGAGGGGTGTCTATATATA 57.401 40.000 0.00 0.00 0.00 0.86
794 797 7.644062 TCTCTTGGAGGGGTGTCTATATATAG 58.356 42.308 12.84 12.84 0.00 1.31
795 798 7.464589 TCTCTTGGAGGGGTGTCTATATATAGA 59.535 40.741 16.95 16.95 37.07 1.98
796 799 8.008104 TCTTGGAGGGGTGTCTATATATAGAA 57.992 38.462 21.45 10.95 40.77 2.10
797 800 8.461854 TCTTGGAGGGGTGTCTATATATAGAAA 58.538 37.037 21.45 15.12 40.77 2.52
798 801 9.273137 CTTGGAGGGGTGTCTATATATAGAAAT 57.727 37.037 21.45 4.08 40.77 2.17
800 803 9.710818 TGGAGGGGTGTCTATATATAGAAATAC 57.289 37.037 21.45 18.78 40.77 1.89
801 804 9.710818 GGAGGGGTGTCTATATATAGAAATACA 57.289 37.037 21.45 13.97 40.77 2.29
815 818 9.698309 ATATAGAAATACATATAGTCGGCATGC 57.302 33.333 9.90 9.90 0.00 4.06
816 819 5.793817 AGAAATACATATAGTCGGCATGCA 58.206 37.500 21.36 0.00 0.00 3.96
817 820 5.639506 AGAAATACATATAGTCGGCATGCAC 59.360 40.000 21.36 10.23 0.00 4.57
818 821 2.169832 ACATATAGTCGGCATGCACC 57.830 50.000 21.36 6.19 0.00 5.01
819 822 1.270839 ACATATAGTCGGCATGCACCC 60.271 52.381 21.36 5.79 0.00 4.61
826 829 2.046988 GGCATGCACCCCAAAAGC 60.047 61.111 21.36 0.00 0.00 3.51
829 832 0.607620 GCATGCACCCCAAAAGCTAA 59.392 50.000 14.21 0.00 0.00 3.09
832 835 0.678950 TGCACCCCAAAAGCTAAAGC 59.321 50.000 0.00 0.00 42.49 3.51
834 837 1.337167 GCACCCCAAAAGCTAAAGCAG 60.337 52.381 4.54 0.00 45.16 4.24
841 844 5.299949 CCCAAAAGCTAAAGCAGTCATTTT 58.700 37.500 4.54 0.00 45.16 1.82
842 845 5.178067 CCCAAAAGCTAAAGCAGTCATTTTG 59.822 40.000 14.58 14.58 45.16 2.44
856 859 9.146984 AGCAGTCATTTTGTCATTCATTTATTG 57.853 29.630 0.00 0.00 0.00 1.90
857 860 9.142515 GCAGTCATTTTGTCATTCATTTATTGA 57.857 29.630 0.00 0.00 0.00 2.57
885 888 8.272545 TGATTTGCCATCATATTCTATGTAGC 57.727 34.615 0.00 0.00 0.00 3.58
891 894 7.938490 TGCCATCATATTCTATGTAGCAAAAGA 59.062 33.333 0.00 0.00 0.00 2.52
925 928 7.882791 ACTATGTGACTAGTATGGAGATCTGAG 59.117 40.741 0.00 0.00 30.16 3.35
941 944 6.652053 AGATCTGAGAAGGATTTTCTCTTGG 58.348 40.000 15.53 7.98 43.91 3.61
946 949 3.919554 AGAAGGATTTTCTCTTGGAGGGT 59.080 43.478 0.00 0.00 0.00 4.34
1099 1131 3.262660 TGCTGACACTGATTTCATCTCCT 59.737 43.478 0.00 0.00 0.00 3.69
1107 1139 3.945921 CTGATTTCATCTCCTGCACATGT 59.054 43.478 0.00 0.00 0.00 3.21
1144 1176 1.704387 CGCATTGTGCATAGCCGTGA 61.704 55.000 2.63 0.00 45.36 4.35
1151 1183 0.462375 TGCATAGCCGTGATTACCGT 59.538 50.000 0.00 0.00 0.00 4.83
1240 1272 0.660005 CACCGCCAAACACAATGTCG 60.660 55.000 0.00 0.00 0.00 4.35
1338 1370 0.392193 CTGAAGCCACTAGTGCCCTG 60.392 60.000 17.86 4.93 0.00 4.45
1346 1378 2.025887 CCACTAGTGCCCTGGAGATTTT 60.026 50.000 17.86 0.00 0.00 1.82
1464 1496 1.916181 TGGATCAAGAAGAAGTCCCCC 59.084 52.381 0.00 0.00 0.00 5.40
1508 1540 0.601558 ACGGAGCATTGTAGTGTCGT 59.398 50.000 0.00 0.00 0.00 4.34
1521 1553 1.893137 AGTGTCGTCAGCAACCTCATA 59.107 47.619 0.00 0.00 0.00 2.15
1550 1582 1.704628 TGTCCCCAAGTGATGACATGT 59.295 47.619 0.00 0.00 33.09 3.21
1603 1635 7.946655 TTCAATAATTAGCCGACTGTATCTG 57.053 36.000 0.00 0.00 0.00 2.90
1616 1648 6.422223 CGACTGTATCTGAAAATGTTATGGC 58.578 40.000 0.00 0.00 0.00 4.40
1687 1719 8.633724 AGATGAACCCTAGGAATACCATATAGA 58.366 37.037 11.48 0.00 38.94 1.98
1832 1865 6.726764 ACACTAGGAGAAATCCTACTGTTTCT 59.273 38.462 9.49 0.41 44.82 2.52
1840 1873 8.535690 AGAAATCCTACTGTTTCTCGTAAAAG 57.464 34.615 0.00 0.00 39.75 2.27
1860 1893 6.840780 AAAGAATGAATGGGAAGTAACCTG 57.159 37.500 0.00 0.00 0.00 4.00
1870 1903 3.067833 GGAAGTAACCTGTGAGTGAAGC 58.932 50.000 0.00 0.00 0.00 3.86
1872 1905 2.047061 AGTAACCTGTGAGTGAAGCCA 58.953 47.619 0.00 0.00 0.00 4.75
1880 1913 1.956477 GTGAGTGAAGCCAAACATGGT 59.044 47.619 0.00 0.00 0.00 3.55
1887 1920 3.244735 TGAAGCCAAACATGGTAGTAGCA 60.245 43.478 4.19 4.19 0.00 3.49
1917 1950 1.313812 ATGCAGCCAAGAAGCAGAGC 61.314 55.000 0.00 0.00 42.14 4.09
1973 2006 7.425606 TCTAAGACAAACTTTTTGAATGGAGC 58.574 34.615 5.67 0.00 39.72 4.70
2004 2037 9.606631 ACTATGGTAGATAAGAAAAAGAAGCAG 57.393 33.333 0.00 0.00 0.00 4.24
2078 2111 7.775397 AGACAAAAATGACAAAGGAACATTG 57.225 32.000 0.00 0.00 43.28 2.82
2079 2112 7.555087 AGACAAAAATGACAAAGGAACATTGA 58.445 30.769 0.00 0.00 39.65 2.57
2097 2130 8.732746 AACATTGACTACAAAGTGTAAAGAGT 57.267 30.769 0.00 0.00 37.86 3.24
2155 2188 7.670364 CCCGCATGTATATATTGATAGGATGA 58.330 38.462 0.00 0.00 0.00 2.92
2173 2206 4.202461 GGATGATCAATGGGTACAAGCCTA 60.202 45.833 0.00 0.00 36.53 3.93
2177 2210 3.726790 TCAATGGGTACAAGCCTAGGTA 58.273 45.455 11.31 0.00 36.53 3.08
2191 2224 6.694445 AGCCTAGGTAGAGATTGCATAATT 57.306 37.500 11.31 0.00 0.00 1.40
2207 2240 4.994852 GCATAATTGAGAGCGGTGGTTATA 59.005 41.667 0.00 0.00 0.00 0.98
2216 2249 4.521256 AGAGCGGTGGTTATAGAGAGAATC 59.479 45.833 0.00 0.00 0.00 2.52
2280 2313 3.477530 ACAACCTCAACAGAAAGCCTAC 58.522 45.455 0.00 0.00 0.00 3.18
2297 2330 3.478509 CCTACGCTAGAGTAGTCACCAT 58.521 50.000 25.90 0.00 41.76 3.55
2306 2339 2.099921 GAGTAGTCACCATGTCGAGCAT 59.900 50.000 0.00 0.00 38.60 3.79
2319 2352 2.360350 AGCATGTCAAGGGTGCGG 60.360 61.111 0.00 0.00 43.37 5.69
2353 2386 1.290009 GCCCATGCCAAGTGTCAAC 59.710 57.895 0.00 0.00 0.00 3.18
2364 2397 4.373116 TGTCAACGGCGCCTCCTC 62.373 66.667 26.68 11.41 0.00 3.71
2367 2400 4.821589 CAACGGCGCCTCCTCCTC 62.822 72.222 26.68 0.00 0.00 3.71
2371 2404 2.442272 GGCGCCTCCTCCTCTGTA 60.442 66.667 22.15 0.00 0.00 2.74
2372 2405 2.058595 GGCGCCTCCTCCTCTGTAA 61.059 63.158 22.15 0.00 0.00 2.41
2373 2406 1.142097 GCGCCTCCTCCTCTGTAAC 59.858 63.158 0.00 0.00 0.00 2.50
2374 2407 1.605058 GCGCCTCCTCCTCTGTAACA 61.605 60.000 0.00 0.00 0.00 2.41
2375 2408 1.115467 CGCCTCCTCCTCTGTAACAT 58.885 55.000 0.00 0.00 0.00 2.71
2376 2409 2.307768 CGCCTCCTCCTCTGTAACATA 58.692 52.381 0.00 0.00 0.00 2.29
2377 2410 2.894126 CGCCTCCTCCTCTGTAACATAT 59.106 50.000 0.00 0.00 0.00 1.78
2378 2411 3.322254 CGCCTCCTCCTCTGTAACATATT 59.678 47.826 0.00 0.00 0.00 1.28
2379 2412 4.636249 GCCTCCTCCTCTGTAACATATTG 58.364 47.826 0.00 0.00 0.00 1.90
2380 2413 4.636249 CCTCCTCCTCTGTAACATATTGC 58.364 47.826 0.00 0.00 0.00 3.56
2381 2414 4.101585 CCTCCTCCTCTGTAACATATTGCA 59.898 45.833 0.00 0.00 0.00 4.08
2382 2415 5.221803 CCTCCTCCTCTGTAACATATTGCAT 60.222 44.000 0.00 0.00 29.33 3.96
2383 2416 5.614308 TCCTCCTCTGTAACATATTGCATG 58.386 41.667 0.00 0.00 29.33 4.06
2384 2417 5.130975 TCCTCCTCTGTAACATATTGCATGT 59.869 40.000 0.00 0.00 29.33 3.21
2385 2418 5.824624 CCTCCTCTGTAACATATTGCATGTT 59.175 40.000 9.03 9.03 43.74 2.71
2386 2419 6.017605 CCTCCTCTGTAACATATTGCATGTTC 60.018 42.308 7.42 1.94 41.81 3.18
2387 2420 6.413892 TCCTCTGTAACATATTGCATGTTCA 58.586 36.000 7.42 5.79 41.81 3.18
2388 2421 6.883756 TCCTCTGTAACATATTGCATGTTCAA 59.116 34.615 7.42 0.00 41.81 2.69
2389 2422 6.968904 CCTCTGTAACATATTGCATGTTCAAC 59.031 38.462 7.42 3.14 41.81 3.18
2390 2423 7.361971 CCTCTGTAACATATTGCATGTTCAACA 60.362 37.037 7.42 7.14 41.81 3.33
2391 2424 7.304735 TCTGTAACATATTGCATGTTCAACAC 58.695 34.615 7.42 2.19 41.81 3.32
2392 2425 6.385843 TGTAACATATTGCATGTTCAACACC 58.614 36.000 7.42 0.00 41.81 4.16
2393 2426 4.454728 ACATATTGCATGTTCAACACCC 57.545 40.909 0.00 0.00 0.00 4.61
2394 2427 4.088634 ACATATTGCATGTTCAACACCCT 58.911 39.130 0.00 0.00 0.00 4.34
2395 2428 4.158394 ACATATTGCATGTTCAACACCCTC 59.842 41.667 0.00 0.00 0.00 4.30
2396 2429 1.327303 TTGCATGTTCAACACCCTCC 58.673 50.000 0.00 0.00 0.00 4.30
2397 2430 0.539438 TGCATGTTCAACACCCTCCC 60.539 55.000 0.00 0.00 0.00 4.30
2398 2431 0.251341 GCATGTTCAACACCCTCCCT 60.251 55.000 0.00 0.00 0.00 4.20
2399 2432 1.823250 GCATGTTCAACACCCTCCCTT 60.823 52.381 0.00 0.00 0.00 3.95
2400 2433 2.554344 GCATGTTCAACACCCTCCCTTA 60.554 50.000 0.00 0.00 0.00 2.69
2401 2434 3.761897 CATGTTCAACACCCTCCCTTAA 58.238 45.455 0.00 0.00 0.00 1.85
2402 2435 4.344104 CATGTTCAACACCCTCCCTTAAT 58.656 43.478 0.00 0.00 0.00 1.40
2403 2436 4.028993 TGTTCAACACCCTCCCTTAATC 57.971 45.455 0.00 0.00 0.00 1.75
2404 2437 3.655777 TGTTCAACACCCTCCCTTAATCT 59.344 43.478 0.00 0.00 0.00 2.40
2405 2438 4.010349 GTTCAACACCCTCCCTTAATCTG 58.990 47.826 0.00 0.00 0.00 2.90
2406 2439 3.526899 TCAACACCCTCCCTTAATCTGA 58.473 45.455 0.00 0.00 0.00 3.27
2407 2440 3.913799 TCAACACCCTCCCTTAATCTGAA 59.086 43.478 0.00 0.00 0.00 3.02
2408 2441 4.010349 CAACACCCTCCCTTAATCTGAAC 58.990 47.826 0.00 0.00 0.00 3.18
2409 2442 3.532102 ACACCCTCCCTTAATCTGAACT 58.468 45.455 0.00 0.00 0.00 3.01
2410 2443 3.916989 ACACCCTCCCTTAATCTGAACTT 59.083 43.478 0.00 0.00 0.00 2.66
2411 2444 4.019231 ACACCCTCCCTTAATCTGAACTTC 60.019 45.833 0.00 0.00 0.00 3.01
2412 2445 4.226168 CACCCTCCCTTAATCTGAACTTCT 59.774 45.833 0.00 0.00 0.00 2.85
2413 2446 4.471747 ACCCTCCCTTAATCTGAACTTCTC 59.528 45.833 0.00 0.00 0.00 2.87
2414 2447 4.471386 CCCTCCCTTAATCTGAACTTCTCA 59.529 45.833 0.00 0.00 0.00 3.27
2427 2460 7.215696 CTGAACTTCTCAGCTTAAGATTACG 57.784 40.000 6.67 0.00 45.11 3.18
2428 2461 6.688578 TGAACTTCTCAGCTTAAGATTACGT 58.311 36.000 6.67 0.00 0.00 3.57
2429 2462 7.152645 TGAACTTCTCAGCTTAAGATTACGTT 58.847 34.615 6.67 0.00 0.00 3.99
2430 2463 7.656137 TGAACTTCTCAGCTTAAGATTACGTTT 59.344 33.333 6.67 0.00 0.00 3.60
2431 2464 7.352719 ACTTCTCAGCTTAAGATTACGTTTG 57.647 36.000 6.67 0.00 0.00 2.93
2432 2465 7.152645 ACTTCTCAGCTTAAGATTACGTTTGA 58.847 34.615 6.67 0.00 0.00 2.69
2433 2466 7.656137 ACTTCTCAGCTTAAGATTACGTTTGAA 59.344 33.333 6.67 0.00 0.00 2.69
2434 2467 7.347508 TCTCAGCTTAAGATTACGTTTGAAC 57.652 36.000 6.67 0.00 0.00 3.18
2435 2468 7.152645 TCTCAGCTTAAGATTACGTTTGAACT 58.847 34.615 6.67 0.00 0.00 3.01
2436 2469 7.328737 TCTCAGCTTAAGATTACGTTTGAACTC 59.671 37.037 6.67 0.00 0.00 3.01
2437 2470 7.152645 TCAGCTTAAGATTACGTTTGAACTCT 58.847 34.615 6.67 0.00 0.00 3.24
2438 2471 7.656137 TCAGCTTAAGATTACGTTTGAACTCTT 59.344 33.333 6.67 0.00 0.00 2.85
2439 2472 7.952637 CAGCTTAAGATTACGTTTGAACTCTTC 59.047 37.037 6.67 0.00 0.00 2.87
2440 2473 7.656137 AGCTTAAGATTACGTTTGAACTCTTCA 59.344 33.333 6.67 0.00 38.04 3.02
2454 2487 6.959361 TGAACTCTTCAAATTGTCTTGTAGC 58.041 36.000 0.00 0.00 36.59 3.58
2455 2488 5.948992 ACTCTTCAAATTGTCTTGTAGCC 57.051 39.130 0.00 0.00 0.00 3.93
2456 2489 5.376625 ACTCTTCAAATTGTCTTGTAGCCA 58.623 37.500 0.00 0.00 0.00 4.75
2457 2490 5.827797 ACTCTTCAAATTGTCTTGTAGCCAA 59.172 36.000 0.00 0.00 0.00 4.52
2459 2492 5.241506 TCTTCAAATTGTCTTGTAGCCAAGG 59.758 40.000 3.30 0.00 46.65 3.61
2463 2496 3.652581 GTCTTGTAGCCAAGGCCTT 57.347 52.632 13.78 13.78 45.60 4.35
2464 2497 1.911057 GTCTTGTAGCCAAGGCCTTT 58.089 50.000 17.61 3.94 45.60 3.11
2465 2498 1.541588 GTCTTGTAGCCAAGGCCTTTG 59.458 52.381 17.61 14.62 45.60 2.77
2466 2499 1.144913 TCTTGTAGCCAAGGCCTTTGT 59.855 47.619 17.61 5.70 46.65 2.83
2467 2500 2.373836 TCTTGTAGCCAAGGCCTTTGTA 59.626 45.455 17.61 4.59 46.65 2.41
2468 2501 2.961531 TGTAGCCAAGGCCTTTGTAA 57.038 45.000 17.61 1.83 43.17 2.41
2469 2502 3.231207 TGTAGCCAAGGCCTTTGTAAA 57.769 42.857 17.61 0.00 43.17 2.01
2470 2503 2.888414 TGTAGCCAAGGCCTTTGTAAAC 59.112 45.455 17.61 12.38 43.17 2.01
2471 2504 1.338107 AGCCAAGGCCTTTGTAAACC 58.662 50.000 17.61 0.00 43.17 3.27
2472 2505 0.320374 GCCAAGGCCTTTGTAAACCC 59.680 55.000 17.61 0.00 34.87 4.11
2473 2506 1.710816 CCAAGGCCTTTGTAAACCCA 58.289 50.000 17.61 0.00 34.87 4.51
2474 2507 2.256306 CCAAGGCCTTTGTAAACCCAT 58.744 47.619 17.61 0.00 34.87 4.00
2475 2508 2.233676 CCAAGGCCTTTGTAAACCCATC 59.766 50.000 17.61 0.00 34.87 3.51
2476 2509 3.165071 CAAGGCCTTTGTAAACCCATCT 58.835 45.455 17.61 0.00 31.92 2.90
2477 2510 2.807676 AGGCCTTTGTAAACCCATCTG 58.192 47.619 0.00 0.00 0.00 2.90
2478 2511 1.204704 GGCCTTTGTAAACCCATCTGC 59.795 52.381 0.00 0.00 0.00 4.26
2479 2512 1.892474 GCCTTTGTAAACCCATCTGCA 59.108 47.619 0.00 0.00 0.00 4.41
2480 2513 2.298729 GCCTTTGTAAACCCATCTGCAA 59.701 45.455 0.00 0.00 0.00 4.08
2481 2514 3.860754 GCCTTTGTAAACCCATCTGCAAC 60.861 47.826 0.00 0.00 0.00 4.17
2482 2515 3.573967 CCTTTGTAAACCCATCTGCAACT 59.426 43.478 0.00 0.00 0.00 3.16
2483 2516 4.039124 CCTTTGTAAACCCATCTGCAACTT 59.961 41.667 0.00 0.00 0.00 2.66
2484 2517 4.582701 TTGTAAACCCATCTGCAACTTG 57.417 40.909 0.00 0.00 0.00 3.16
2485 2518 2.890311 TGTAAACCCATCTGCAACTTGG 59.110 45.455 2.89 2.89 0.00 3.61
2486 2519 2.086610 AAACCCATCTGCAACTTGGT 57.913 45.000 8.07 1.03 0.00 3.67
2487 2520 1.620822 AACCCATCTGCAACTTGGTC 58.379 50.000 8.07 0.00 0.00 4.02
2488 2521 0.773644 ACCCATCTGCAACTTGGTCT 59.226 50.000 8.07 0.00 0.00 3.85
2489 2522 1.145738 ACCCATCTGCAACTTGGTCTT 59.854 47.619 8.07 0.00 0.00 3.01
2490 2523 2.242043 CCCATCTGCAACTTGGTCTTT 58.758 47.619 8.07 0.00 0.00 2.52
2491 2524 2.629617 CCCATCTGCAACTTGGTCTTTT 59.370 45.455 8.07 0.00 0.00 2.27
2492 2525 3.553508 CCCATCTGCAACTTGGTCTTTTG 60.554 47.826 8.07 0.00 0.00 2.44
2493 2526 3.318839 CCATCTGCAACTTGGTCTTTTGA 59.681 43.478 0.00 0.00 0.00 2.69
2494 2527 4.202141 CCATCTGCAACTTGGTCTTTTGAA 60.202 41.667 0.00 0.00 0.00 2.69
2495 2528 4.637483 TCTGCAACTTGGTCTTTTGAAG 57.363 40.909 0.00 0.00 0.00 3.02
2496 2529 3.381272 TCTGCAACTTGGTCTTTTGAAGG 59.619 43.478 0.00 0.00 0.00 3.46
2497 2530 3.360867 TGCAACTTGGTCTTTTGAAGGA 58.639 40.909 0.00 0.00 0.00 3.36
2498 2531 3.766591 TGCAACTTGGTCTTTTGAAGGAA 59.233 39.130 0.00 0.00 0.00 3.36
2499 2532 4.405358 TGCAACTTGGTCTTTTGAAGGAAT 59.595 37.500 0.00 0.00 0.00 3.01
2500 2533 5.596361 TGCAACTTGGTCTTTTGAAGGAATA 59.404 36.000 0.00 0.00 0.00 1.75
2501 2534 6.097554 TGCAACTTGGTCTTTTGAAGGAATAA 59.902 34.615 0.00 0.00 0.00 1.40
2502 2535 6.983890 GCAACTTGGTCTTTTGAAGGAATAAA 59.016 34.615 0.00 0.00 0.00 1.40
2503 2536 7.657354 GCAACTTGGTCTTTTGAAGGAATAAAT 59.343 33.333 0.00 0.00 0.00 1.40
2504 2537 9.196552 CAACTTGGTCTTTTGAAGGAATAAATC 57.803 33.333 0.00 0.00 0.00 2.17
2505 2538 8.477419 ACTTGGTCTTTTGAAGGAATAAATCA 57.523 30.769 0.00 0.00 0.00 2.57
2506 2539 8.923270 ACTTGGTCTTTTGAAGGAATAAATCAA 58.077 29.630 0.00 0.00 0.00 2.57
2507 2540 9.762933 CTTGGTCTTTTGAAGGAATAAATCAAA 57.237 29.630 0.00 0.00 0.00 2.69
2509 2542 9.927668 TGGTCTTTTGAAGGAATAAATCAAATC 57.072 29.630 1.51 0.00 31.58 2.17
2515 2548 9.927668 TTTGAAGGAATAAATCAAATCTCCAAC 57.072 29.630 0.00 0.00 0.00 3.77
2516 2549 8.884124 TGAAGGAATAAATCAAATCTCCAACT 57.116 30.769 0.00 0.00 0.00 3.16
2517 2550 8.960591 TGAAGGAATAAATCAAATCTCCAACTC 58.039 33.333 0.00 0.00 0.00 3.01
2518 2551 7.888250 AGGAATAAATCAAATCTCCAACTCC 57.112 36.000 0.00 0.00 0.00 3.85
2519 2552 7.646884 AGGAATAAATCAAATCTCCAACTCCT 58.353 34.615 0.00 0.00 0.00 3.69
2520 2553 8.118600 AGGAATAAATCAAATCTCCAACTCCTT 58.881 33.333 0.00 0.00 0.00 3.36
2521 2554 8.193438 GGAATAAATCAAATCTCCAACTCCTTG 58.807 37.037 0.00 0.00 0.00 3.61
2522 2555 5.397142 AAATCAAATCTCCAACTCCTTGC 57.603 39.130 0.00 0.00 0.00 4.01
2523 2556 3.795688 TCAAATCTCCAACTCCTTGCT 57.204 42.857 0.00 0.00 0.00 3.91
2524 2557 4.104383 TCAAATCTCCAACTCCTTGCTT 57.896 40.909 0.00 0.00 0.00 3.91
2525 2558 3.822735 TCAAATCTCCAACTCCTTGCTTG 59.177 43.478 0.00 0.00 0.00 4.01
2526 2559 1.831580 ATCTCCAACTCCTTGCTTGC 58.168 50.000 0.00 0.00 0.00 4.01
2527 2560 0.473755 TCTCCAACTCCTTGCTTGCA 59.526 50.000 0.00 0.00 0.00 4.08
2528 2561 1.133823 TCTCCAACTCCTTGCTTGCAA 60.134 47.619 7.83 7.83 0.00 4.08
2529 2562 1.000938 CTCCAACTCCTTGCTTGCAAC 60.001 52.381 3.70 0.00 0.00 4.17
2530 2563 0.032540 CCAACTCCTTGCTTGCAACC 59.967 55.000 3.70 0.00 0.00 3.77
2531 2564 0.032540 CAACTCCTTGCTTGCAACCC 59.967 55.000 3.70 0.00 0.00 4.11
2532 2565 0.106015 AACTCCTTGCTTGCAACCCT 60.106 50.000 3.70 0.00 0.00 4.34
2533 2566 0.106015 ACTCCTTGCTTGCAACCCTT 60.106 50.000 3.70 0.00 0.00 3.95
2534 2567 0.316204 CTCCTTGCTTGCAACCCTTG 59.684 55.000 3.70 0.00 0.00 3.61
2535 2568 0.396974 TCCTTGCTTGCAACCCTTGT 60.397 50.000 3.70 0.00 0.00 3.16
2536 2569 0.465287 CCTTGCTTGCAACCCTTGTT 59.535 50.000 3.70 0.00 34.14 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.798725 CATTTTGTGCGCGCCTCTG 60.799 57.895 30.77 13.29 0.00 3.35
21 22 3.174573 GGCTCATTTTGTGCGCGC 61.175 61.111 27.26 27.26 39.44 6.86
22 23 2.082366 GTGGCTCATTTTGTGCGCG 61.082 57.895 0.00 0.00 39.44 6.86
28 29 1.788308 CGTTGCAAGTGGCTCATTTTG 59.212 47.619 0.00 0.00 45.15 2.44
29 30 1.869342 GCGTTGCAAGTGGCTCATTTT 60.869 47.619 0.00 0.00 45.15 1.82
30 31 0.318955 GCGTTGCAAGTGGCTCATTT 60.319 50.000 0.00 0.00 45.15 2.32
37 38 2.095969 TCTAAAATCGCGTTGCAAGTGG 60.096 45.455 5.77 0.00 0.00 4.00
144 145 3.202001 CCCCTTGCACGCGTATGG 61.202 66.667 13.44 9.33 0.00 2.74
145 146 1.705337 CTTCCCCTTGCACGCGTATG 61.705 60.000 13.44 0.60 0.00 2.39
150 151 0.321298 TAAGACTTCCCCTTGCACGC 60.321 55.000 0.00 0.00 0.00 5.34
201 204 7.742089 CAGTGACGAAGAATGAAATAGAAACAC 59.258 37.037 0.00 0.00 0.00 3.32
266 269 2.821437 TCCCTTAACTCTGCAGCTAGT 58.179 47.619 9.47 5.42 0.00 2.57
269 272 3.245052 ACATTTCCCTTAACTCTGCAGCT 60.245 43.478 9.47 0.00 0.00 4.24
311 314 2.102925 CACAAATCAGCCCCACAACTTT 59.897 45.455 0.00 0.00 0.00 2.66
443 446 6.145338 TCTAACTCCCGTGAATTCATCTAC 57.855 41.667 12.12 0.00 0.00 2.59
456 459 2.932614 CAAATGAGTGCTCTAACTCCCG 59.067 50.000 2.12 0.00 45.03 5.14
462 465 8.515695 AATGAATGATCAAATGAGTGCTCTAA 57.484 30.769 0.00 0.00 39.49 2.10
482 485 9.504708 AGCAAACCAAATAAATGAATGAATGAA 57.495 25.926 0.00 0.00 0.00 2.57
489 492 9.206870 CTGTAACAGCAAACCAAATAAATGAAT 57.793 29.630 0.00 0.00 0.00 2.57
547 550 4.521146 CTTGTGGTCTGATCTGCCTTAAT 58.479 43.478 12.04 0.00 0.00 1.40
561 564 7.509546 TCTCTATATGGAAAATCCTTGTGGTC 58.490 38.462 0.00 0.00 37.46 4.02
677 680 9.925268 GGCAAATCATTTCAATAAATCAATGAC 57.075 29.630 0.00 0.00 38.22 3.06
701 704 7.025963 GCTTTTGCTACATAGAATATGATGGC 58.974 38.462 3.87 5.50 43.35 4.40
775 778 9.710818 TGTATTTCTATATATAGACACCCCTCC 57.289 37.037 19.94 5.96 39.00 4.30
789 792 9.698309 GCATGCCGACTATATGTATTTCTATAT 57.302 33.333 6.36 0.00 0.00 0.86
790 793 8.691797 TGCATGCCGACTATATGTATTTCTATA 58.308 33.333 16.68 0.00 0.00 1.31
791 794 7.492669 GTGCATGCCGACTATATGTATTTCTAT 59.507 37.037 16.68 0.00 0.00 1.98
792 795 6.811665 GTGCATGCCGACTATATGTATTTCTA 59.188 38.462 16.68 0.00 0.00 2.10
793 796 5.639506 GTGCATGCCGACTATATGTATTTCT 59.360 40.000 16.68 0.00 0.00 2.52
794 797 5.163854 GGTGCATGCCGACTATATGTATTTC 60.164 44.000 16.68 0.00 0.00 2.17
795 798 4.695455 GGTGCATGCCGACTATATGTATTT 59.305 41.667 16.68 0.00 0.00 1.40
796 799 4.253685 GGTGCATGCCGACTATATGTATT 58.746 43.478 16.68 0.00 0.00 1.89
797 800 3.369471 GGGTGCATGCCGACTATATGTAT 60.369 47.826 16.68 0.00 0.00 2.29
798 801 2.028476 GGGTGCATGCCGACTATATGTA 60.028 50.000 16.68 0.00 0.00 2.29
799 802 1.270839 GGGTGCATGCCGACTATATGT 60.271 52.381 16.68 0.00 0.00 2.29
800 803 1.442769 GGGTGCATGCCGACTATATG 58.557 55.000 16.68 0.00 0.00 1.78
801 804 0.324943 GGGGTGCATGCCGACTATAT 59.675 55.000 16.68 0.00 0.00 0.86
802 805 1.051556 TGGGGTGCATGCCGACTATA 61.052 55.000 16.68 0.00 0.00 1.31
803 806 1.920734 TTGGGGTGCATGCCGACTAT 61.921 55.000 16.68 0.00 0.00 2.12
804 807 2.130821 TTTGGGGTGCATGCCGACTA 62.131 55.000 16.68 0.00 0.00 2.59
805 808 2.992817 TTTTGGGGTGCATGCCGACT 62.993 55.000 16.68 0.00 0.00 4.18
806 809 2.490993 CTTTTGGGGTGCATGCCGAC 62.491 60.000 16.68 7.49 0.00 4.79
807 810 2.203552 TTTTGGGGTGCATGCCGA 60.204 55.556 16.68 0.00 0.00 5.54
808 811 2.262292 CTTTTGGGGTGCATGCCG 59.738 61.111 16.68 0.00 0.00 5.69
809 812 1.257055 TAGCTTTTGGGGTGCATGCC 61.257 55.000 16.68 6.42 0.00 4.40
810 813 0.607620 TTAGCTTTTGGGGTGCATGC 59.392 50.000 11.82 11.82 0.00 4.06
811 814 2.932187 GCTTTAGCTTTTGGGGTGCATG 60.932 50.000 0.00 0.00 38.21 4.06
812 815 1.276138 GCTTTAGCTTTTGGGGTGCAT 59.724 47.619 0.00 0.00 38.21 3.96
813 816 0.678950 GCTTTAGCTTTTGGGGTGCA 59.321 50.000 0.00 0.00 38.21 4.57
814 817 0.678950 TGCTTTAGCTTTTGGGGTGC 59.321 50.000 0.00 0.00 42.66 5.01
815 818 1.963515 ACTGCTTTAGCTTTTGGGGTG 59.036 47.619 0.00 0.00 42.66 4.61
816 819 2.239400 GACTGCTTTAGCTTTTGGGGT 58.761 47.619 0.00 0.00 42.66 4.95
817 820 2.238521 TGACTGCTTTAGCTTTTGGGG 58.761 47.619 0.00 0.00 42.66 4.96
818 821 4.525912 AATGACTGCTTTAGCTTTTGGG 57.474 40.909 0.00 0.00 42.66 4.12
819 822 5.754890 ACAAAATGACTGCTTTAGCTTTTGG 59.245 36.000 20.54 9.98 42.66 3.28
826 829 8.752766 AATGAATGACAAAATGACTGCTTTAG 57.247 30.769 0.00 0.00 0.00 1.85
829 832 9.715121 AATAAATGAATGACAAAATGACTGCTT 57.285 25.926 0.00 0.00 0.00 3.91
899 902 7.750655 TCAGATCTCCATACTAGTCACATAGT 58.249 38.462 0.00 0.00 39.35 2.12
900 903 8.100164 TCTCAGATCTCCATACTAGTCACATAG 58.900 40.741 0.00 0.00 0.00 2.23
901 904 7.978925 TCTCAGATCTCCATACTAGTCACATA 58.021 38.462 0.00 0.00 0.00 2.29
905 908 6.101881 TCCTTCTCAGATCTCCATACTAGTCA 59.898 42.308 0.00 0.00 0.00 3.41
911 914 7.734942 AGAAAATCCTTCTCAGATCTCCATAC 58.265 38.462 0.00 0.00 0.00 2.39
916 919 6.762661 CCAAGAGAAAATCCTTCTCAGATCTC 59.237 42.308 15.00 0.00 45.48 2.75
921 924 5.184711 CCTCCAAGAGAAAATCCTTCTCAG 58.815 45.833 15.00 8.10 45.48 3.35
925 928 4.308526 ACCCTCCAAGAGAAAATCCTTC 57.691 45.455 0.00 0.00 0.00 3.46
1005 1037 7.362662 ACATAGCTACAAATGTTGAAACACTG 58.637 34.615 0.00 2.26 42.51 3.66
1053 1085 1.279271 GCAACAAGGAGGCTAGAGGAA 59.721 52.381 0.00 0.00 0.00 3.36
1099 1131 3.282885 TGTTGGTCTTGTTACATGTGCA 58.717 40.909 9.11 4.65 0.00 4.57
1107 1139 1.671845 GCGGTGTTGTTGGTCTTGTTA 59.328 47.619 0.00 0.00 0.00 2.41
1144 1176 1.539827 GCTTTGTGGCTTGACGGTAAT 59.460 47.619 0.00 0.00 0.00 1.89
1151 1183 0.112995 ATGGGAGCTTTGTGGCTTGA 59.887 50.000 0.00 0.00 43.20 3.02
1209 1241 1.142314 GGCGGTGTTAGTGGCGATA 59.858 57.895 0.00 0.00 0.00 2.92
1286 1318 1.081094 GCAGATGGCAATTGCAAACC 58.919 50.000 30.32 16.16 44.36 3.27
1338 1370 6.509677 CGAAGTATAAGTCGGCAAAAATCTCC 60.510 42.308 0.00 0.00 33.62 3.71
1346 1378 5.063180 TCTTTCGAAGTATAAGTCGGCAA 57.937 39.130 0.00 1.23 37.84 4.52
1381 1413 6.416455 GCAAATGAAACAACGTTCAATGTAGA 59.584 34.615 0.00 0.00 40.76 2.59
1382 1414 6.198029 TGCAAATGAAACAACGTTCAATGTAG 59.802 34.615 0.00 0.00 40.76 2.74
1386 1418 6.420588 CATTGCAAATGAAACAACGTTCAAT 58.579 32.000 1.71 0.00 40.76 2.57
1391 1423 3.129871 CCCATTGCAAATGAAACAACGT 58.870 40.909 1.71 0.00 0.00 3.99
1464 1496 3.808174 TCTCACGATCTATGTAGGACACG 59.192 47.826 0.00 0.00 0.00 4.49
1508 1540 5.221843 ACAAGTAGGTTTATGAGGTTGCTGA 60.222 40.000 0.00 0.00 0.00 4.26
1550 1582 2.487805 GGCATACATGAGGCAGGAATGA 60.488 50.000 0.00 0.00 36.23 2.57
1559 1591 7.514784 TTGAAATCAATAGGCATACATGAGG 57.485 36.000 0.00 0.00 0.00 3.86
1591 1623 6.511767 GCCATAACATTTTCAGATACAGTCGG 60.512 42.308 0.00 0.00 0.00 4.79
1603 1635 3.115554 GCATGACCGCCATAACATTTTC 58.884 45.455 0.00 0.00 33.31 2.29
1616 1648 6.073369 CGATAACTCATAAATTGCATGACCG 58.927 40.000 0.00 0.00 0.00 4.79
1730 1762 5.325239 AGTTTAGGATCCCAGGAAAAACAG 58.675 41.667 8.55 0.00 0.00 3.16
1832 1865 7.120138 GGTTACTTCCCATTCATTCTTTTACGA 59.880 37.037 0.00 0.00 0.00 3.43
1840 1873 5.253330 TCACAGGTTACTTCCCATTCATTC 58.747 41.667 0.00 0.00 0.00 2.67
1860 1893 2.712057 CCATGTTTGGCTTCACTCAC 57.288 50.000 0.00 0.00 35.85 3.51
1872 1905 5.193099 AGGGAAATGCTACTACCATGTTT 57.807 39.130 0.00 0.00 0.00 2.83
1880 1913 2.106511 GCATGGGAGGGAAATGCTACTA 59.893 50.000 0.00 0.00 42.70 1.82
1887 1920 1.075748 GGCTGCATGGGAGGGAAAT 60.076 57.895 0.50 0.00 0.00 2.17
1959 1992 9.125026 ACCATAGTATTAGCTCCATTCAAAAAG 57.875 33.333 0.00 0.00 0.00 2.27
1983 2016 6.595716 TGCTCTGCTTCTTTTTCTTATCTACC 59.404 38.462 0.00 0.00 0.00 3.18
1997 2030 2.297129 GGAGGGGTGCTCTGCTTCT 61.297 63.158 0.00 0.00 0.00 2.85
2000 2033 2.285969 ATGGAGGGGTGCTCTGCT 60.286 61.111 0.00 0.00 0.00 4.24
2078 2111 9.485206 TTCCATAACTCTTTACACTTTGTAGTC 57.515 33.333 0.00 0.00 33.92 2.59
2079 2112 9.490379 CTTCCATAACTCTTTACACTTTGTAGT 57.510 33.333 0.00 0.00 33.92 2.73
2097 2130 3.523157 TGAGGGTTGAGATGCTTCCATAA 59.477 43.478 0.00 0.00 0.00 1.90
2155 2188 3.123273 ACCTAGGCTTGTACCCATTGAT 58.877 45.455 9.30 0.00 0.00 2.57
2173 2206 6.229733 GCTCTCAATTATGCAATCTCTACCT 58.770 40.000 0.00 0.00 0.00 3.08
2177 2210 4.063689 CCGCTCTCAATTATGCAATCTCT 58.936 43.478 0.00 0.00 0.00 3.10
2191 2224 3.118000 TCTCTCTATAACCACCGCTCTCA 60.118 47.826 0.00 0.00 0.00 3.27
2207 2240 7.392766 TCTATCTCTTCCTCTGATTCTCTCT 57.607 40.000 0.00 0.00 0.00 3.10
2280 2313 2.286477 CGACATGGTGACTACTCTAGCG 60.286 54.545 0.00 0.00 0.00 4.26
2297 2330 0.320683 CACCCTTGACATGCTCGACA 60.321 55.000 0.00 0.00 0.00 4.35
2306 2339 4.947147 GTGGCCGCACCCTTGACA 62.947 66.667 12.58 0.00 37.83 3.58
2345 2378 4.681978 GGAGGCGCCGTTGACACT 62.682 66.667 23.20 0.00 0.00 3.55
2357 2390 4.636249 CAATATGTTACAGAGGAGGAGGC 58.364 47.826 0.00 0.00 0.00 4.70
2364 2397 6.682423 TGAACATGCAATATGTTACAGAGG 57.318 37.500 4.21 0.00 41.76 3.69
2365 2398 7.482743 GTGTTGAACATGCAATATGTTACAGAG 59.517 37.037 0.00 0.00 41.76 3.35
2366 2399 7.304735 GTGTTGAACATGCAATATGTTACAGA 58.695 34.615 0.00 0.00 41.76 3.41
2367 2400 6.527722 GGTGTTGAACATGCAATATGTTACAG 59.472 38.462 0.00 0.00 41.76 2.74
2368 2401 6.385843 GGTGTTGAACATGCAATATGTTACA 58.614 36.000 0.00 4.12 41.76 2.41
2369 2402 5.804979 GGGTGTTGAACATGCAATATGTTAC 59.195 40.000 0.00 1.73 41.76 2.50
2370 2403 5.714333 AGGGTGTTGAACATGCAATATGTTA 59.286 36.000 0.00 0.00 41.76 2.41
2371 2404 4.527816 AGGGTGTTGAACATGCAATATGTT 59.472 37.500 0.00 3.87 44.08 2.71
2372 2405 4.088634 AGGGTGTTGAACATGCAATATGT 58.911 39.130 0.00 0.00 0.00 2.29
2373 2406 4.440525 GGAGGGTGTTGAACATGCAATATG 60.441 45.833 0.00 0.00 0.00 1.78
2374 2407 3.701040 GGAGGGTGTTGAACATGCAATAT 59.299 43.478 0.00 0.00 0.00 1.28
2375 2408 3.088532 GGAGGGTGTTGAACATGCAATA 58.911 45.455 0.00 0.00 0.00 1.90
2376 2409 1.895131 GGAGGGTGTTGAACATGCAAT 59.105 47.619 0.00 0.00 0.00 3.56
2377 2410 1.327303 GGAGGGTGTTGAACATGCAA 58.673 50.000 0.00 0.00 0.00 4.08
2378 2411 0.539438 GGGAGGGTGTTGAACATGCA 60.539 55.000 0.00 0.00 0.00 3.96
2379 2412 0.251341 AGGGAGGGTGTTGAACATGC 60.251 55.000 0.00 0.00 0.00 4.06
2380 2413 2.292828 AAGGGAGGGTGTTGAACATG 57.707 50.000 0.00 0.00 0.00 3.21
2381 2414 4.292306 AGATTAAGGGAGGGTGTTGAACAT 59.708 41.667 0.00 0.00 0.00 2.71
2382 2415 3.655777 AGATTAAGGGAGGGTGTTGAACA 59.344 43.478 0.00 0.00 0.00 3.18
2383 2416 4.010349 CAGATTAAGGGAGGGTGTTGAAC 58.990 47.826 0.00 0.00 0.00 3.18
2384 2417 3.913799 TCAGATTAAGGGAGGGTGTTGAA 59.086 43.478 0.00 0.00 0.00 2.69
2385 2418 3.526899 TCAGATTAAGGGAGGGTGTTGA 58.473 45.455 0.00 0.00 0.00 3.18
2386 2419 4.010349 GTTCAGATTAAGGGAGGGTGTTG 58.990 47.826 0.00 0.00 0.00 3.33
2387 2420 3.916989 AGTTCAGATTAAGGGAGGGTGTT 59.083 43.478 0.00 0.00 0.00 3.32
2388 2421 3.532102 AGTTCAGATTAAGGGAGGGTGT 58.468 45.455 0.00 0.00 0.00 4.16
2389 2422 4.226168 AGAAGTTCAGATTAAGGGAGGGTG 59.774 45.833 5.50 0.00 0.00 4.61
2390 2423 4.439860 AGAAGTTCAGATTAAGGGAGGGT 58.560 43.478 5.50 0.00 0.00 4.34
2391 2424 4.471386 TGAGAAGTTCAGATTAAGGGAGGG 59.529 45.833 5.50 0.00 0.00 4.30
2392 2425 5.683876 TGAGAAGTTCAGATTAAGGGAGG 57.316 43.478 5.50 0.00 0.00 4.30
2404 2437 6.688578 ACGTAATCTTAAGCTGAGAAGTTCA 58.311 36.000 5.50 0.00 0.00 3.18
2405 2438 7.583860 AACGTAATCTTAAGCTGAGAAGTTC 57.416 36.000 0.00 0.00 0.00 3.01
2406 2439 7.656137 TCAAACGTAATCTTAAGCTGAGAAGTT 59.344 33.333 0.00 6.26 0.00 2.66
2407 2440 7.152645 TCAAACGTAATCTTAAGCTGAGAAGT 58.847 34.615 0.00 1.41 0.00 3.01
2408 2441 7.582435 TCAAACGTAATCTTAAGCTGAGAAG 57.418 36.000 0.00 1.20 0.00 2.85
2409 2442 7.656137 AGTTCAAACGTAATCTTAAGCTGAGAA 59.344 33.333 0.00 0.00 0.00 2.87
2410 2443 7.152645 AGTTCAAACGTAATCTTAAGCTGAGA 58.847 34.615 0.00 2.84 0.00 3.27
2411 2444 7.329717 AGAGTTCAAACGTAATCTTAAGCTGAG 59.670 37.037 0.00 0.00 0.00 3.35
2412 2445 7.152645 AGAGTTCAAACGTAATCTTAAGCTGA 58.847 34.615 0.00 0.00 0.00 4.26
2413 2446 7.352719 AGAGTTCAAACGTAATCTTAAGCTG 57.647 36.000 0.00 0.00 0.00 4.24
2414 2447 7.656137 TGAAGAGTTCAAACGTAATCTTAAGCT 59.344 33.333 0.00 0.00 36.59 3.74
2415 2448 7.793902 TGAAGAGTTCAAACGTAATCTTAAGC 58.206 34.615 0.00 0.00 36.59 3.09
2430 2463 6.017109 GGCTACAAGACAATTTGAAGAGTTCA 60.017 38.462 2.79 0.00 38.04 3.18
2431 2464 6.017109 TGGCTACAAGACAATTTGAAGAGTTC 60.017 38.462 2.79 0.00 23.92 3.01
2432 2465 5.827797 TGGCTACAAGACAATTTGAAGAGTT 59.172 36.000 2.79 0.00 23.92 3.01
2433 2466 5.376625 TGGCTACAAGACAATTTGAAGAGT 58.623 37.500 2.79 0.00 23.92 3.24
2434 2467 5.947228 TGGCTACAAGACAATTTGAAGAG 57.053 39.130 2.79 0.00 23.92 2.85
2448 2481 2.961531 TACAAAGGCCTTGGCTACAA 57.038 45.000 21.33 0.00 39.56 2.41
2449 2482 2.888414 GTTTACAAAGGCCTTGGCTACA 59.112 45.455 21.33 1.63 39.56 2.74
2450 2483 2.230508 GGTTTACAAAGGCCTTGGCTAC 59.769 50.000 21.33 14.26 39.56 3.58
2451 2484 2.521126 GGTTTACAAAGGCCTTGGCTA 58.479 47.619 21.33 8.37 39.56 3.93
2452 2485 1.338107 GGTTTACAAAGGCCTTGGCT 58.662 50.000 21.33 9.43 39.56 4.75
2453 2486 0.320374 GGGTTTACAAAGGCCTTGGC 59.680 55.000 21.33 2.31 39.56 4.52
2454 2487 1.710816 TGGGTTTACAAAGGCCTTGG 58.289 50.000 21.33 20.11 39.56 3.61
2455 2488 3.056607 CAGATGGGTTTACAAAGGCCTTG 60.057 47.826 21.33 15.57 41.19 3.61
2456 2489 3.165071 CAGATGGGTTTACAAAGGCCTT 58.835 45.455 13.78 13.78 0.00 4.35
2457 2490 2.807676 CAGATGGGTTTACAAAGGCCT 58.192 47.619 0.00 0.00 0.00 5.19
2458 2491 1.204704 GCAGATGGGTTTACAAAGGCC 59.795 52.381 0.00 0.00 0.00 5.19
2459 2492 1.892474 TGCAGATGGGTTTACAAAGGC 59.108 47.619 0.00 0.00 0.00 4.35
2460 2493 3.573967 AGTTGCAGATGGGTTTACAAAGG 59.426 43.478 0.00 0.00 0.00 3.11
2461 2494 4.853924 AGTTGCAGATGGGTTTACAAAG 57.146 40.909 0.00 0.00 0.00 2.77
2462 2495 4.202202 CCAAGTTGCAGATGGGTTTACAAA 60.202 41.667 0.00 0.00 0.00 2.83
2463 2496 3.320541 CCAAGTTGCAGATGGGTTTACAA 59.679 43.478 0.00 0.00 0.00 2.41
2464 2497 2.890311 CCAAGTTGCAGATGGGTTTACA 59.110 45.455 0.00 0.00 0.00 2.41
2465 2498 2.890945 ACCAAGTTGCAGATGGGTTTAC 59.109 45.455 16.07 0.00 38.58 2.01
2466 2499 3.153919 GACCAAGTTGCAGATGGGTTTA 58.846 45.455 16.07 0.00 38.58 2.01
2467 2500 1.963515 GACCAAGTTGCAGATGGGTTT 59.036 47.619 16.07 0.00 38.58 3.27
2468 2501 1.145738 AGACCAAGTTGCAGATGGGTT 59.854 47.619 16.07 4.16 38.58 4.11
2469 2502 0.773644 AGACCAAGTTGCAGATGGGT 59.226 50.000 16.07 8.83 38.58 4.51
2470 2503 1.915141 AAGACCAAGTTGCAGATGGG 58.085 50.000 16.07 5.90 38.58 4.00
2471 2504 3.318839 TCAAAAGACCAAGTTGCAGATGG 59.681 43.478 11.64 11.64 40.16 3.51
2472 2505 4.572985 TCAAAAGACCAAGTTGCAGATG 57.427 40.909 0.00 0.00 0.00 2.90
2473 2506 4.038402 CCTTCAAAAGACCAAGTTGCAGAT 59.962 41.667 0.00 0.00 0.00 2.90
2474 2507 3.381272 CCTTCAAAAGACCAAGTTGCAGA 59.619 43.478 0.00 0.00 0.00 4.26
2475 2508 3.381272 TCCTTCAAAAGACCAAGTTGCAG 59.619 43.478 0.00 0.00 0.00 4.41
2476 2509 3.360867 TCCTTCAAAAGACCAAGTTGCA 58.639 40.909 0.00 0.00 0.00 4.08
2477 2510 4.385358 TTCCTTCAAAAGACCAAGTTGC 57.615 40.909 0.00 0.00 0.00 4.17
2478 2511 9.196552 GATTTATTCCTTCAAAAGACCAAGTTG 57.803 33.333 0.00 0.00 0.00 3.16
2479 2512 8.923270 TGATTTATTCCTTCAAAAGACCAAGTT 58.077 29.630 0.00 0.00 0.00 2.66
2480 2513 8.477419 TGATTTATTCCTTCAAAAGACCAAGT 57.523 30.769 0.00 0.00 0.00 3.16
2481 2514 9.762933 TTTGATTTATTCCTTCAAAAGACCAAG 57.237 29.630 0.00 0.00 36.66 3.61
2483 2516 9.927668 GATTTGATTTATTCCTTCAAAAGACCA 57.072 29.630 1.92 0.00 41.26 4.02
2489 2522 9.927668 GTTGGAGATTTGATTTATTCCTTCAAA 57.072 29.630 0.00 0.00 41.90 2.69
2490 2523 9.312904 AGTTGGAGATTTGATTTATTCCTTCAA 57.687 29.630 0.00 0.00 0.00 2.69
2491 2524 8.884124 AGTTGGAGATTTGATTTATTCCTTCA 57.116 30.769 0.00 0.00 0.00 3.02
2492 2525 8.409371 GGAGTTGGAGATTTGATTTATTCCTTC 58.591 37.037 0.00 0.00 0.00 3.46
2493 2526 8.118600 AGGAGTTGGAGATTTGATTTATTCCTT 58.881 33.333 0.00 0.00 0.00 3.36
2494 2527 7.646884 AGGAGTTGGAGATTTGATTTATTCCT 58.353 34.615 0.00 0.00 0.00 3.36
2495 2528 7.888250 AGGAGTTGGAGATTTGATTTATTCC 57.112 36.000 0.00 0.00 0.00 3.01
2496 2529 7.704047 GCAAGGAGTTGGAGATTTGATTTATTC 59.296 37.037 0.00 0.00 33.87 1.75
2497 2530 7.398332 AGCAAGGAGTTGGAGATTTGATTTATT 59.602 33.333 0.00 0.00 33.87 1.40
2498 2531 6.894103 AGCAAGGAGTTGGAGATTTGATTTAT 59.106 34.615 0.00 0.00 33.87 1.40
2499 2532 6.248433 AGCAAGGAGTTGGAGATTTGATTTA 58.752 36.000 0.00 0.00 33.87 1.40
2500 2533 5.082425 AGCAAGGAGTTGGAGATTTGATTT 58.918 37.500 0.00 0.00 33.87 2.17
2501 2534 4.670765 AGCAAGGAGTTGGAGATTTGATT 58.329 39.130 0.00 0.00 33.87 2.57
2502 2535 4.313020 AGCAAGGAGTTGGAGATTTGAT 57.687 40.909 0.00 0.00 33.87 2.57
2503 2536 3.795688 AGCAAGGAGTTGGAGATTTGA 57.204 42.857 0.00 0.00 33.87 2.69
2504 2537 3.613432 GCAAGCAAGGAGTTGGAGATTTG 60.613 47.826 0.00 0.00 33.87 2.32
2505 2538 2.560105 GCAAGCAAGGAGTTGGAGATTT 59.440 45.455 0.00 0.00 33.87 2.17
2506 2539 2.165998 GCAAGCAAGGAGTTGGAGATT 58.834 47.619 0.00 0.00 33.87 2.40
2507 2540 1.074405 TGCAAGCAAGGAGTTGGAGAT 59.926 47.619 0.00 0.00 33.87 2.75
2508 2541 0.473755 TGCAAGCAAGGAGTTGGAGA 59.526 50.000 0.00 0.00 33.87 3.71
2509 2542 1.000938 GTTGCAAGCAAGGAGTTGGAG 60.001 52.381 7.88 0.00 36.52 3.86
2510 2543 1.032014 GTTGCAAGCAAGGAGTTGGA 58.968 50.000 7.88 0.00 36.52 3.53
2511 2544 0.032540 GGTTGCAAGCAAGGAGTTGG 59.967 55.000 23.18 0.00 36.52 3.77
2512 2545 0.032540 GGGTTGCAAGCAAGGAGTTG 59.967 55.000 28.22 0.00 36.52 3.16
2513 2546 0.106015 AGGGTTGCAAGCAAGGAGTT 60.106 50.000 28.22 3.63 36.52 3.01
2514 2547 0.106015 AAGGGTTGCAAGCAAGGAGT 60.106 50.000 28.22 5.23 36.52 3.85
2515 2548 0.316204 CAAGGGTTGCAAGCAAGGAG 59.684 55.000 28.22 10.51 36.52 3.69
2516 2549 0.396974 ACAAGGGTTGCAAGCAAGGA 60.397 50.000 28.22 0.00 36.52 3.36
2517 2550 0.465287 AACAAGGGTTGCAAGCAAGG 59.535 50.000 28.22 18.36 36.52 3.61
2518 2551 1.574134 CAACAAGGGTTGCAAGCAAG 58.426 50.000 28.22 18.96 46.98 4.01
2519 2552 3.756739 CAACAAGGGTTGCAAGCAA 57.243 47.368 28.22 2.89 46.98 3.91


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

AutoCloner maintained by Alex Coulton.