Multiple sequence alignment - TraesCS1D01G218400

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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 TraesCS1D01G218400 chr1D 100.000 5941 0 0 1 5941 305222951 305228891 0.000000e+00 10972
1 TraesCS1D01G218400 chr1D 92.258 155 11 1 3344 3498 7349856 7349703 1.000000e-52 219
2 TraesCS1D01G218400 chr1A 96.970 2178 56 7 1840 4008 382247994 382250170 0.000000e+00 3648
3 TraesCS1D01G218400 chr1A 93.795 1934 62 18 4037 5941 382250166 382252070 0.000000e+00 2854
4 TraesCS1D01G218400 chr1A 94.877 976 29 9 707 1667 382247032 382248001 0.000000e+00 1506
5 TraesCS1D01G218400 chr1A 93.253 667 37 6 1 660 382246193 382246858 0.000000e+00 976
6 TraesCS1D01G218400 chr1A 91.756 279 19 4 1 277 382245667 382245943 9.340000e-103 385
7 TraesCS1D01G218400 chr1A 89.286 168 17 1 3341 3508 361357410 361357576 6.030000e-50 209
8 TraesCS1D01G218400 chr1B 95.185 1890 51 10 4080 5941 412245984 412244107 0.000000e+00 2950
9 TraesCS1D01G218400 chr1B 95.696 1580 34 14 1842 3415 412247548 412245997 0.000000e+00 2510
10 TraesCS1D01G218400 chr1B 95.756 966 27 8 707 1667 412248499 412247543 0.000000e+00 1544
11 TraesCS1D01G218400 chr1B 92.354 667 38 9 1 660 412249334 412248674 0.000000e+00 937
12 TraesCS1D01G218400 chr3D 100.000 173 0 0 1668 1840 551629576 551629748 2.670000e-83 320
13 TraesCS1D01G218400 chr3D 98.256 172 3 0 1668 1839 4973369 4973540 9.680000e-78 302
14 TraesCS1D01G218400 chr3D 91.250 160 13 1 3345 3503 288550611 288550452 3.610000e-52 217
15 TraesCS1D01G218400 chr7D 97.093 172 5 0 1668 1839 25036263 25036434 2.090000e-74 291
16 TraesCS1D01G218400 chr7D 92.308 156 12 0 3342 3497 375400761 375400916 7.750000e-54 222
17 TraesCS1D01G218400 chr7A 95.930 172 7 0 1668 1839 650404010 650403839 4.530000e-71 279
18 TraesCS1D01G218400 chr7A 91.463 164 9 4 3336 3497 421784998 421785158 2.790000e-53 220
19 TraesCS1D01G218400 chr6B 95.376 173 7 1 1668 1839 642913092 642913264 2.110000e-69 274
20 TraesCS1D01G218400 chr6B 95.808 167 7 0 1673 1839 113328033 113328199 2.730000e-68 270
21 TraesCS1D01G218400 chr6B 94.186 172 8 2 1668 1839 473090542 473090373 1.640000e-65 261
22 TraesCS1D01G218400 chr4B 94.828 174 9 0 1667 1840 343725962 343726135 7.590000e-69 272
23 TraesCS1D01G218400 chr4B 91.848 184 14 1 1665 1848 666754175 666753993 7.640000e-64 255
24 TraesCS1D01G218400 chr2A 92.453 159 11 1 3341 3498 79316000 79316158 5.990000e-55 226
25 TraesCS1D01G218400 chr2D 91.824 159 12 1 3341 3498 79056162 79056320 2.790000e-53 220
26 TraesCS1D01G218400 chr7B 90.798 163 14 1 3336 3498 369872711 369872872 3.610000e-52 217


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 TraesCS1D01G218400 chr1D 305222951 305228891 5940 False 10972.00 10972 100.00000 1 5941 1 chr1D.!!$F1 5940
1 TraesCS1D01G218400 chr1A 382245667 382252070 6403 False 1873.80 3648 94.13020 1 5941 5 chr1A.!!$F2 5940
2 TraesCS1D01G218400 chr1B 412244107 412249334 5227 True 1985.25 2950 94.74775 1 5941 4 chr1B.!!$R1 5940

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
23 24 0.243365 TGGCAATGTTTAGGCAAGCG 59.757 50.0 0.00 0.00 37.37 4.68 F
539 1070 0.602638 CCGTGAAGCCAGCTTGTGTA 60.603 55.0 10.13 0.00 36.26 2.90 F
1265 1938 0.511653 GCGTTTCGAGGGTTTGAGAC 59.488 55.0 0.00 0.00 0.00 3.36 F
1711 2389 0.039035 AAAATAGCGTGGCCCCTGAA 59.961 50.0 0.00 0.00 0.00 3.02 F
1712 2390 0.039035 AAATAGCGTGGCCCCTGAAA 59.961 50.0 0.00 0.00 0.00 2.69 F
1751 2429 0.039437 TAGCGTGCTATTAGCGAGGC 60.039 55.0 17.41 17.41 46.26 4.70 F
3700 4389 0.385390 GCAACCCCAAAGGATATGCG 59.615 55.0 0.00 0.00 39.89 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1870 0.026933 CTGTAACACACGCACGCAAA 59.973 50.000 0.00 0.0 0.00 3.68 R
1692 2370 0.039035 TTCAGGGGCCACGCTATTTT 59.961 50.000 4.39 0.0 37.87 1.82 R
2228 2906 2.229062 ACGAGTTGCGAGAAGAAGATGA 59.771 45.455 0.00 0.0 44.57 2.92 R
3478 4166 0.037975 GTACTCCCTCCGTTCGCAAA 60.038 55.000 0.00 0.0 0.00 3.68 R
3482 4170 1.401199 GAGAAGTACTCCCTCCGTTCG 59.599 57.143 12.00 0.0 39.53 3.95 R
3715 4404 0.473755 TTTGGACTGCCTCAGCTTCA 59.526 50.000 0.00 0.0 40.80 3.02 R
5036 5745 1.266718 GAAACGAATCCTTGTGCTGCA 59.733 47.619 0.00 0.0 0.00 4.41 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
23 24 0.243365 TGGCAATGTTTAGGCAAGCG 59.757 50.000 0.00 0.00 37.37 4.68
92 621 8.168058 AGCCTTAGAAAACTTACCAATTTCCTA 58.832 33.333 0.00 0.00 34.39 2.94
125 654 4.100479 CCAAGAGTTGGCATGCCA 57.900 55.556 35.59 35.59 45.17 4.92
162 691 3.047857 TGGCATTCATGGAGATGGTCTA 58.952 45.455 0.00 0.00 0.00 2.59
166 695 6.012245 TGGCATTCATGGAGATGGTCTATAAT 60.012 38.462 0.00 0.00 0.00 1.28
193 722 3.432186 CGCCCTCTTGATTATGTCCTTCA 60.432 47.826 0.00 0.00 0.00 3.02
286 816 4.282195 TGTTCCAAAATACGCCAAGGATTT 59.718 37.500 0.00 0.00 45.00 2.17
461 991 2.102252 GTCATCTTAGAGCTCCACCCTG 59.898 54.545 10.93 3.49 0.00 4.45
500 1031 6.150809 GTCGAGTAAGTAGAAAAGAAGAGGGA 59.849 42.308 0.00 0.00 0.00 4.20
506 1037 6.608539 AGTAGAAAAGAAGAGGGAGTAACC 57.391 41.667 0.00 0.00 38.08 2.85
531 1062 3.414700 GTGACGCCGTGAAGCCAG 61.415 66.667 0.00 0.00 0.00 4.85
539 1070 0.602638 CCGTGAAGCCAGCTTGTGTA 60.603 55.000 10.13 0.00 36.26 2.90
545 1076 4.455877 GTGAAGCCAGCTTGTGTAACTAAT 59.544 41.667 10.13 0.00 38.04 1.73
672 1297 3.910627 AGACTTCTTGTTGTCTACCCCAT 59.089 43.478 0.00 0.00 41.19 4.00
785 1452 8.800370 ATTTTCTCTAGGGATTTCTCTTGAAC 57.200 34.615 0.00 0.00 31.02 3.18
847 1515 5.221283 GGTTTTATTTTGGAACGAGAACCCA 60.221 40.000 0.00 0.00 0.00 4.51
928 1596 2.202866 TGGGATCTTCCACTCGCTC 58.797 57.895 0.00 0.00 38.64 5.03
1202 1870 2.280592 GTGGACCAGGTTCGCGTT 60.281 61.111 5.77 0.00 0.00 4.84
1203 1871 1.890510 GTGGACCAGGTTCGCGTTT 60.891 57.895 5.77 0.00 0.00 3.60
1264 1937 0.942410 CGCGTTTCGAGGGTTTGAGA 60.942 55.000 0.00 0.00 41.67 3.27
1265 1938 0.511653 GCGTTTCGAGGGTTTGAGAC 59.488 55.000 0.00 0.00 0.00 3.36
1266 1939 1.860676 CGTTTCGAGGGTTTGAGACA 58.139 50.000 0.00 0.00 0.00 3.41
1417 2093 3.630148 CGCCGCTTCGCATGGTAG 61.630 66.667 0.00 0.00 0.00 3.18
1613 2291 4.020573 TGACACTAGGTGATCGGTTTGATT 60.021 41.667 4.62 0.00 37.47 2.57
1628 2306 4.976116 GGTTTGATTTTCACTTTCCAGTCG 59.024 41.667 0.00 0.00 0.00 4.18
1667 2345 2.932167 GTTTCTGACGACTTCTGTGC 57.068 50.000 0.00 0.00 0.00 4.57
1668 2346 2.201732 GTTTCTGACGACTTCTGTGCA 58.798 47.619 0.00 0.00 0.00 4.57
1669 2347 2.595124 TTCTGACGACTTCTGTGCAA 57.405 45.000 0.00 0.00 0.00 4.08
1670 2348 2.820059 TCTGACGACTTCTGTGCAAT 57.180 45.000 0.00 0.00 0.00 3.56
1671 2349 2.407090 TCTGACGACTTCTGTGCAATG 58.593 47.619 0.00 0.00 0.00 2.82
1672 2350 2.035832 TCTGACGACTTCTGTGCAATGA 59.964 45.455 0.00 0.00 0.00 2.57
1673 2351 2.802247 CTGACGACTTCTGTGCAATGAA 59.198 45.455 0.00 0.00 0.00 2.57
1674 2352 3.202097 TGACGACTTCTGTGCAATGAAA 58.798 40.909 0.00 0.00 0.00 2.69
1675 2353 3.625313 TGACGACTTCTGTGCAATGAAAA 59.375 39.130 0.00 0.00 0.00 2.29
1676 2354 4.095632 TGACGACTTCTGTGCAATGAAAAA 59.904 37.500 0.00 0.00 0.00 1.94
1695 2373 4.413495 AAAAATAGCGCGCTACAGAAAA 57.587 36.364 40.42 21.55 0.00 2.29
1696 2374 4.616181 AAAATAGCGCGCTACAGAAAAT 57.384 36.364 40.42 22.89 0.00 1.82
1697 2375 5.728351 AAAATAGCGCGCTACAGAAAATA 57.272 34.783 40.42 19.94 0.00 1.40
1698 2376 4.974103 AATAGCGCGCTACAGAAAATAG 57.026 40.909 40.42 0.00 0.00 1.73
1699 2377 0.931005 AGCGCGCTACAGAAAATAGC 59.069 50.000 35.79 0.00 41.43 2.97
1704 2382 2.739293 GCTACAGAAAATAGCGTGGC 57.261 50.000 0.00 0.00 36.02 5.01
1705 2383 1.330829 GCTACAGAAAATAGCGTGGCC 59.669 52.381 0.00 0.00 36.02 5.36
1706 2384 1.940613 CTACAGAAAATAGCGTGGCCC 59.059 52.381 0.00 0.00 0.00 5.80
1707 2385 0.679960 ACAGAAAATAGCGTGGCCCC 60.680 55.000 0.00 0.00 0.00 5.80
1708 2386 0.394352 CAGAAAATAGCGTGGCCCCT 60.394 55.000 0.00 0.00 0.00 4.79
1709 2387 0.394352 AGAAAATAGCGTGGCCCCTG 60.394 55.000 0.00 0.00 0.00 4.45
1710 2388 0.393808 GAAAATAGCGTGGCCCCTGA 60.394 55.000 0.00 0.00 0.00 3.86
1711 2389 0.039035 AAAATAGCGTGGCCCCTGAA 59.961 50.000 0.00 0.00 0.00 3.02
1712 2390 0.039035 AAATAGCGTGGCCCCTGAAA 59.961 50.000 0.00 0.00 0.00 2.69
1713 2391 0.039035 AATAGCGTGGCCCCTGAAAA 59.961 50.000 0.00 0.00 0.00 2.29
1714 2392 0.258774 ATAGCGTGGCCCCTGAAAAT 59.741 50.000 0.00 0.00 0.00 1.82
1715 2393 0.913205 TAGCGTGGCCCCTGAAAATA 59.087 50.000 0.00 0.00 0.00 1.40
1716 2394 0.258774 AGCGTGGCCCCTGAAAATAT 59.741 50.000 0.00 0.00 0.00 1.28
1717 2395 0.385390 GCGTGGCCCCTGAAAATATG 59.615 55.000 0.00 0.00 0.00 1.78
1718 2396 0.385390 CGTGGCCCCTGAAAATATGC 59.615 55.000 0.00 0.00 0.00 3.14
1719 2397 1.780503 GTGGCCCCTGAAAATATGCT 58.219 50.000 0.00 0.00 0.00 3.79
1720 2398 2.748132 CGTGGCCCCTGAAAATATGCTA 60.748 50.000 0.00 0.00 0.00 3.49
1721 2399 3.500343 GTGGCCCCTGAAAATATGCTAT 58.500 45.455 0.00 0.00 0.00 2.97
1722 2400 3.897505 GTGGCCCCTGAAAATATGCTATT 59.102 43.478 0.00 0.00 0.00 1.73
1723 2401 5.076873 GTGGCCCCTGAAAATATGCTATTA 58.923 41.667 0.00 0.00 0.00 0.98
1724 2402 5.183904 GTGGCCCCTGAAAATATGCTATTAG 59.816 44.000 0.00 0.00 0.00 1.73
1725 2403 4.158579 GGCCCCTGAAAATATGCTATTAGC 59.841 45.833 8.80 8.80 42.82 3.09
1726 2404 4.142600 GCCCCTGAAAATATGCTATTAGCG 60.143 45.833 10.94 0.00 46.26 4.26
1727 2405 5.003804 CCCCTGAAAATATGCTATTAGCGT 58.996 41.667 14.53 14.53 46.26 5.07
1728 2406 5.106555 CCCCTGAAAATATGCTATTAGCGTG 60.107 44.000 18.61 2.19 46.26 5.34
1729 2407 5.385617 CCTGAAAATATGCTATTAGCGTGC 58.614 41.667 18.61 5.49 46.26 5.34
1730 2408 5.180117 CCTGAAAATATGCTATTAGCGTGCT 59.820 40.000 18.61 0.00 46.26 4.40
1731 2409 6.368791 CCTGAAAATATGCTATTAGCGTGCTA 59.631 38.462 18.61 0.00 46.26 3.49
1732 2410 7.065085 CCTGAAAATATGCTATTAGCGTGCTAT 59.935 37.037 18.61 5.81 46.26 2.97
1733 2411 8.996024 TGAAAATATGCTATTAGCGTGCTATA 57.004 30.769 18.61 7.66 46.26 1.31
1734 2412 9.087424 TGAAAATATGCTATTAGCGTGCTATAG 57.913 33.333 18.61 7.85 46.26 1.31
1735 2413 7.470289 AAATATGCTATTAGCGTGCTATAGC 57.530 36.000 18.18 18.18 46.26 2.97
1736 2414 2.863739 TGCTATTAGCGTGCTATAGCG 58.136 47.619 19.55 7.69 46.26 4.26
1737 2415 2.228103 TGCTATTAGCGTGCTATAGCGT 59.772 45.455 19.55 7.04 46.26 5.07
1738 2416 2.594654 GCTATTAGCGTGCTATAGCGTG 59.405 50.000 19.55 14.81 45.83 5.34
1739 2417 1.419374 ATTAGCGTGCTATAGCGTGC 58.581 50.000 25.35 25.35 45.83 5.34
1740 2418 2.808315 AGCGTGCTATAGCGTGCT 59.192 55.556 28.16 28.16 45.20 4.40
1741 2419 4.628160 GCGTGCTATAGCGTGCTA 57.372 55.556 25.40 3.73 45.83 3.49
1742 2420 3.108521 GCGTGCTATAGCGTGCTAT 57.891 52.632 25.40 17.65 45.83 2.97
1743 2421 1.419374 GCGTGCTATAGCGTGCTATT 58.581 50.000 25.40 4.72 45.83 1.73
1744 2422 2.592194 GCGTGCTATAGCGTGCTATTA 58.408 47.619 25.40 3.80 45.83 0.98
1745 2423 2.594654 GCGTGCTATAGCGTGCTATTAG 59.405 50.000 25.40 14.04 45.83 1.73
1746 2424 2.594654 CGTGCTATAGCGTGCTATTAGC 59.405 50.000 18.62 21.07 45.83 3.09
1747 2425 2.594654 GTGCTATAGCGTGCTATTAGCG 59.405 50.000 18.62 7.48 44.30 4.26
1748 2426 2.486592 TGCTATAGCGTGCTATTAGCGA 59.513 45.455 18.62 12.37 44.30 4.93
1749 2427 3.102276 GCTATAGCGTGCTATTAGCGAG 58.898 50.000 18.62 11.00 46.26 5.03
1750 2428 2.638556 ATAGCGTGCTATTAGCGAGG 57.361 50.000 8.54 7.17 46.26 4.63
1751 2429 0.039437 TAGCGTGCTATTAGCGAGGC 60.039 55.000 17.41 17.41 46.26 4.70
1752 2430 1.591594 GCGTGCTATTAGCGAGGCA 60.592 57.895 18.94 0.00 46.26 4.75
1753 2431 0.946221 GCGTGCTATTAGCGAGGCAT 60.946 55.000 18.94 0.00 46.26 4.40
1754 2432 1.502231 CGTGCTATTAGCGAGGCATT 58.498 50.000 10.94 0.00 46.26 3.56
1755 2433 1.193203 CGTGCTATTAGCGAGGCATTG 59.807 52.381 10.94 0.00 46.26 2.82
1756 2434 2.213499 GTGCTATTAGCGAGGCATTGT 58.787 47.619 10.94 0.00 46.26 2.71
1757 2435 3.390135 GTGCTATTAGCGAGGCATTGTA 58.610 45.455 10.94 0.00 46.26 2.41
1758 2436 3.184581 GTGCTATTAGCGAGGCATTGTAC 59.815 47.826 10.94 0.00 46.26 2.90
1759 2437 3.181470 TGCTATTAGCGAGGCATTGTACA 60.181 43.478 10.94 0.00 46.26 2.90
1760 2438 3.997021 GCTATTAGCGAGGCATTGTACAT 59.003 43.478 0.00 0.00 0.00 2.29
1761 2439 4.452455 GCTATTAGCGAGGCATTGTACATT 59.548 41.667 0.00 0.00 0.00 2.71
1762 2440 4.818534 ATTAGCGAGGCATTGTACATTG 57.181 40.909 12.41 12.41 0.00 2.82
1763 2441 2.401583 AGCGAGGCATTGTACATTGA 57.598 45.000 19.36 0.00 0.00 2.57
1764 2442 2.923121 AGCGAGGCATTGTACATTGAT 58.077 42.857 19.36 8.37 0.00 2.57
1765 2443 3.282021 AGCGAGGCATTGTACATTGATT 58.718 40.909 19.36 7.76 0.00 2.57
1766 2444 3.696051 AGCGAGGCATTGTACATTGATTT 59.304 39.130 19.36 5.61 0.00 2.17
1767 2445 4.881273 AGCGAGGCATTGTACATTGATTTA 59.119 37.500 19.36 0.00 0.00 1.40
1768 2446 5.532406 AGCGAGGCATTGTACATTGATTTAT 59.468 36.000 19.36 0.00 0.00 1.40
1769 2447 6.039717 AGCGAGGCATTGTACATTGATTTATT 59.960 34.615 19.36 0.67 0.00 1.40
1770 2448 6.697019 GCGAGGCATTGTACATTGATTTATTT 59.303 34.615 19.36 0.00 0.00 1.40
1771 2449 7.860373 GCGAGGCATTGTACATTGATTTATTTA 59.140 33.333 19.36 0.00 0.00 1.40
1772 2450 9.385902 CGAGGCATTGTACATTGATTTATTTAG 57.614 33.333 19.36 0.09 0.00 1.85
1773 2451 9.185192 GAGGCATTGTACATTGATTTATTTAGC 57.815 33.333 19.36 2.30 0.00 3.09
1774 2452 7.862372 AGGCATTGTACATTGATTTATTTAGCG 59.138 33.333 19.36 0.00 0.00 4.26
1775 2453 7.860373 GGCATTGTACATTGATTTATTTAGCGA 59.140 33.333 19.36 0.00 0.00 4.93
1776 2454 8.895845 GCATTGTACATTGATTTATTTAGCGAG 58.104 33.333 19.36 0.00 0.00 5.03
1779 2457 8.710835 TGTACATTGATTTATTTAGCGAGACA 57.289 30.769 0.00 0.00 0.00 3.41
1780 2458 9.157104 TGTACATTGATTTATTTAGCGAGACAA 57.843 29.630 0.00 0.00 0.00 3.18
1783 2461 9.722056 ACATTGATTTATTTAGCGAGACAATTC 57.278 29.630 0.00 0.00 0.00 2.17
1784 2462 9.941664 CATTGATTTATTTAGCGAGACAATTCT 57.058 29.630 0.00 0.00 33.37 2.40
1786 2464 8.948631 TGATTTATTTAGCGAGACAATTCTCT 57.051 30.769 0.46 0.00 45.61 3.10
1792 2470 7.875316 TTTAGCGAGACAATTCTCTATATGC 57.125 36.000 0.46 0.00 45.61 3.14
1793 2471 5.720371 AGCGAGACAATTCTCTATATGCT 57.280 39.130 0.46 0.00 45.61 3.79
1794 2472 6.825944 AGCGAGACAATTCTCTATATGCTA 57.174 37.500 0.46 0.00 45.61 3.49
1795 2473 7.403312 AGCGAGACAATTCTCTATATGCTAT 57.597 36.000 0.46 0.00 45.61 2.97
1796 2474 8.512966 AGCGAGACAATTCTCTATATGCTATA 57.487 34.615 0.46 0.00 45.61 1.31
1797 2475 8.620416 AGCGAGACAATTCTCTATATGCTATAG 58.380 37.037 0.00 0.00 45.61 1.31
1798 2476 7.378461 GCGAGACAATTCTCTATATGCTATAGC 59.622 40.741 18.18 18.18 45.61 2.97
1799 2477 7.585936 CGAGACAATTCTCTATATGCTATAGCG 59.414 40.741 19.55 5.29 45.61 4.26
1800 2478 8.287439 AGACAATTCTCTATATGCTATAGCGT 57.713 34.615 22.53 22.53 45.83 5.07
1801 2479 8.187480 AGACAATTCTCTATATGCTATAGCGTG 58.813 37.037 26.43 12.19 45.83 5.34
1802 2480 6.754209 ACAATTCTCTATATGCTATAGCGTGC 59.246 38.462 26.43 2.18 45.83 5.34
1803 2481 6.707440 ATTCTCTATATGCTATAGCGTGCT 57.293 37.500 26.43 16.66 45.83 4.40
1804 2482 7.809546 ATTCTCTATATGCTATAGCGTGCTA 57.190 36.000 26.43 16.86 45.83 3.49
1805 2483 7.809546 TTCTCTATATGCTATAGCGTGCTAT 57.190 36.000 26.43 17.65 45.83 2.97
1806 2484 7.809546 TCTCTATATGCTATAGCGTGCTATT 57.190 36.000 26.43 10.41 45.83 1.73
1807 2485 8.904099 TCTCTATATGCTATAGCGTGCTATTA 57.096 34.615 26.43 8.34 45.83 0.98
1808 2486 8.994170 TCTCTATATGCTATAGCGTGCTATTAG 58.006 37.037 26.43 17.73 45.83 1.73
1809 2487 7.585867 TCTATATGCTATAGCGTGCTATTAGC 58.414 38.462 26.43 21.07 45.83 3.09
1810 2488 2.863739 TGCTATAGCGTGCTATTAGCG 58.136 47.619 18.62 7.48 44.30 4.26
1811 2489 2.186076 GCTATAGCGTGCTATTAGCGG 58.814 52.381 18.62 6.68 46.26 5.52
1812 2490 2.186076 CTATAGCGTGCTATTAGCGGC 58.814 52.381 18.62 18.55 46.26 6.53
1813 2491 0.732880 ATAGCGTGCTATTAGCGGCG 60.733 55.000 20.72 20.72 46.26 6.46
1815 2493 2.658593 CGTGCTATTAGCGGCGCT 60.659 61.111 37.84 37.84 46.26 5.92
1816 2494 1.371267 CGTGCTATTAGCGGCGCTA 60.371 57.895 35.39 35.39 46.26 4.26
1817 2495 0.732880 CGTGCTATTAGCGGCGCTAT 60.733 55.000 38.35 28.53 46.26 2.97
1818 2496 1.466866 CGTGCTATTAGCGGCGCTATA 60.467 52.381 38.35 28.19 46.26 1.31
1819 2497 2.186076 GTGCTATTAGCGGCGCTATAG 58.814 52.381 38.35 34.01 46.26 1.31
1820 2498 1.201343 GCTATTAGCGGCGCTATAGC 58.799 55.000 37.08 37.08 41.01 2.97
1963 2641 4.036262 TCTGTTGATTTGTGTTGTACCAGC 59.964 41.667 0.00 0.00 0.00 4.85
1995 2673 7.601856 CATTTGAACTGCTTTGGTAAGGATTA 58.398 34.615 0.00 0.00 30.84 1.75
2002 2680 6.318900 ACTGCTTTGGTAAGGATTATTACAGC 59.681 38.462 0.00 0.00 37.38 4.40
2138 2816 2.876079 GCTGTCTTTTGGAGTAGGGGTG 60.876 54.545 0.00 0.00 0.00 4.61
2445 3127 5.523552 GCACTAAATAATGCCCCAAATCAAC 59.476 40.000 0.00 0.00 35.73 3.18
2630 3312 7.148474 GGTTTATATACACCGATAATGCCACTG 60.148 40.741 2.32 0.00 0.00 3.66
2822 3504 6.985059 GCCTCACCCTTTACATACTTACTTAG 59.015 42.308 0.00 0.00 0.00 2.18
2871 3554 6.835174 AGATGCTGATTAAAGATCCTAAGCA 58.165 36.000 0.00 0.00 42.97 3.91
2907 3590 8.402472 TCTTTCTTTTGCGTTTGATTCTTTCTA 58.598 29.630 0.00 0.00 0.00 2.10
2922 3610 8.212995 TGATTCTTTCTAATCATGAGTGCCATA 58.787 33.333 5.80 0.00 40.17 2.74
3077 3765 0.407139 AAAGGCAGAGGTGGATGCTT 59.593 50.000 0.00 0.00 42.19 3.91
3216 3904 6.690194 AAGTTTTGCATTGCCATTTGTTAA 57.310 29.167 6.12 0.00 0.00 2.01
3313 4001 2.834638 ACCATCCCATTTCTTCCTGG 57.165 50.000 0.00 0.00 0.00 4.45
3490 4178 2.869801 TGGCTTATATTTGCGAACGGAG 59.130 45.455 0.00 0.00 0.00 4.63
3569 4258 5.046591 ACTCCAGTGCAGCTGTTTAAGTATA 60.047 40.000 16.64 0.00 43.55 1.47
3700 4389 0.385390 GCAACCCCAAAGGATATGCG 59.615 55.000 0.00 0.00 39.89 4.73
3715 4404 2.380084 ATGCGTACGTGGAGTTTCAT 57.620 45.000 17.90 6.04 0.00 2.57
3722 4411 2.146342 ACGTGGAGTTTCATGAAGCTG 58.854 47.619 27.02 15.68 31.89 4.24
3725 4414 2.746362 GTGGAGTTTCATGAAGCTGAGG 59.254 50.000 27.02 0.00 31.89 3.86
3744 4433 1.538047 GCAGTCCAAAATGCTCTCCA 58.462 50.000 0.00 0.00 39.38 3.86
3854 4543 3.813529 AACATTTACTTGCGTGCTCTC 57.186 42.857 0.00 0.00 0.00 3.20
3900 4589 4.851639 ACTAATGTTCCAGGAATGAGCT 57.148 40.909 4.80 0.00 0.00 4.09
4006 4695 7.517614 TTGCACTTAGATGTGGAAACATTAA 57.482 32.000 0.00 0.00 43.38 1.40
4007 4696 7.144722 TGCACTTAGATGTGGAAACATTAAG 57.855 36.000 13.34 13.34 46.14 1.85
4008 4697 6.939730 TGCACTTAGATGTGGAAACATTAAGA 59.060 34.615 17.70 4.16 46.14 2.10
4009 4698 7.446931 TGCACTTAGATGTGGAAACATTAAGAA 59.553 33.333 17.70 8.15 46.14 2.52
4010 4699 8.296713 GCACTTAGATGTGGAAACATTAAGAAA 58.703 33.333 17.70 2.59 46.14 2.52
4051 4740 4.083271 GGTTGGACTTAAGTCAGCATGTTC 60.083 45.833 31.30 15.30 46.47 3.18
4058 4747 6.245408 ACTTAAGTCAGCATGTTCCCAATTA 58.755 36.000 1.12 0.00 37.40 1.40
4307 4999 3.893813 GGAGGCCATTCTTCTAATGCATT 59.106 43.478 17.56 17.56 0.00 3.56
4379 5071 3.676093 CCTCTTTTCCTGAGGTTACCAC 58.324 50.000 3.51 0.00 44.42 4.16
4414 5106 2.615912 GGCCCAAGATGAGAGAAATTCG 59.384 50.000 0.00 0.00 0.00 3.34
4526 5218 1.675310 CTGATTCTGCCGGGTTGCA 60.675 57.895 2.18 0.00 39.37 4.08
4607 5299 2.612972 CCCTGAAAAGCTGCGACTTCTA 60.613 50.000 11.00 0.99 0.00 2.10
4781 5478 4.036734 TGAGTCAGAATTGTTGGCAAAGTC 59.963 41.667 0.00 0.00 38.21 3.01
4800 5497 2.161808 GTCGTGTACTCTGCTTGCTCTA 59.838 50.000 0.00 0.00 0.00 2.43
4809 5506 4.020751 ACTCTGCTTGCTCTAATGAGTTCA 60.021 41.667 0.00 0.00 42.13 3.18
4923 5629 1.339631 CCGATGGACTGGTTGCCTTTA 60.340 52.381 0.00 0.00 0.00 1.85
4924 5630 2.432444 CGATGGACTGGTTGCCTTTAA 58.568 47.619 0.00 0.00 0.00 1.52
4995 5702 5.409520 TCAAATTTGATCTGTCGAGTCCTTG 59.590 40.000 16.91 0.00 31.01 3.61
5028 5737 2.485835 GGTGTAGGGTGTGTAGTTGCAA 60.486 50.000 0.00 0.00 0.00 4.08
5036 5745 4.277423 GGGTGTGTAGTTGCAAGTTTACAT 59.723 41.667 12.95 0.00 0.00 2.29
5048 5757 2.862541 AGTTTACATGCAGCACAAGGA 58.137 42.857 0.00 0.00 0.00 3.36
5066 5775 4.559862 AGGATTCGTTTCTTCCATGAGT 57.440 40.909 0.00 0.00 31.65 3.41
5342 6079 6.701841 TGAGAAGAACAAATATCGTATCCAGC 59.298 38.462 0.00 0.00 0.00 4.85
5380 6117 1.000506 CAGCTTGCAACTTTCATGCCT 59.999 47.619 0.00 0.00 43.16 4.75
5450 6187 1.169661 TGTGGCGCCTTTTGATTCGT 61.170 50.000 29.70 0.00 0.00 3.85
5459 6197 4.495844 CGCCTTTTGATTCGTAGGAATTCC 60.496 45.833 17.31 17.31 42.86 3.01
5460 6198 4.398044 GCCTTTTGATTCGTAGGAATTCCA 59.602 41.667 26.22 9.69 42.86 3.53
5461 6199 5.067805 GCCTTTTGATTCGTAGGAATTCCAT 59.932 40.000 26.22 10.51 42.86 3.41
5462 6200 6.262273 GCCTTTTGATTCGTAGGAATTCCATA 59.738 38.462 26.22 12.52 42.86 2.74
5463 6201 7.520614 GCCTTTTGATTCGTAGGAATTCCATAG 60.521 40.741 26.22 15.57 42.86 2.23
5464 6202 7.041098 CCTTTTGATTCGTAGGAATTCCATAGG 60.041 40.741 26.22 18.36 42.86 2.57
5465 6203 6.740944 TTGATTCGTAGGAATTCCATAGGA 57.259 37.500 26.22 20.00 42.86 2.94
5466 6204 6.740944 TGATTCGTAGGAATTCCATAGGAA 57.259 37.500 26.22 25.33 46.39 3.36
5521 6259 1.064758 TGTGAAACTCAACAGTGCCCT 60.065 47.619 0.00 0.00 38.04 5.19
5604 6342 3.305964 CTGCAGCAACTGTGAAATTCAG 58.694 45.455 0.00 0.00 38.68 3.02
5651 6389 3.372025 GGGCCATCCATAACAAACTCTCT 60.372 47.826 4.39 0.00 35.00 3.10
5898 6636 4.284490 ACAGCCATATCCTACACCTACATG 59.716 45.833 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
125 654 2.181125 TGCCATGATCATGCTTGGTTT 58.819 42.857 27.24 0.00 37.49 3.27
162 691 6.886459 ACATAATCAAGAGGGCGCAATATTAT 59.114 34.615 10.83 5.74 0.00 1.28
166 695 4.065088 GACATAATCAAGAGGGCGCAATA 58.935 43.478 10.83 0.00 0.00 1.90
193 722 6.957631 TCACTAACATGGACCATAAAGTGAT 58.042 36.000 26.59 9.68 34.36 3.06
240 769 4.336889 TTCAGACGGAGAAACTGACAAT 57.663 40.909 0.00 0.00 39.80 2.71
241 770 3.812156 TTCAGACGGAGAAACTGACAA 57.188 42.857 0.00 0.00 39.80 3.18
255 784 4.857037 GGCGTATTTTGGAACATTTCAGAC 59.143 41.667 0.00 0.00 39.30 3.51
258 787 4.855715 TGGCGTATTTTGGAACATTTCA 57.144 36.364 0.00 0.00 39.30 2.69
286 816 1.438469 CCATATGCAAGGAGGAGGGA 58.562 55.000 0.00 0.00 0.00 4.20
461 991 5.634020 ACTTACTCGACAAATGTCAGTTAGC 59.366 40.000 19.81 0.00 44.99 3.09
506 1037 3.467226 ACGGCGTCACCCCTATGG 61.467 66.667 6.77 0.00 41.37 2.74
531 1062 1.737793 AGGCGCATTAGTTACACAAGC 59.262 47.619 10.83 0.00 0.00 4.01
584 1118 5.487488 ACAACTCCAACATATACCTCCTTCA 59.513 40.000 0.00 0.00 0.00 3.02
594 1128 6.294176 GCTTTCTTGTGACAACTCCAACATAT 60.294 38.462 0.00 0.00 0.00 1.78
595 1129 5.008613 GCTTTCTTGTGACAACTCCAACATA 59.991 40.000 0.00 0.00 0.00 2.29
807 1474 2.327325 AACCCTAGAGGAAGCACTGA 57.673 50.000 0.00 0.00 39.89 3.41
816 1483 5.941647 TCGTTCCAAAATAAAACCCTAGAGG 59.058 40.000 0.00 0.00 43.78 3.69
847 1515 2.993863 ACCCACCCTAGAAAATGGAAGT 59.006 45.455 0.00 0.00 33.80 3.01
928 1596 2.296471 ACTTGTACACTTCAGACGGGAG 59.704 50.000 0.00 0.00 0.00 4.30
1202 1870 0.026933 CTGTAACACACGCACGCAAA 59.973 50.000 0.00 0.00 0.00 3.68
1203 1871 1.639000 CTGTAACACACGCACGCAA 59.361 52.632 0.00 0.00 0.00 4.85
1417 2093 0.109226 GTGGTGGCGACTAGACAGAC 60.109 60.000 0.00 0.00 39.56 3.51
1613 2291 2.833794 CCTGTCGACTGGAAAGTGAAA 58.166 47.619 31.52 0.00 37.15 2.69
1628 2306 2.231721 ACGAAGAAACTAGGAGCCTGTC 59.768 50.000 0.00 0.00 0.00 3.51
1674 2352 4.413495 TTTTCTGTAGCGCGCTATTTTT 57.587 36.364 39.99 18.75 0.00 1.94
1675 2353 4.616181 ATTTTCTGTAGCGCGCTATTTT 57.384 36.364 39.99 19.54 0.00 1.82
1676 2354 4.318831 GCTATTTTCTGTAGCGCGCTATTT 60.319 41.667 39.99 19.95 35.68 1.40
1677 2355 3.184581 GCTATTTTCTGTAGCGCGCTATT 59.815 43.478 39.99 20.35 35.68 1.73
1678 2356 2.731976 GCTATTTTCTGTAGCGCGCTAT 59.268 45.455 39.99 26.62 35.68 2.97
1679 2357 2.124903 GCTATTTTCTGTAGCGCGCTA 58.875 47.619 35.48 35.48 35.68 4.26
1680 2358 0.931005 GCTATTTTCTGTAGCGCGCT 59.069 50.000 38.01 38.01 35.68 5.92
1681 2359 3.422646 GCTATTTTCTGTAGCGCGC 57.577 52.632 26.66 26.66 35.68 6.86
1685 2363 1.330829 GGCCACGCTATTTTCTGTAGC 59.669 52.381 0.00 0.00 40.83 3.58
1686 2364 1.940613 GGGCCACGCTATTTTCTGTAG 59.059 52.381 4.39 0.00 0.00 2.74
1687 2365 1.407712 GGGGCCACGCTATTTTCTGTA 60.408 52.381 4.39 0.00 0.00 2.74
1688 2366 0.679960 GGGGCCACGCTATTTTCTGT 60.680 55.000 4.39 0.00 0.00 3.41
1689 2367 0.394352 AGGGGCCACGCTATTTTCTG 60.394 55.000 4.39 0.00 38.23 3.02
1690 2368 0.394352 CAGGGGCCACGCTATTTTCT 60.394 55.000 4.39 0.00 37.87 2.52
1691 2369 0.393808 TCAGGGGCCACGCTATTTTC 60.394 55.000 4.39 0.00 37.87 2.29
1692 2370 0.039035 TTCAGGGGCCACGCTATTTT 59.961 50.000 4.39 0.00 37.87 1.82
1693 2371 0.039035 TTTCAGGGGCCACGCTATTT 59.961 50.000 4.39 0.00 37.87 1.40
1694 2372 0.039035 TTTTCAGGGGCCACGCTATT 59.961 50.000 4.39 0.00 37.87 1.73
1695 2373 0.258774 ATTTTCAGGGGCCACGCTAT 59.741 50.000 4.39 0.00 37.87 2.97
1696 2374 0.913205 TATTTTCAGGGGCCACGCTA 59.087 50.000 4.39 0.00 37.87 4.26
1697 2375 0.258774 ATATTTTCAGGGGCCACGCT 59.741 50.000 4.39 0.00 41.05 5.07
1698 2376 0.385390 CATATTTTCAGGGGCCACGC 59.615 55.000 4.39 0.00 0.00 5.34
1699 2377 0.385390 GCATATTTTCAGGGGCCACG 59.615 55.000 4.39 0.00 0.00 4.94
1700 2378 1.780503 AGCATATTTTCAGGGGCCAC 58.219 50.000 4.39 0.00 0.00 5.01
1701 2379 3.901570 ATAGCATATTTTCAGGGGCCA 57.098 42.857 4.39 0.00 0.00 5.36
1702 2380 4.158579 GCTAATAGCATATTTTCAGGGGCC 59.841 45.833 7.49 0.00 41.89 5.80
1703 2381 4.142600 CGCTAATAGCATATTTTCAGGGGC 60.143 45.833 13.15 0.00 42.58 5.80
1704 2382 5.003804 ACGCTAATAGCATATTTTCAGGGG 58.996 41.667 13.15 0.00 42.58 4.79
1705 2383 5.617751 GCACGCTAATAGCATATTTTCAGGG 60.618 44.000 13.15 0.00 42.58 4.45
1706 2384 5.180117 AGCACGCTAATAGCATATTTTCAGG 59.820 40.000 13.15 0.00 42.58 3.86
1707 2385 6.233430 AGCACGCTAATAGCATATTTTCAG 57.767 37.500 13.15 0.00 42.58 3.02
1708 2386 7.905604 ATAGCACGCTAATAGCATATTTTCA 57.094 32.000 13.15 0.00 42.58 2.69
1709 2387 8.058915 GCTATAGCACGCTAATAGCATATTTTC 58.941 37.037 20.01 0.00 40.38 2.29
1710 2388 7.254117 CGCTATAGCACGCTAATAGCATATTTT 60.254 37.037 23.99 0.00 40.58 1.82
1711 2389 6.199154 CGCTATAGCACGCTAATAGCATATTT 59.801 38.462 23.99 0.00 40.58 1.40
1712 2390 5.687730 CGCTATAGCACGCTAATAGCATATT 59.312 40.000 23.99 0.00 40.58 1.28
1713 2391 5.215903 CGCTATAGCACGCTAATAGCATAT 58.784 41.667 23.99 7.17 40.58 1.78
1714 2392 4.095932 ACGCTATAGCACGCTAATAGCATA 59.904 41.667 23.99 1.56 40.58 3.14
1715 2393 3.119459 ACGCTATAGCACGCTAATAGCAT 60.119 43.478 23.99 15.58 40.58 3.79
1716 2394 2.228103 ACGCTATAGCACGCTAATAGCA 59.772 45.455 23.99 0.00 40.58 3.49
1717 2395 2.594654 CACGCTATAGCACGCTAATAGC 59.405 50.000 23.99 19.62 42.21 2.97
1718 2396 2.594654 GCACGCTATAGCACGCTAATAG 59.405 50.000 23.99 7.18 42.21 1.73
1719 2397 2.228103 AGCACGCTATAGCACGCTAATA 59.772 45.455 27.72 0.00 43.56 0.98
1720 2398 1.000163 AGCACGCTATAGCACGCTAAT 60.000 47.619 27.72 11.41 43.56 1.73
1721 2399 0.384309 AGCACGCTATAGCACGCTAA 59.616 50.000 27.72 0.00 43.56 3.09
1722 2400 1.232119 TAGCACGCTATAGCACGCTA 58.768 50.000 28.42 28.42 43.56 4.26
1723 2401 0.598562 ATAGCACGCTATAGCACGCT 59.401 50.000 30.02 30.02 45.99 5.07
1724 2402 1.419374 AATAGCACGCTATAGCACGC 58.581 50.000 23.99 22.83 42.21 5.34
1725 2403 2.594654 GCTAATAGCACGCTATAGCACG 59.405 50.000 23.99 14.72 41.89 5.34
1726 2404 2.594654 CGCTAATAGCACGCTATAGCAC 59.405 50.000 23.99 12.65 42.58 4.40
1727 2405 2.486592 TCGCTAATAGCACGCTATAGCA 59.513 45.455 23.99 4.83 42.58 3.49
1728 2406 3.102276 CTCGCTAATAGCACGCTATAGC 58.898 50.000 15.09 15.09 42.58 2.97
1729 2407 3.686128 CCTCGCTAATAGCACGCTATAG 58.314 50.000 13.15 10.32 42.58 1.31
1730 2408 2.159421 GCCTCGCTAATAGCACGCTATA 60.159 50.000 13.15 1.16 42.58 1.31
1731 2409 1.402984 GCCTCGCTAATAGCACGCTAT 60.403 52.381 13.15 5.72 42.58 2.97
1732 2410 0.039437 GCCTCGCTAATAGCACGCTA 60.039 55.000 13.15 0.39 42.58 4.26
1733 2411 1.300233 GCCTCGCTAATAGCACGCT 60.300 57.895 13.15 0.00 42.58 5.07
1734 2412 0.946221 ATGCCTCGCTAATAGCACGC 60.946 55.000 13.15 10.17 42.58 5.34
1735 2413 1.193203 CAATGCCTCGCTAATAGCACG 59.807 52.381 13.15 2.14 42.58 5.34
1736 2414 2.213499 ACAATGCCTCGCTAATAGCAC 58.787 47.619 13.15 0.00 42.58 4.40
1737 2415 2.620251 ACAATGCCTCGCTAATAGCA 57.380 45.000 13.15 0.00 42.58 3.49
1738 2416 3.390135 TGTACAATGCCTCGCTAATAGC 58.610 45.455 1.41 1.41 38.02 2.97
1739 2417 5.696270 TCAATGTACAATGCCTCGCTAATAG 59.304 40.000 6.02 0.00 0.00 1.73
1740 2418 5.606505 TCAATGTACAATGCCTCGCTAATA 58.393 37.500 6.02 0.00 0.00 0.98
1741 2419 4.450976 TCAATGTACAATGCCTCGCTAAT 58.549 39.130 6.02 0.00 0.00 1.73
1742 2420 3.867857 TCAATGTACAATGCCTCGCTAA 58.132 40.909 6.02 0.00 0.00 3.09
1743 2421 3.535280 TCAATGTACAATGCCTCGCTA 57.465 42.857 6.02 0.00 0.00 4.26
1744 2422 2.401583 TCAATGTACAATGCCTCGCT 57.598 45.000 6.02 0.00 0.00 4.93
1745 2423 3.698029 AATCAATGTACAATGCCTCGC 57.302 42.857 6.02 0.00 0.00 5.03
1746 2424 9.385902 CTAAATAAATCAATGTACAATGCCTCG 57.614 33.333 6.02 0.00 0.00 4.63
1747 2425 9.185192 GCTAAATAAATCAATGTACAATGCCTC 57.815 33.333 6.02 0.00 0.00 4.70
1748 2426 7.862372 CGCTAAATAAATCAATGTACAATGCCT 59.138 33.333 6.02 0.00 0.00 4.75
1749 2427 7.860373 TCGCTAAATAAATCAATGTACAATGCC 59.140 33.333 6.02 0.00 0.00 4.40
1750 2428 8.781067 TCGCTAAATAAATCAATGTACAATGC 57.219 30.769 6.02 0.00 0.00 3.56
1753 2431 9.157104 TGTCTCGCTAAATAAATCAATGTACAA 57.843 29.630 0.00 0.00 0.00 2.41
1754 2432 8.710835 TGTCTCGCTAAATAAATCAATGTACA 57.289 30.769 0.00 0.00 0.00 2.90
1757 2435 9.722056 GAATTGTCTCGCTAAATAAATCAATGT 57.278 29.630 0.00 0.00 0.00 2.71
1758 2436 9.941664 AGAATTGTCTCGCTAAATAAATCAATG 57.058 29.630 0.00 0.00 0.00 2.82
1772 2450 7.378461 GCTATAGCATATAGAGAATTGTCTCGC 59.622 40.741 20.01 8.03 46.73 5.03
1773 2451 8.781067 GCTATAGCATATAGAGAATTGTCTCG 57.219 38.462 20.01 0.00 46.73 4.04
1774 2452 8.402472 ACGCTATAGCATATAGAGAATTGTCTC 58.598 37.037 23.99 0.00 45.16 3.36
1775 2453 8.187480 CACGCTATAGCATATAGAGAATTGTCT 58.813 37.037 23.99 10.33 42.21 3.41
1776 2454 7.043722 GCACGCTATAGCATATAGAGAATTGTC 60.044 40.741 23.99 0.00 42.21 3.18
1777 2455 6.754209 GCACGCTATAGCATATAGAGAATTGT 59.246 38.462 23.99 6.41 42.21 2.71
1778 2456 6.977502 AGCACGCTATAGCATATAGAGAATTG 59.022 38.462 23.99 5.79 42.21 2.32
1779 2457 7.106439 AGCACGCTATAGCATATAGAGAATT 57.894 36.000 23.99 0.00 42.21 2.17
1780 2458 6.707440 AGCACGCTATAGCATATAGAGAAT 57.293 37.500 23.99 0.00 42.21 2.40
1781 2459 7.809546 ATAGCACGCTATAGCATATAGAGAA 57.190 36.000 23.99 1.16 42.21 2.87
1782 2460 7.809546 AATAGCACGCTATAGCATATAGAGA 57.190 36.000 23.99 2.22 42.21 3.10
1783 2461 7.748683 GCTAATAGCACGCTATAGCATATAGAG 59.251 40.741 23.99 15.18 41.89 2.43
1784 2462 7.571428 CGCTAATAGCACGCTATAGCATATAGA 60.571 40.741 23.99 5.24 42.58 1.98
1785 2463 6.521477 CGCTAATAGCACGCTATAGCATATAG 59.479 42.308 23.99 14.95 42.58 1.31
1786 2464 6.371389 CGCTAATAGCACGCTATAGCATATA 58.629 40.000 23.99 11.13 42.58 0.86
1787 2465 5.215903 CGCTAATAGCACGCTATAGCATAT 58.784 41.667 23.99 12.75 42.58 1.78
1788 2466 4.497507 CCGCTAATAGCACGCTATAGCATA 60.498 45.833 23.99 11.14 42.58 3.14
1789 2467 3.439293 CGCTAATAGCACGCTATAGCAT 58.561 45.455 23.99 6.50 42.58 3.79
1790 2468 2.415491 CCGCTAATAGCACGCTATAGCA 60.415 50.000 23.99 4.83 42.58 3.49
1791 2469 2.186076 CCGCTAATAGCACGCTATAGC 58.814 52.381 15.09 15.09 42.58 2.97
1792 2470 2.186076 GCCGCTAATAGCACGCTATAG 58.814 52.381 13.15 10.32 42.58 1.31
1793 2471 1.466866 CGCCGCTAATAGCACGCTATA 60.467 52.381 13.15 1.16 42.58 1.31
1794 2472 0.732880 CGCCGCTAATAGCACGCTAT 60.733 55.000 13.15 5.72 42.58 2.97
1795 2473 1.371267 CGCCGCTAATAGCACGCTA 60.371 57.895 13.15 0.39 42.58 4.26
1796 2474 2.658593 CGCCGCTAATAGCACGCT 60.659 61.111 13.15 0.00 42.58 5.07
1798 2476 0.732880 ATAGCGCCGCTAATAGCACG 60.733 55.000 23.98 17.04 44.62 5.34
1799 2477 2.186076 CTATAGCGCCGCTAATAGCAC 58.814 52.381 23.98 2.74 44.62 4.40
1800 2478 1.469251 GCTATAGCGCCGCTAATAGCA 60.469 52.381 32.01 14.85 44.62 3.49
1801 2479 1.201343 GCTATAGCGCCGCTAATAGC 58.799 55.000 27.92 27.92 44.62 2.97
1835 2513 0.255890 ACCAACCACACAGAAGCACT 59.744 50.000 0.00 0.00 0.00 4.40
1836 2514 1.102978 AACCAACCACACAGAAGCAC 58.897 50.000 0.00 0.00 0.00 4.40
1837 2515 1.102154 CAACCAACCACACAGAAGCA 58.898 50.000 0.00 0.00 0.00 3.91
1838 2516 1.065551 GACAACCAACCACACAGAAGC 59.934 52.381 0.00 0.00 0.00 3.86
1839 2517 1.330521 CGACAACCAACCACACAGAAG 59.669 52.381 0.00 0.00 0.00 2.85
1840 2518 1.374560 CGACAACCAACCACACAGAA 58.625 50.000 0.00 0.00 0.00 3.02
1841 2519 0.462937 CCGACAACCAACCACACAGA 60.463 55.000 0.00 0.00 0.00 3.41
1842 2520 0.462937 TCCGACAACCAACCACACAG 60.463 55.000 0.00 0.00 0.00 3.66
1963 2641 5.640357 ACCAAAGCAGTTCAAATGCATATTG 59.360 36.000 13.16 13.09 46.31 1.90
1979 2657 5.295787 CGCTGTAATAATCCTTACCAAAGCA 59.704 40.000 0.00 0.00 32.13 3.91
1995 2673 4.814771 GGCTATCACCTTAAACGCTGTAAT 59.185 41.667 0.00 0.00 0.00 1.89
2002 2680 1.940613 GCCTGGCTATCACCTTAAACG 59.059 52.381 12.43 0.00 0.00 3.60
2138 2816 9.542462 TGAGTCTAAGTAATGCACCATTATTAC 57.458 33.333 0.00 0.00 38.37 1.89
2228 2906 2.229062 ACGAGTTGCGAGAAGAAGATGA 59.771 45.455 0.00 0.00 44.57 2.92
2445 3127 7.417612 CCTTTCCTAATTTACATCGTTCATGG 58.582 38.462 0.00 0.00 36.72 3.66
2770 3452 6.203915 TGAAGCAAACACTTAATCGTGTACAT 59.796 34.615 0.00 0.00 46.71 2.29
2871 3554 3.642705 GCAAAAGAAAGAAGATGCCGTT 58.357 40.909 0.00 0.00 0.00 4.44
2907 3590 2.889045 GCATGGTATGGCACTCATGATT 59.111 45.455 22.39 0.00 37.71 2.57
2922 3610 4.799564 AATAATGAAACAACGGCATGGT 57.200 36.364 0.00 0.00 0.00 3.55
3216 3904 2.648059 CCGAAATCCAGATTCTTGGCT 58.352 47.619 0.00 0.00 38.16 4.75
3313 4001 3.152341 CAGATGAGGATGCCATAAACCC 58.848 50.000 0.00 0.00 0.00 4.11
3407 4095 8.633075 AATGAGTGAACAAACACACTAAAATG 57.367 30.769 0.00 0.00 45.54 2.32
3408 4096 9.301153 GAAATGAGTGAACAAACACACTAAAAT 57.699 29.630 0.00 0.00 45.54 1.82
3415 4103 5.163663 GGACTGAAATGAGTGAACAAACACA 60.164 40.000 0.00 0.00 42.45 3.72
3469 4157 2.869801 CTCCGTTCGCAAATATAAGCCA 59.130 45.455 0.00 0.00 0.00 4.75
3478 4166 0.037975 GTACTCCCTCCGTTCGCAAA 60.038 55.000 0.00 0.00 0.00 3.68
3482 4170 1.401199 GAGAAGTACTCCCTCCGTTCG 59.599 57.143 12.00 0.00 39.53 3.95
3569 4258 2.505819 CCTGAGGCAAGGTGGTAATAGT 59.494 50.000 0.00 0.00 32.17 2.12
3700 4389 3.123621 CAGCTTCATGAAACTCCACGTAC 59.876 47.826 8.41 0.00 0.00 3.67
3715 4404 0.473755 TTTGGACTGCCTCAGCTTCA 59.526 50.000 0.00 0.00 40.80 3.02
3722 4411 1.742268 GAGAGCATTTTGGACTGCCTC 59.258 52.381 0.00 0.00 39.22 4.70
3725 4414 1.471684 CTGGAGAGCATTTTGGACTGC 59.528 52.381 0.00 0.00 38.69 4.40
3744 4433 4.212143 TGCAGTTCTGTATCATTCAGCT 57.788 40.909 1.78 0.00 33.48 4.24
3854 4543 9.244799 GTTCTTTTTGGACACACCTATAAAAAG 57.755 33.333 0.00 0.00 43.18 2.27
3900 4589 2.144738 GGCGCCTTCCCCTATGGTA 61.145 63.158 22.15 0.00 34.77 3.25
3947 4636 2.644798 AGAGACACCTTACCCAAATGCT 59.355 45.455 0.00 0.00 0.00 3.79
4017 4706 8.919145 TGACTTAAGTCCAACCAAATTTACAAT 58.081 29.630 28.43 0.00 44.15 2.71
4018 4707 8.294954 TGACTTAAGTCCAACCAAATTTACAA 57.705 30.769 28.43 5.28 44.15 2.41
4019 4708 7.469456 GCTGACTTAAGTCCAACCAAATTTACA 60.469 37.037 28.43 8.14 44.15 2.41
4020 4709 6.861572 GCTGACTTAAGTCCAACCAAATTTAC 59.138 38.462 28.43 4.02 44.15 2.01
4021 4710 6.547880 TGCTGACTTAAGTCCAACCAAATTTA 59.452 34.615 28.43 8.14 44.15 1.40
4022 4711 5.362430 TGCTGACTTAAGTCCAACCAAATTT 59.638 36.000 28.43 0.00 44.15 1.82
4023 4712 4.892934 TGCTGACTTAAGTCCAACCAAATT 59.107 37.500 28.43 0.00 44.15 1.82
4024 4713 4.469657 TGCTGACTTAAGTCCAACCAAAT 58.530 39.130 28.43 0.00 44.15 2.32
4025 4714 3.892284 TGCTGACTTAAGTCCAACCAAA 58.108 40.909 28.43 10.57 44.15 3.28
4026 4715 3.569194 TGCTGACTTAAGTCCAACCAA 57.431 42.857 28.43 11.23 44.15 3.67
4027 4716 3.181445 ACATGCTGACTTAAGTCCAACCA 60.181 43.478 28.43 20.03 44.15 3.67
4028 4717 3.412386 ACATGCTGACTTAAGTCCAACC 58.588 45.455 28.43 15.93 44.15 3.77
4029 4718 4.083271 GGAACATGCTGACTTAAGTCCAAC 60.083 45.833 28.43 19.05 44.15 3.77
4030 4719 4.072131 GGAACATGCTGACTTAAGTCCAA 58.928 43.478 28.43 16.37 44.15 3.53
4031 4720 3.559171 GGGAACATGCTGACTTAAGTCCA 60.559 47.826 28.43 21.15 44.15 4.02
4032 4721 3.010420 GGGAACATGCTGACTTAAGTCC 58.990 50.000 28.43 16.74 44.15 3.85
4033 4722 3.674997 TGGGAACATGCTGACTTAAGTC 58.325 45.455 25.73 25.73 39.70 3.01
4034 4723 3.788227 TGGGAACATGCTGACTTAAGT 57.212 42.857 8.13 8.13 33.40 2.24
4035 4724 5.649782 AATTGGGAACATGCTGACTTAAG 57.350 39.130 0.00 0.00 42.32 1.85
4051 4740 4.351111 AGTCCTACCTAAGCCATAATTGGG 59.649 45.833 0.00 0.00 43.84 4.12
4058 4747 4.827789 TCCATTAGTCCTACCTAAGCCAT 58.172 43.478 0.00 0.00 30.84 4.40
4138 4827 9.101655 CAATGAAATCAGGATAACCCAAAATTC 57.898 33.333 0.00 0.00 37.41 2.17
4307 4999 2.206750 GTTTGGTGCACAACTAGTCGA 58.793 47.619 20.43 0.00 39.19 4.20
4379 5071 0.990374 TGGGCCCCATTTTGGATTTG 59.010 50.000 22.27 0.00 40.96 2.32
4414 5106 3.054065 AGGTCATCCTGGGAATTCTGTTC 60.054 47.826 5.23 0.00 43.33 3.18
4594 5286 4.628074 TGTAACTTTTAGAAGTCGCAGCT 58.372 39.130 0.00 0.00 45.18 4.24
4607 5299 7.990886 TGACAACAAGGAGACTATGTAACTTTT 59.009 33.333 0.00 0.00 42.68 2.27
4781 5478 2.921634 TAGAGCAAGCAGAGTACACG 57.078 50.000 0.00 0.00 0.00 4.49
4800 5497 3.319122 GGTCCAACTGCTTTGAACTCATT 59.681 43.478 0.64 0.00 37.39 2.57
4809 5506 5.416952 CAGATAATTCAGGTCCAACTGCTTT 59.583 40.000 0.00 0.00 38.36 3.51
4995 5702 4.697756 TACACCTGCAGCGGCCAC 62.698 66.667 8.66 0.00 40.13 5.01
5028 5737 2.862541 TCCTTGTGCTGCATGTAAACT 58.137 42.857 5.27 0.00 0.00 2.66
5036 5745 1.266718 GAAACGAATCCTTGTGCTGCA 59.733 47.619 0.00 0.00 0.00 4.41
5048 5757 5.152623 TCAGACTCATGGAAGAAACGAAT 57.847 39.130 0.00 0.00 0.00 3.34
5066 5775 5.489792 ACAAAAGTAGCCAGAAGATCAGA 57.510 39.130 0.00 0.00 0.00 3.27
5342 6079 1.588404 CTGCGGCTGTAACTAATGTCG 59.412 52.381 0.00 0.00 0.00 4.35
5380 6117 2.083774 GGACGGCTGAACATCAATGAA 58.916 47.619 0.00 0.00 0.00 2.57
5459 6197 8.475331 AACTGTTTGTAGTACGAATTCCTATG 57.525 34.615 6.25 0.00 0.00 2.23
5460 6198 8.308931 TGAACTGTTTGTAGTACGAATTCCTAT 58.691 33.333 6.25 0.00 0.00 2.57
5461 6199 7.660112 TGAACTGTTTGTAGTACGAATTCCTA 58.340 34.615 6.25 0.00 0.00 2.94
5462 6200 6.518493 TGAACTGTTTGTAGTACGAATTCCT 58.482 36.000 6.25 0.00 0.00 3.36
5463 6201 6.774354 TGAACTGTTTGTAGTACGAATTCC 57.226 37.500 6.25 0.00 0.00 3.01
5464 6202 9.314501 GAATTGAACTGTTTGTAGTACGAATTC 57.685 33.333 6.25 7.09 30.77 2.17
5465 6203 8.287503 GGAATTGAACTGTTTGTAGTACGAATT 58.712 33.333 6.25 0.00 0.00 2.17
5466 6204 7.660208 AGGAATTGAACTGTTTGTAGTACGAAT 59.340 33.333 6.25 0.00 0.00 3.34
5467 6205 6.987992 AGGAATTGAACTGTTTGTAGTACGAA 59.012 34.615 0.00 0.00 0.00 3.85
5468 6206 6.422701 CAGGAATTGAACTGTTTGTAGTACGA 59.577 38.462 0.00 0.00 0.00 3.43
5469 6207 6.590357 CAGGAATTGAACTGTTTGTAGTACG 58.410 40.000 0.00 0.00 0.00 3.67
5470 6208 6.017440 TGCAGGAATTGAACTGTTTGTAGTAC 60.017 38.462 0.00 0.00 37.07 2.73
5604 6342 5.974108 TGCTTAACTATCAACTGGGTACTC 58.026 41.667 0.00 0.00 0.00 2.59
5898 6636 4.584327 TTTAAGAAGTGAAGGGCAAAGC 57.416 40.909 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.