Multiple sequence alignment - TraesCS3A01G067400

Loading Multiple Alignment...

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 TraesCS3A01G067400 chr3A 100.000 2546 0 0 1 2546 40391079 40388534 0.000000e+00 4702.0
1 TraesCS3A01G067400 chr3A 85.592 1166 86 46 361 1477 40556837 40555705 0.000000e+00 1147.0
2 TraesCS3A01G067400 chr3A 80.325 493 59 23 1749 2216 436273188 436272709 3.140000e-89 339.0
3 TraesCS3A01G067400 chr3B 89.252 1377 84 29 358 1701 50942457 50943802 0.000000e+00 1664.0
4 TraesCS3A01G067400 chr3B 85.943 1060 82 30 358 1386 50655085 50654062 0.000000e+00 1070.0
5 TraesCS3A01G067400 chr3B 84.318 931 70 28 683 1568 50959693 50958794 0.000000e+00 841.0
6 TraesCS3A01G067400 chr3B 85.396 404 20 16 1722 2097 50943791 50944183 1.430000e-102 383.0
7 TraesCS3A01G067400 chr3B 81.212 495 51 25 1749 2216 421531190 421530711 6.700000e-96 361.0
8 TraesCS3A01G067400 chr3B 92.742 248 12 5 1913 2155 50958343 50958097 1.120000e-93 353.0
9 TraesCS3A01G067400 chr3B 79.310 493 51 21 2004 2468 51010228 51009759 5.330000e-77 298.0
10 TraesCS3A01G067400 chr3B 80.333 300 32 14 2143 2437 50952359 50952636 4.300000e-48 202.0
11 TraesCS3A01G067400 chr3B 90.066 151 9 4 1790 1939 50653409 50653264 9.300000e-45 191.0
12 TraesCS3A01G067400 chr3B 90.598 117 8 1 45 158 50942347 50942463 4.390000e-33 152.0
13 TraesCS3A01G067400 chr3B 80.838 167 9 9 1395 1561 50653917 50653774 2.680000e-20 110.0
14 TraesCS3A01G067400 chr3D 86.721 1348 84 47 230 1549 29801686 29800406 0.000000e+00 1410.0
15 TraesCS3A01G067400 chr3D 84.906 1431 92 62 358 1699 29813128 29811733 0.000000e+00 1332.0
16 TraesCS3A01G067400 chr3D 90.763 747 43 12 635 1364 29790158 29789421 0.000000e+00 974.0
17 TraesCS3A01G067400 chr3D 86.310 935 56 26 415 1315 29862118 29861222 0.000000e+00 952.0
18 TraesCS3A01G067400 chr3D 93.644 236 13 2 1921 2155 29852995 29852761 4.030000e-93 351.0
19 TraesCS3A01G067400 chr3D 90.840 262 21 2 1856 2114 29788768 29788507 5.210000e-92 348.0
20 TraesCS3A01G067400 chr3D 92.887 239 15 2 1918 2155 29799771 29799534 1.880000e-91 346.0
21 TraesCS3A01G067400 chr3D 80.448 491 55 25 1749 2216 299746033 299746505 1.130000e-88 337.0
22 TraesCS3A01G067400 chr3D 90.870 230 13 5 1 228 29803641 29803418 4.120000e-78 302.0
23 TraesCS3A01G067400 chr3D 88.800 250 16 11 1722 1969 29811741 29811502 1.920000e-76 296.0
24 TraesCS3A01G067400 chr3D 82.573 241 17 10 358 586 29790387 29790160 3.340000e-44 189.0
25 TraesCS3A01G067400 chr3D 85.263 190 10 10 1395 1568 29789307 29789120 2.010000e-41 180.0
26 TraesCS3A01G067400 chr3D 94.690 113 6 0 45 157 29796850 29796738 2.600000e-40 176.0
27 TraesCS3A01G067400 chr3D 86.667 150 12 5 1562 1710 29860931 29860789 2.620000e-35 159.0
28 TraesCS3A01G067400 chr3D 98.718 78 1 0 81 158 29813199 29813122 3.420000e-29 139.0
29 TraesCS3A01G067400 chr3D 92.473 93 6 1 2126 2218 29788384 29788293 5.720000e-27 132.0
30 TraesCS3A01G067400 chr3D 84.397 141 11 6 1562 1698 29800130 29799997 7.390000e-26 128.0
31 TraesCS3A01G067400 chr3D 89.610 77 4 2 1489 1561 29861106 29861030 7.500000e-16 95.3
32 TraesCS3A01G067400 chr3D 96.875 32 1 0 2241 2272 29788293 29788262 1.000000e-03 54.7
33 TraesCS3A01G067400 chr7B 90.748 735 46 12 680 1398 707946989 707946261 0.000000e+00 961.0
34 TraesCS3A01G067400 chr7B 84.770 348 24 13 358 683 707947609 707947269 3.160000e-84 322.0
35 TraesCS3A01G067400 chr7B 88.670 203 9 4 1722 1923 707945974 707945785 4.230000e-58 235.0
36 TraesCS3A01G067400 chr7B 79.233 313 23 14 1434 1710 707946261 707945955 2.010000e-41 180.0
37 TraesCS3A01G067400 chr7B 96.429 56 2 0 103 158 707947658 707947603 2.700000e-15 93.5
38 TraesCS3A01G067400 chr4B 92.857 42 3 0 6 47 36340296 36340337 7.610000e-06 62.1
39 TraesCS3A01G067400 chr4B 94.872 39 2 0 6 44 664432231 664432193 7.610000e-06 62.1


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 TraesCS3A01G067400 chr3A 40388534 40391079 2545 True 4702.00 4702 100.000000 1 2546 1 chr3A.!!$R1 2545
1 TraesCS3A01G067400 chr3A 40555705 40556837 1132 True 1147.00 1147 85.592000 361 1477 1 chr3A.!!$R2 1116
2 TraesCS3A01G067400 chr3B 50942347 50944183 1836 False 733.00 1664 88.415333 45 2097 3 chr3B.!!$F2 2052
3 TraesCS3A01G067400 chr3B 50958097 50959693 1596 True 597.00 841 88.530000 683 2155 2 chr3B.!!$R4 1472
4 TraesCS3A01G067400 chr3B 50653264 50655085 1821 True 457.00 1070 85.615667 358 1939 3 chr3B.!!$R3 1581
5 TraesCS3A01G067400 chr3D 29811502 29813199 1697 True 589.00 1332 90.808000 81 1969 3 chr3D.!!$R4 1888
6 TraesCS3A01G067400 chr3D 29796738 29803641 6903 True 472.40 1410 89.913000 1 2155 5 chr3D.!!$R3 2154
7 TraesCS3A01G067400 chr3D 29860789 29862118 1329 True 402.10 952 87.529000 415 1710 3 chr3D.!!$R5 1295
8 TraesCS3A01G067400 chr3D 29788262 29790387 2125 True 312.95 974 89.797833 358 2272 6 chr3D.!!$R2 1914
9 TraesCS3A01G067400 chr7B 707945785 707947658 1873 True 358.30 961 87.970000 103 1923 5 chr7B.!!$R1 1820

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
217 221 0.035317 TGCGGATCAGCTGACTTGTT 59.965 50.0 20.97 1.58 38.13 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 4563 0.040425 ACGCAAAATGAAGTCGCACC 60.04 50.0 0.0 0.0 0.0 5.01 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
38 39 3.364889 TGGCGTATAACTCGATTCCAG 57.635 47.619 0.00 0.00 0.00 3.86
43 44 4.910456 GCGTATAACTCGATTCCAGTAGTG 59.090 45.833 0.00 0.00 0.00 2.74
71 75 2.738643 GCGGATGTTTGAGGATTCGAGA 60.739 50.000 0.00 0.00 0.00 4.04
74 78 4.508662 GGATGTTTGAGGATTCGAGAAGT 58.491 43.478 0.00 0.00 0.00 3.01
151 155 0.815615 GGCAATCTTCCGGCACTAGG 60.816 60.000 0.00 0.00 0.00 3.02
217 221 0.035317 TGCGGATCAGCTGACTTGTT 59.965 50.000 20.97 1.58 38.13 2.83
218 222 0.723981 GCGGATCAGCTGACTTGTTC 59.276 55.000 20.97 12.26 0.00 3.18
224 228 5.456265 GGATCAGCTGACTTGTTCTTTTTC 58.544 41.667 20.97 7.79 0.00 2.29
225 229 5.240403 GGATCAGCTGACTTGTTCTTTTTCT 59.760 40.000 20.97 0.00 0.00 2.52
227 231 7.041098 GGATCAGCTGACTTGTTCTTTTTCTAA 60.041 37.037 20.97 0.00 0.00 2.10
228 232 7.807977 TCAGCTGACTTGTTCTTTTTCTAAT 57.192 32.000 13.74 0.00 0.00 1.73
246 1979 7.422465 TTCTAATTGGGCAAAATAGCATTCT 57.578 32.000 0.00 0.00 35.83 2.40
327 2061 4.331717 CCCCGTAATTGTCTGTTGATGTAC 59.668 45.833 0.00 0.00 0.00 2.90
328 2062 5.175859 CCCGTAATTGTCTGTTGATGTACT 58.824 41.667 0.00 0.00 0.00 2.73
329 2063 6.334989 CCCGTAATTGTCTGTTGATGTACTA 58.665 40.000 0.00 0.00 0.00 1.82
330 2064 6.255020 CCCGTAATTGTCTGTTGATGTACTAC 59.745 42.308 0.00 0.00 0.00 2.73
331 2065 6.020916 CCGTAATTGTCTGTTGATGTACTACG 60.021 42.308 0.00 0.00 0.00 3.51
332 2066 6.525628 CGTAATTGTCTGTTGATGTACTACGT 59.474 38.462 0.00 0.00 0.00 3.57
333 2067 6.706055 AATTGTCTGTTGATGTACTACGTG 57.294 37.500 0.00 0.00 0.00 4.49
334 2068 3.571571 TGTCTGTTGATGTACTACGTGC 58.428 45.455 0.00 0.00 0.00 5.34
335 2069 2.921754 GTCTGTTGATGTACTACGTGCC 59.078 50.000 0.00 0.00 0.00 5.01
336 2070 2.559231 TCTGTTGATGTACTACGTGCCA 59.441 45.455 0.00 0.00 0.00 4.92
337 2071 3.194755 TCTGTTGATGTACTACGTGCCAT 59.805 43.478 0.00 0.00 0.00 4.40
338 2072 3.258228 TGTTGATGTACTACGTGCCATG 58.742 45.455 0.00 0.00 0.00 3.66
339 2073 3.056465 TGTTGATGTACTACGTGCCATGA 60.056 43.478 0.00 0.00 0.00 3.07
340 2074 4.119862 GTTGATGTACTACGTGCCATGAT 58.880 43.478 0.00 0.00 0.00 2.45
341 2075 3.716601 TGATGTACTACGTGCCATGATG 58.283 45.455 0.00 0.00 0.00 3.07
342 2076 3.383185 TGATGTACTACGTGCCATGATGA 59.617 43.478 0.00 0.00 0.00 2.92
343 2077 3.436700 TGTACTACGTGCCATGATGAG 57.563 47.619 0.00 0.00 0.00 2.90
344 2078 2.758423 TGTACTACGTGCCATGATGAGT 59.242 45.455 0.00 0.00 0.00 3.41
345 2079 3.949113 TGTACTACGTGCCATGATGAGTA 59.051 43.478 0.00 0.00 0.00 2.59
476 2227 8.344098 GCTAGTCGTCTTTGTTCATACTAGTAT 58.656 37.037 9.71 9.71 38.02 2.12
561 2338 6.439599 GCGACAGAATATATATATCCGCACT 58.560 40.000 19.60 9.17 38.88 4.40
613 2394 2.285083 CCCGAGATGCCGTTGATAAAA 58.715 47.619 0.00 0.00 0.00 1.52
630 2411 4.787280 AGGCTCCCTGGACCTCGG 62.787 72.222 0.00 0.00 29.57 4.63
671 2460 2.552031 GGTTCTAGCTAGCCTTTTCCG 58.448 52.381 16.35 0.00 0.00 4.30
695 2767 4.452733 GTTAGCTCGCTGCCCGGT 62.453 66.667 0.00 0.00 44.23 5.28
1003 3081 0.661780 CGCGGCTATACTCTGCAGAC 60.662 60.000 13.74 1.21 35.64 3.51
1047 3142 2.018355 TAGCTCCACCAACACCACTA 57.982 50.000 0.00 0.00 0.00 2.74
1107 3228 1.159285 CTCAAGCTTGTGATTCGGCA 58.841 50.000 25.19 2.50 0.00 5.69
1129 3255 2.363680 GCATACTCAAGCTAGCTCCTCA 59.636 50.000 19.65 3.02 0.00 3.86
1140 3266 2.827423 CTCCTCATCATGGCGCCT 59.173 61.111 29.70 10.60 0.00 5.52
1161 3290 0.179100 CGTCGAAGGTCATGAGCCAT 60.179 55.000 20.92 10.74 0.00 4.40
1315 3447 2.551270 CCTGAAGTGCACGTTCGC 59.449 61.111 12.01 0.00 0.00 4.70
1413 3703 6.300703 AGTATAGGTGTGCTTTTTGTAACCA 58.699 36.000 0.00 0.00 0.00 3.67
1590 4271 2.745821 TGTTGTTGCTCTGCTGATCATC 59.254 45.455 0.00 0.00 0.00 2.92
1660 4504 8.779303 TCGCTTGACTTGTTTAATTTTCATCTA 58.221 29.630 0.00 0.00 0.00 1.98
1701 4551 4.668289 GGTTATCCGATTTCATTTTGCGT 58.332 39.130 0.00 0.00 0.00 5.24
1702 4552 5.099575 GGTTATCCGATTTCATTTTGCGTT 58.900 37.500 0.00 0.00 0.00 4.84
1703 4553 5.575218 GGTTATCCGATTTCATTTTGCGTTT 59.425 36.000 0.00 0.00 0.00 3.60
1704 4554 6.090223 GGTTATCCGATTTCATTTTGCGTTTT 59.910 34.615 0.00 0.00 0.00 2.43
1705 4555 7.359681 GGTTATCCGATTTCATTTTGCGTTTTT 60.360 33.333 0.00 0.00 0.00 1.94
1723 4573 3.936585 TTTTTGCAGGTGCGACTTC 57.063 47.368 0.00 0.00 45.83 3.01
1813 4673 7.934120 AGCAGGCTACGATATATTCTTTCTTTT 59.066 33.333 0.00 0.00 0.00 2.27
1890 4806 6.887626 AGCTAGTAGCCAGTAAGATTCTAC 57.112 41.667 18.65 0.00 43.77 2.59
2000 4949 8.571336 CCACTCGATCATATATATACATCTGCA 58.429 37.037 0.00 0.00 0.00 4.41
2024 4973 3.005050 ACATTCATATTTCTGCATGCCGG 59.995 43.478 16.68 8.37 0.00 6.13
2124 5154 8.741603 TTGTTTTAGTTATTATAGCTGGGTCC 57.258 34.615 0.00 0.00 0.00 4.46
2128 5158 5.407407 AGTTATTATAGCTGGGTCCATCG 57.593 43.478 0.00 0.00 0.00 3.84
2174 5239 3.127548 ACAGATGAAAATAAGCGCCACAG 59.872 43.478 2.29 0.00 0.00 3.66
2189 5254 1.000739 ACAGGCATCATTGGGTGGG 59.999 57.895 0.00 0.00 0.00 4.61
2217 5282 1.135112 TGGCTAGACATGTAGTGTGCG 60.135 52.381 0.00 0.00 42.36 5.34
2218 5283 0.924090 GCTAGACATGTAGTGTGCGC 59.076 55.000 0.00 0.00 42.36 6.09
2219 5284 1.560923 CTAGACATGTAGTGTGCGCC 58.439 55.000 4.18 0.00 42.36 6.53
2220 5285 1.135139 CTAGACATGTAGTGTGCGCCT 59.865 52.381 4.18 0.00 42.36 5.52
2221 5286 0.108615 AGACATGTAGTGTGCGCCTC 60.109 55.000 4.18 0.00 42.36 4.70
2223 5288 0.321671 ACATGTAGTGTGCGCCTCTT 59.678 50.000 4.18 0.00 40.28 2.85
2225 5290 1.394917 CATGTAGTGTGCGCCTCTTTC 59.605 52.381 4.18 1.33 0.00 2.62
2226 5291 0.391228 TGTAGTGTGCGCCTCTTTCA 59.609 50.000 4.18 3.72 0.00 2.69
2227 5292 1.001974 TGTAGTGTGCGCCTCTTTCAT 59.998 47.619 4.18 0.00 0.00 2.57
2229 5294 1.160137 AGTGTGCGCCTCTTTCATTC 58.840 50.000 4.18 0.00 0.00 2.67
2230 5295 0.874390 GTGTGCGCCTCTTTCATTCA 59.126 50.000 4.18 0.00 0.00 2.57
2231 5296 1.470098 GTGTGCGCCTCTTTCATTCAT 59.530 47.619 4.18 0.00 0.00 2.57
2233 5298 2.095110 TGTGCGCCTCTTTCATTCATTG 60.095 45.455 4.18 0.00 0.00 2.82
2234 5299 2.095059 GTGCGCCTCTTTCATTCATTGT 60.095 45.455 4.18 0.00 0.00 2.71
2235 5300 2.095110 TGCGCCTCTTTCATTCATTGTG 60.095 45.455 4.18 0.00 0.00 3.33
2236 5301 2.162208 GCGCCTCTTTCATTCATTGTGA 59.838 45.455 0.00 0.00 0.00 3.58
2238 5303 3.181503 CGCCTCTTTCATTCATTGTGAGG 60.182 47.826 0.00 0.00 39.28 3.86
2239 5304 3.129988 GCCTCTTTCATTCATTGTGAGGG 59.870 47.826 0.00 0.00 38.07 4.30
2269 6626 5.063204 ACACCGGGATGATGTATGTATTTG 58.937 41.667 6.32 0.00 0.00 2.32
2275 6632 6.208644 GGGATGATGTATGTATTTGTTGCAC 58.791 40.000 0.00 0.00 0.00 4.57
2276 6633 6.208644 GGATGATGTATGTATTTGTTGCACC 58.791 40.000 0.00 0.00 0.00 5.01
2287 6644 8.397575 TGTATTTGTTGCACCTATTTTAGTCA 57.602 30.769 0.00 0.00 0.00 3.41
2288 6645 9.019656 TGTATTTGTTGCACCTATTTTAGTCAT 57.980 29.630 0.00 0.00 0.00 3.06
2289 6646 9.289303 GTATTTGTTGCACCTATTTTAGTCATG 57.711 33.333 0.00 0.00 0.00 3.07
2290 6647 5.895636 TGTTGCACCTATTTTAGTCATGG 57.104 39.130 0.00 0.00 0.00 3.66
2291 6648 5.565509 TGTTGCACCTATTTTAGTCATGGA 58.434 37.500 0.00 0.00 0.00 3.41
2292 6649 6.007076 TGTTGCACCTATTTTAGTCATGGAA 58.993 36.000 0.00 0.00 0.00 3.53
2293 6650 6.663093 TGTTGCACCTATTTTAGTCATGGAAT 59.337 34.615 0.00 0.00 0.00 3.01
2295 6652 5.593909 TGCACCTATTTTAGTCATGGAATGG 59.406 40.000 0.00 0.00 46.73 3.16
2296 6653 5.594317 GCACCTATTTTAGTCATGGAATGGT 59.406 40.000 0.00 0.00 46.73 3.55
2297 6654 6.096846 GCACCTATTTTAGTCATGGAATGGTT 59.903 38.462 0.00 0.00 46.73 3.67
2298 6655 7.284489 GCACCTATTTTAGTCATGGAATGGTTA 59.716 37.037 0.00 0.00 46.73 2.85
2301 6658 7.998964 CCTATTTTAGTCATGGAATGGTTACCT 59.001 37.037 2.07 0.00 46.73 3.08
2304 6661 4.772886 AGTCATGGAATGGTTACCTACC 57.227 45.455 2.07 4.18 46.73 3.18
2320 6677 7.649705 GGTTACCTACCGAACTAAAGTAATAGC 59.350 40.741 0.00 0.00 37.12 2.97
2321 6678 8.409371 GTTACCTACCGAACTAAAGTAATAGCT 58.591 37.037 0.00 0.00 0.00 3.32
2322 6679 7.036996 ACCTACCGAACTAAAGTAATAGCTC 57.963 40.000 0.00 0.00 0.00 4.09
2323 6680 6.141462 CCTACCGAACTAAAGTAATAGCTCG 58.859 44.000 0.00 1.33 39.81 5.03
2325 6682 5.576895 ACCGAACTAAAGTAATAGCTCGAC 58.423 41.667 8.28 0.00 41.62 4.20
2326 6683 4.974888 CCGAACTAAAGTAATAGCTCGACC 59.025 45.833 8.28 0.00 41.62 4.79
2327 6684 5.449588 CCGAACTAAAGTAATAGCTCGACCA 60.450 44.000 8.28 0.00 41.62 4.02
2329 6686 6.696148 CGAACTAAAGTAATAGCTCGACCATT 59.304 38.462 0.00 0.00 41.62 3.16
2330 6687 7.306051 CGAACTAAAGTAATAGCTCGACCATTG 60.306 40.741 0.00 0.00 41.62 2.82
2332 6689 3.819564 AGTAATAGCTCGACCATTGCA 57.180 42.857 0.00 0.00 0.00 4.08
2333 6690 4.342862 AGTAATAGCTCGACCATTGCAT 57.657 40.909 0.00 0.00 0.00 3.96
2335 6692 1.233019 ATAGCTCGACCATTGCATGC 58.767 50.000 11.82 11.82 0.00 4.06
2337 6694 1.226491 GCTCGACCATTGCATGCAC 60.226 57.895 22.58 7.61 0.00 4.57
2338 6695 1.430632 CTCGACCATTGCATGCACC 59.569 57.895 22.58 6.52 0.00 5.01
2339 6696 1.002257 TCGACCATTGCATGCACCT 60.002 52.632 22.58 8.15 0.00 4.00
2340 6697 0.608856 TCGACCATTGCATGCACCTT 60.609 50.000 22.58 5.42 0.00 3.50
2341 6698 0.244450 CGACCATTGCATGCACCTTT 59.756 50.000 22.58 5.20 0.00 3.11
2342 6699 1.717194 GACCATTGCATGCACCTTTG 58.283 50.000 22.58 15.08 0.00 2.77
2344 6701 1.417145 ACCATTGCATGCACCTTTGTT 59.583 42.857 22.58 1.47 0.00 2.83
2346 6703 1.195900 CATTGCATGCACCTTTGTTGC 59.804 47.619 22.58 0.00 35.64 4.17
2347 6704 0.532417 TTGCATGCACCTTTGTTGCC 60.532 50.000 22.58 0.00 34.74 4.52
2348 6705 1.069427 GCATGCACCTTTGTTGCCA 59.931 52.632 14.21 0.00 31.46 4.92
2349 6706 0.320946 GCATGCACCTTTGTTGCCAT 60.321 50.000 14.21 0.00 31.46 4.40
2351 6708 2.496111 CATGCACCTTTGTTGCCATTT 58.504 42.857 0.00 0.00 0.00 2.32
2352 6709 2.706339 TGCACCTTTGTTGCCATTTT 57.294 40.000 0.00 0.00 0.00 1.82
2353 6710 2.559440 TGCACCTTTGTTGCCATTTTC 58.441 42.857 0.00 0.00 0.00 2.29
2354 6711 1.872952 GCACCTTTGTTGCCATTTTCC 59.127 47.619 0.00 0.00 0.00 3.13
2355 6712 2.493035 CACCTTTGTTGCCATTTTCCC 58.507 47.619 0.00 0.00 0.00 3.97
2357 6714 2.158827 ACCTTTGTTGCCATTTTCCCAC 60.159 45.455 0.00 0.00 0.00 4.61
2358 6715 2.493035 CTTTGTTGCCATTTTCCCACC 58.507 47.619 0.00 0.00 0.00 4.61
2359 6716 0.390860 TTGTTGCCATTTTCCCACCG 59.609 50.000 0.00 0.00 0.00 4.94
2369 6856 5.925969 GCCATTTTCCCACCGATTATTATTG 59.074 40.000 0.00 0.00 0.00 1.90
2371 6858 7.255660 GCCATTTTCCCACCGATTATTATTGTA 60.256 37.037 0.00 0.00 0.00 2.41
2402 6889 4.844998 TCTTCGATGAAGAGCCAGATAG 57.155 45.455 5.19 0.00 42.78 2.08
2403 6890 4.211125 TCTTCGATGAAGAGCCAGATAGT 58.789 43.478 5.19 0.00 42.78 2.12
2404 6891 5.377478 TCTTCGATGAAGAGCCAGATAGTA 58.623 41.667 5.19 0.00 42.78 1.82
2405 6892 5.828328 TCTTCGATGAAGAGCCAGATAGTAA 59.172 40.000 5.19 0.00 42.78 2.24
2406 6893 6.491745 TCTTCGATGAAGAGCCAGATAGTAAT 59.508 38.462 5.19 0.00 42.78 1.89
2407 6894 6.260870 TCGATGAAGAGCCAGATAGTAATC 57.739 41.667 0.00 0.00 0.00 1.75
2409 6896 7.168905 TCGATGAAGAGCCAGATAGTAATCTA 58.831 38.462 0.00 0.00 40.65 1.98
2410 6897 7.335673 TCGATGAAGAGCCAGATAGTAATCTAG 59.664 40.741 0.00 0.00 40.65 2.43
2411 6898 6.582677 TGAAGAGCCAGATAGTAATCTAGC 57.417 41.667 0.00 0.00 44.42 3.42
2417 6904 5.646606 GCCAGATAGTAATCTAGCTAGTGC 58.353 45.833 20.10 6.03 41.85 4.40
2418 6905 5.393678 GCCAGATAGTAATCTAGCTAGTGCC 60.394 48.000 20.10 7.37 41.85 5.01
2420 6907 6.379703 CCAGATAGTAATCTAGCTAGTGCCAT 59.620 42.308 20.10 3.79 40.37 4.40
2421 6908 7.257003 CAGATAGTAATCTAGCTAGTGCCATG 58.743 42.308 20.10 5.83 40.37 3.66
2425 6912 3.951775 ATCTAGCTAGTGCCATGTAGC 57.048 47.619 20.10 5.19 41.77 3.58
2427 6914 2.625314 TCTAGCTAGTGCCATGTAGCAG 59.375 50.000 20.10 9.57 45.14 4.24
2428 6915 0.179062 AGCTAGTGCCATGTAGCAGC 60.179 55.000 13.67 7.06 45.14 5.25
2429 6916 0.462581 GCTAGTGCCATGTAGCAGCA 60.463 55.000 7.90 0.00 45.14 4.41
2430 6917 1.813092 GCTAGTGCCATGTAGCAGCAT 60.813 52.381 7.90 0.00 45.14 3.79
2431 6918 1.871676 CTAGTGCCATGTAGCAGCATG 59.128 52.381 11.95 11.95 45.14 4.06
2432 6919 0.034767 AGTGCCATGTAGCAGCATGT 60.035 50.000 15.96 0.00 45.14 3.21
2433 6920 0.099968 GTGCCATGTAGCAGCATGTG 59.900 55.000 15.96 10.34 45.14 3.21
2434 6921 0.035247 TGCCATGTAGCAGCATGTGA 60.035 50.000 15.96 3.37 43.33 3.58
2435 6922 1.097232 GCCATGTAGCAGCATGTGAA 58.903 50.000 15.96 0.00 43.33 3.18
2436 6923 1.473677 GCCATGTAGCAGCATGTGAAA 59.526 47.619 15.96 0.00 43.33 2.69
2437 6924 2.094597 GCCATGTAGCAGCATGTGAAAA 60.095 45.455 15.96 0.00 43.33 2.29
2439 6926 3.922240 CCATGTAGCAGCATGTGAAAAAC 59.078 43.478 15.96 0.00 43.33 2.43
2455 6942 6.928820 GTGAAAAACACCTGGAAAAATAACG 58.071 36.000 0.00 0.00 43.05 3.18
2456 6943 6.532302 GTGAAAAACACCTGGAAAAATAACGT 59.468 34.615 0.00 0.00 43.05 3.99
2457 6944 6.752815 TGAAAAACACCTGGAAAAATAACGTC 59.247 34.615 0.00 0.00 0.00 4.34
2458 6945 4.477302 AACACCTGGAAAAATAACGTCG 57.523 40.909 0.00 0.00 0.00 5.12
2459 6946 3.469739 ACACCTGGAAAAATAACGTCGT 58.530 40.909 0.00 0.00 0.00 4.34
2460 6947 3.249080 ACACCTGGAAAAATAACGTCGTG 59.751 43.478 0.00 0.00 0.00 4.35
2461 6948 2.224784 ACCTGGAAAAATAACGTCGTGC 59.775 45.455 0.00 0.00 0.00 5.34
2462 6949 2.413634 CCTGGAAAAATAACGTCGTGCC 60.414 50.000 0.00 0.00 0.00 5.01
2464 6951 2.814919 TGGAAAAATAACGTCGTGCCAT 59.185 40.909 0.00 0.00 0.00 4.40
2466 6953 3.365565 GGAAAAATAACGTCGTGCCATGT 60.366 43.478 0.00 0.00 0.00 3.21
2467 6954 4.142859 GGAAAAATAACGTCGTGCCATGTA 60.143 41.667 0.00 0.00 0.00 2.29
2468 6955 4.593597 AAAATAACGTCGTGCCATGTAG 57.406 40.909 0.00 0.00 0.00 2.74
2469 6956 2.953466 ATAACGTCGTGCCATGTAGT 57.047 45.000 0.00 0.00 0.00 2.73
2470 6957 4.374843 AATAACGTCGTGCCATGTAGTA 57.625 40.909 0.00 0.00 0.00 1.82
2471 6958 2.953466 AACGTCGTGCCATGTAGTAT 57.047 45.000 0.00 0.00 0.00 2.12
2472 6959 5.694231 ATAACGTCGTGCCATGTAGTATA 57.306 39.130 0.00 0.00 0.00 1.47
2474 6961 3.897325 ACGTCGTGCCATGTAGTATATG 58.103 45.455 0.00 0.05 0.00 1.78
2475 6962 3.566742 ACGTCGTGCCATGTAGTATATGA 59.433 43.478 8.37 0.00 0.00 2.15
2476 6963 3.912563 CGTCGTGCCATGTAGTATATGAC 59.087 47.826 8.37 0.00 0.00 3.06
2477 6964 4.320275 CGTCGTGCCATGTAGTATATGACT 60.320 45.833 8.37 0.00 42.69 3.41
2478 6965 5.529791 GTCGTGCCATGTAGTATATGACTT 58.470 41.667 8.37 0.00 39.81 3.01
2480 6967 6.802348 GTCGTGCCATGTAGTATATGACTTAG 59.198 42.308 8.37 0.00 39.81 2.18
2482 6969 6.582672 CGTGCCATGTAGTATATGACTTAGTG 59.417 42.308 8.37 0.00 39.81 2.74
2483 6970 6.366332 GTGCCATGTAGTATATGACTTAGTGC 59.634 42.308 8.37 2.59 39.81 4.40
2485 6972 6.809196 GCCATGTAGTATATGACTTAGTGCTC 59.191 42.308 8.37 0.00 39.81 4.26
2488 6975 6.370453 TGTAGTATATGACTTAGTGCTCCCA 58.630 40.000 0.00 0.00 39.81 4.37
2489 6976 6.837048 TGTAGTATATGACTTAGTGCTCCCAA 59.163 38.462 0.00 0.00 39.81 4.12
2490 6977 6.808321 AGTATATGACTTAGTGCTCCCAAA 57.192 37.500 0.00 0.00 33.13 3.28
2492 6979 7.220030 AGTATATGACTTAGTGCTCCCAAATG 58.780 38.462 0.00 0.00 33.13 2.32
2493 6980 3.071874 TGACTTAGTGCTCCCAAATGG 57.928 47.619 0.00 0.00 0.00 3.16
2494 6981 2.375174 TGACTTAGTGCTCCCAAATGGT 59.625 45.455 0.00 0.00 34.77 3.55
2495 6982 3.010420 GACTTAGTGCTCCCAAATGGTC 58.990 50.000 0.00 0.00 34.77 4.02
2496 6983 2.375174 ACTTAGTGCTCCCAAATGGTCA 59.625 45.455 0.00 0.00 34.77 4.02
2497 6984 3.010584 ACTTAGTGCTCCCAAATGGTCAT 59.989 43.478 0.00 0.00 34.77 3.06
2498 6985 2.134789 AGTGCTCCCAAATGGTCATC 57.865 50.000 0.00 0.00 34.77 2.92
2500 6987 2.042162 AGTGCTCCCAAATGGTCATCTT 59.958 45.455 0.00 0.00 34.77 2.40
2502 6989 2.827322 TGCTCCCAAATGGTCATCTTTG 59.173 45.455 0.00 0.00 34.77 2.77
2503 6990 3.091545 GCTCCCAAATGGTCATCTTTGA 58.908 45.455 0.00 0.00 34.93 2.69
2504 6991 3.129988 GCTCCCAAATGGTCATCTTTGAG 59.870 47.826 0.00 0.00 34.93 3.02
2505 6992 4.338879 CTCCCAAATGGTCATCTTTGAGT 58.661 43.478 0.00 0.00 34.93 3.41
2506 6993 5.500234 CTCCCAAATGGTCATCTTTGAGTA 58.500 41.667 0.00 0.00 34.93 2.59
2507 6994 6.078456 TCCCAAATGGTCATCTTTGAGTAT 57.922 37.500 0.00 0.00 34.93 2.12
2509 6996 6.603201 TCCCAAATGGTCATCTTTGAGTATTC 59.397 38.462 0.00 0.00 34.93 1.75
2510 6997 6.604795 CCCAAATGGTCATCTTTGAGTATTCT 59.395 38.462 0.00 0.00 34.93 2.40
2511 6998 7.775093 CCCAAATGGTCATCTTTGAGTATTCTA 59.225 37.037 0.00 0.00 34.93 2.10
2512 6999 8.616076 CCAAATGGTCATCTTTGAGTATTCTAC 58.384 37.037 0.00 0.00 34.93 2.59
2515 7002 9.606631 AATGGTCATCTTTGAGTATTCTACTTC 57.393 33.333 0.00 0.00 39.59 3.01
2516 7003 7.258441 TGGTCATCTTTGAGTATTCTACTTCG 58.742 38.462 0.00 0.00 39.59 3.79
2517 7004 7.122204 TGGTCATCTTTGAGTATTCTACTTCGA 59.878 37.037 0.00 0.00 39.59 3.71
2519 7006 7.166804 GTCATCTTTGAGTATTCTACTTCGAGC 59.833 40.741 0.00 0.00 39.59 5.03
2521 7008 7.860918 TCTTTGAGTATTCTACTTCGAGCTA 57.139 36.000 0.00 0.00 39.59 3.32
2522 7009 8.453238 TCTTTGAGTATTCTACTTCGAGCTAT 57.547 34.615 0.00 0.00 39.59 2.97
2523 7010 9.557061 TCTTTGAGTATTCTACTTCGAGCTATA 57.443 33.333 0.00 0.00 39.59 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.447838 CGCCAAGTGCTACGGACAT 60.448 57.895 0.00 0.00 38.05 3.06
18 19 2.691526 ACTGGAATCGAGTTATACGCCA 59.308 45.455 0.00 0.00 0.00 5.69
31 32 2.604914 CGCACACATCACTACTGGAATC 59.395 50.000 0.00 0.00 0.00 2.52
38 39 2.010145 ACATCCGCACACATCACTAC 57.990 50.000 0.00 0.00 0.00 2.73
43 44 1.131126 CCTCAAACATCCGCACACATC 59.869 52.381 0.00 0.00 0.00 3.06
71 75 0.461961 GAGCATCTACAGCCGGACTT 59.538 55.000 5.05 0.00 0.00 3.01
163 167 5.355350 GCTTTAGTCCATGTGTCTAGCATTT 59.645 40.000 0.00 0.00 0.00 2.32
164 168 4.878397 GCTTTAGTCCATGTGTCTAGCATT 59.122 41.667 0.00 0.00 0.00 3.56
165 169 4.446371 GCTTTAGTCCATGTGTCTAGCAT 58.554 43.478 0.00 0.00 0.00 3.79
167 171 2.860735 CGCTTTAGTCCATGTGTCTAGC 59.139 50.000 0.00 0.00 0.00 3.42
168 172 4.371855 TCGCTTTAGTCCATGTGTCTAG 57.628 45.455 0.00 0.00 0.00 2.43
169 173 4.441495 CCATCGCTTTAGTCCATGTGTCTA 60.441 45.833 0.00 0.00 0.00 2.59
170 174 3.525537 CATCGCTTTAGTCCATGTGTCT 58.474 45.455 0.00 0.00 0.00 3.41
172 176 2.632377 CCATCGCTTTAGTCCATGTGT 58.368 47.619 0.00 0.00 0.00 3.72
173 177 1.942657 CCCATCGCTTTAGTCCATGTG 59.057 52.381 0.00 0.00 0.00 3.21
174 178 1.837439 TCCCATCGCTTTAGTCCATGT 59.163 47.619 0.00 0.00 0.00 3.21
175 179 2.620251 TCCCATCGCTTTAGTCCATG 57.380 50.000 0.00 0.00 0.00 3.66
176 180 3.864789 AATCCCATCGCTTTAGTCCAT 57.135 42.857 0.00 0.00 0.00 3.41
177 181 3.644966 AAATCCCATCGCTTTAGTCCA 57.355 42.857 0.00 0.00 0.00 4.02
178 182 3.489229 GCAAAATCCCATCGCTTTAGTCC 60.489 47.826 0.00 0.00 0.00 3.85
179 183 3.695816 GCAAAATCCCATCGCTTTAGTC 58.304 45.455 0.00 0.00 0.00 2.59
180 184 2.097466 CGCAAAATCCCATCGCTTTAGT 59.903 45.455 0.00 0.00 0.00 2.24
217 221 7.675062 TGCTATTTTGCCCAATTAGAAAAAGA 58.325 30.769 1.34 0.00 0.00 2.52
218 222 7.903995 TGCTATTTTGCCCAATTAGAAAAAG 57.096 32.000 1.34 0.00 0.00 2.27
224 228 6.041296 AGGAGAATGCTATTTTGCCCAATTAG 59.959 38.462 0.00 0.00 31.62 1.73
225 229 5.898972 AGGAGAATGCTATTTTGCCCAATTA 59.101 36.000 0.00 0.00 31.62 1.40
227 231 4.292643 AGGAGAATGCTATTTTGCCCAAT 58.707 39.130 0.00 0.00 31.62 3.16
228 232 3.701040 GAGGAGAATGCTATTTTGCCCAA 59.299 43.478 0.00 0.00 36.27 4.12
246 1979 1.134228 GGGGCGGTTAATTAGGAGGA 58.866 55.000 0.00 0.00 0.00 3.71
327 2061 2.223805 TGCTACTCATCATGGCACGTAG 60.224 50.000 0.00 1.26 0.00 3.51
328 2062 1.754226 TGCTACTCATCATGGCACGTA 59.246 47.619 0.00 0.00 0.00 3.57
329 2063 0.536724 TGCTACTCATCATGGCACGT 59.463 50.000 0.00 0.00 0.00 4.49
330 2064 1.655484 TTGCTACTCATCATGGCACG 58.345 50.000 0.00 0.00 32.47 5.34
331 2065 2.223433 GCTTTGCTACTCATCATGGCAC 60.223 50.000 0.00 0.00 32.47 5.01
332 2066 2.019249 GCTTTGCTACTCATCATGGCA 58.981 47.619 0.00 0.00 0.00 4.92
333 2067 2.290093 GAGCTTTGCTACTCATCATGGC 59.710 50.000 0.00 0.00 39.88 4.40
334 2068 3.538591 TGAGCTTTGCTACTCATCATGG 58.461 45.455 0.00 0.00 39.88 3.66
340 2074 4.893608 TGTTGTATGAGCTTTGCTACTCA 58.106 39.130 0.00 0.00 46.34 3.41
341 2075 6.253746 CAATGTTGTATGAGCTTTGCTACTC 58.746 40.000 0.00 0.00 39.88 2.59
342 2076 5.392380 GCAATGTTGTATGAGCTTTGCTACT 60.392 40.000 6.70 0.00 39.88 2.57
343 2077 4.795278 GCAATGTTGTATGAGCTTTGCTAC 59.205 41.667 6.70 1.33 39.88 3.58
344 2078 4.142403 GGCAATGTTGTATGAGCTTTGCTA 60.142 41.667 12.28 0.00 39.88 3.49
345 2079 3.367703 GGCAATGTTGTATGAGCTTTGCT 60.368 43.478 12.28 0.00 43.88 3.91
476 2227 3.108288 TTGCCACACCAGCGGTACA 62.108 57.895 0.00 0.00 32.11 2.90
493 2246 4.640201 CGGTGATCAATGTTAATCCCAGTT 59.360 41.667 0.00 0.00 0.00 3.16
561 2338 3.398406 TCTCGCACTTTACTGCAATTCA 58.602 40.909 0.00 0.00 36.94 2.57
613 2394 4.787280 CCGAGGTCCAGGGAGCCT 62.787 72.222 13.58 10.81 42.97 4.58
630 2411 1.015109 TCGACGCAGATCAGTAGACC 58.985 55.000 0.00 0.00 0.00 3.85
671 2460 3.839432 AGCGAGCTAACGGGAGGC 61.839 66.667 0.00 0.00 0.00 4.70
798 2872 2.644212 CGCTGACAGGTGAGCTCCT 61.644 63.158 12.15 0.00 37.68 3.69
1003 3081 1.888215 AGCTGTGTTGGTGTCTGATG 58.112 50.000 0.00 0.00 0.00 3.07
1032 3110 0.762418 CTGGTAGTGGTGTTGGTGGA 59.238 55.000 0.00 0.00 0.00 4.02
1077 3194 6.605471 TCACAAGCTTGAGGTCTAATAAGA 57.395 37.500 32.50 9.20 0.00 2.10
1079 3196 6.535150 CGAATCACAAGCTTGAGGTCTAATAA 59.465 38.462 32.50 6.77 0.00 1.40
1080 3197 6.042777 CGAATCACAAGCTTGAGGTCTAATA 58.957 40.000 32.50 7.52 0.00 0.98
1081 3198 4.872691 CGAATCACAAGCTTGAGGTCTAAT 59.127 41.667 32.50 10.94 0.00 1.73
1107 3228 2.627699 GAGGAGCTAGCTTGAGTATGCT 59.372 50.000 20.42 5.02 40.13 3.79
1140 3266 1.446099 GCTCATGACCTTCGACGCA 60.446 57.895 0.00 0.00 0.00 5.24
1590 4271 6.753180 ACATATAGGATAATAGGAGCATGCG 58.247 40.000 13.01 0.00 0.00 4.73
1660 4504 1.831652 CGGCCTGTTGACTCTTCCCT 61.832 60.000 0.00 0.00 0.00 4.20
1705 4555 1.098869 TGAAGTCGCACCTGCAAAAA 58.901 45.000 0.00 0.00 42.21 1.94
1706 4556 1.317613 ATGAAGTCGCACCTGCAAAA 58.682 45.000 0.00 0.00 42.21 2.44
1707 4557 1.317613 AATGAAGTCGCACCTGCAAA 58.682 45.000 0.00 0.00 42.21 3.68
1708 4558 1.317613 AAATGAAGTCGCACCTGCAA 58.682 45.000 0.00 0.00 42.21 4.08
1709 4559 1.001487 CAAAATGAAGTCGCACCTGCA 60.001 47.619 0.00 0.00 42.21 4.41
1710 4560 1.689959 CAAAATGAAGTCGCACCTGC 58.310 50.000 0.00 0.00 37.78 4.85
1711 4561 1.689959 GCAAAATGAAGTCGCACCTG 58.310 50.000 0.00 0.00 0.00 4.00
1712 4562 0.238289 CGCAAAATGAAGTCGCACCT 59.762 50.000 0.00 0.00 0.00 4.00
1713 4563 0.040425 ACGCAAAATGAAGTCGCACC 60.040 50.000 0.00 0.00 0.00 5.01
1714 4564 1.447938 CAACGCAAAATGAAGTCGCAC 59.552 47.619 0.00 0.00 0.00 5.34
1715 4565 1.332065 TCAACGCAAAATGAAGTCGCA 59.668 42.857 0.00 0.00 0.00 5.10
1716 4566 2.031037 TCAACGCAAAATGAAGTCGC 57.969 45.000 0.00 0.00 0.00 5.19
1717 4567 5.559694 AAAATCAACGCAAAATGAAGTCG 57.440 34.783 0.00 0.00 0.00 4.18
1718 4568 7.165427 AGAAAAATCAACGCAAAATGAAGTC 57.835 32.000 0.00 0.00 0.00 3.01
1719 4569 7.277539 TCAAGAAAAATCAACGCAAAATGAAGT 59.722 29.630 0.00 0.00 0.00 3.01
1720 4570 7.620215 TCAAGAAAAATCAACGCAAAATGAAG 58.380 30.769 0.00 0.00 0.00 3.02
1721 4571 7.531280 TCAAGAAAAATCAACGCAAAATGAA 57.469 28.000 0.00 0.00 0.00 2.57
1722 4572 7.531280 TTCAAGAAAAATCAACGCAAAATGA 57.469 28.000 0.00 0.00 0.00 2.57
1723 4573 6.355144 GCTTCAAGAAAAATCAACGCAAAATG 59.645 34.615 0.00 0.00 0.00 2.32
1813 4673 1.459450 GGCAAAGCCGTATCTTCCAA 58.541 50.000 0.00 0.00 39.62 3.53
2000 4949 4.498513 CGGCATGCAGAAATATGAATGTGT 60.499 41.667 21.36 0.00 38.34 3.72
2024 4973 4.541779 CAGGAGCTACATATCGAAGTGTC 58.458 47.826 9.04 0.00 0.00 3.67
2124 5154 3.817084 AGCCATGAACATATCCAACGATG 59.183 43.478 0.00 0.00 0.00 3.84
2128 5158 9.448438 TGTATAATAGCCATGAACATATCCAAC 57.552 33.333 0.00 0.00 0.00 3.77
2174 5239 0.397535 ACATCCCACCCAATGATGCC 60.398 55.000 0.00 0.00 39.55 4.40
2178 5243 3.641046 CCATAAACATCCCACCCAATGA 58.359 45.455 0.00 0.00 0.00 2.57
2189 5254 6.986817 ACACTACATGTCTAGCCATAAACATC 59.013 38.462 0.00 0.00 36.54 3.06
2217 5282 3.129988 CCCTCACAATGAATGAAAGAGGC 59.870 47.826 0.00 0.00 40.97 4.70
2218 5283 3.698040 CCCCTCACAATGAATGAAAGAGG 59.302 47.826 0.00 0.00 41.46 3.69
2219 5284 4.338879 ACCCCTCACAATGAATGAAAGAG 58.661 43.478 0.00 0.00 0.00 2.85
2220 5285 4.335416 GACCCCTCACAATGAATGAAAGA 58.665 43.478 0.00 0.00 0.00 2.52
2221 5286 3.127548 CGACCCCTCACAATGAATGAAAG 59.872 47.826 0.00 0.00 0.00 2.62
2223 5288 2.710377 CGACCCCTCACAATGAATGAA 58.290 47.619 0.00 0.00 0.00 2.57
2225 5290 0.734889 GCGACCCCTCACAATGAATG 59.265 55.000 0.00 0.00 0.00 2.67
2226 5291 0.620556 AGCGACCCCTCACAATGAAT 59.379 50.000 0.00 0.00 0.00 2.57
2227 5292 1.066430 GTAGCGACCCCTCACAATGAA 60.066 52.381 0.00 0.00 0.00 2.57
2229 5294 0.249120 TGTAGCGACCCCTCACAATG 59.751 55.000 0.00 0.00 0.00 2.82
2230 5295 0.249398 GTGTAGCGACCCCTCACAAT 59.751 55.000 0.00 0.00 0.00 2.71
2231 5296 1.669440 GTGTAGCGACCCCTCACAA 59.331 57.895 0.00 0.00 0.00 3.33
2233 5298 2.577593 GGTGTAGCGACCCCTCAC 59.422 66.667 0.00 0.00 0.00 3.51
2234 5299 3.066190 CGGTGTAGCGACCCCTCA 61.066 66.667 0.00 0.00 31.57 3.86
2235 5300 3.834799 CCGGTGTAGCGACCCCTC 61.835 72.222 4.90 0.00 31.57 4.30
2238 5303 3.152400 ATCCCGGTGTAGCGACCC 61.152 66.667 0.00 0.00 31.57 4.46
2239 5304 1.745320 ATCATCCCGGTGTAGCGACC 61.745 60.000 0.00 0.00 0.00 4.79
2269 6626 6.509418 TTCCATGACTAAAATAGGTGCAAC 57.491 37.500 0.00 0.00 0.00 4.17
2275 6632 7.998964 AGGTAACCATTCCATGACTAAAATAGG 59.001 37.037 0.00 0.00 37.17 2.57
2276 6633 8.980481 AGGTAACCATTCCATGACTAAAATAG 57.020 34.615 0.00 0.00 37.17 1.73
2294 6651 7.649705 GCTATTACTTTAGTTCGGTAGGTAACC 59.350 40.741 0.00 0.00 45.77 2.85
2295 6652 8.409371 AGCTATTACTTTAGTTCGGTAGGTAAC 58.591 37.037 0.00 0.00 0.00 2.50
2296 6653 8.525290 AGCTATTACTTTAGTTCGGTAGGTAA 57.475 34.615 0.00 0.00 0.00 2.85
2297 6654 7.041780 CGAGCTATTACTTTAGTTCGGTAGGTA 60.042 40.741 9.09 0.00 44.33 3.08
2298 6655 6.238593 CGAGCTATTACTTTAGTTCGGTAGGT 60.239 42.308 9.09 0.00 44.33 3.08
2301 6658 6.238484 GGTCGAGCTATTACTTTAGTTCGGTA 60.238 42.308 7.51 0.00 46.50 4.02
2302 6659 5.449725 GGTCGAGCTATTACTTTAGTTCGGT 60.450 44.000 7.51 0.00 46.50 4.69
2305 6662 7.516943 GCAATGGTCGAGCTATTACTTTAGTTC 60.517 40.741 16.64 0.00 0.00 3.01
2306 6663 6.258068 GCAATGGTCGAGCTATTACTTTAGTT 59.742 38.462 16.64 0.00 0.00 2.24
2308 6665 5.753438 TGCAATGGTCGAGCTATTACTTTAG 59.247 40.000 16.64 3.06 0.00 1.85
2309 6666 5.666462 TGCAATGGTCGAGCTATTACTTTA 58.334 37.500 16.64 0.00 0.00 1.85
2310 6667 4.513442 TGCAATGGTCGAGCTATTACTTT 58.487 39.130 16.64 0.00 0.00 2.66
2311 6668 4.137116 TGCAATGGTCGAGCTATTACTT 57.863 40.909 16.64 0.00 0.00 2.24
2313 6670 3.364366 GCATGCAATGGTCGAGCTATTAC 60.364 47.826 14.21 9.08 46.86 1.89
2314 6671 2.807967 GCATGCAATGGTCGAGCTATTA 59.192 45.455 14.21 0.00 46.86 0.98
2315 6672 1.605710 GCATGCAATGGTCGAGCTATT 59.394 47.619 14.21 10.73 46.86 1.73
2316 6673 1.233019 GCATGCAATGGTCGAGCTAT 58.767 50.000 14.21 5.02 46.86 2.97
2317 6674 0.107752 TGCATGCAATGGTCGAGCTA 60.108 50.000 20.30 2.64 46.86 3.32
2318 6675 1.377594 TGCATGCAATGGTCGAGCT 60.378 52.632 20.30 0.00 46.86 4.09
2319 6676 1.226491 GTGCATGCAATGGTCGAGC 60.226 57.895 24.58 7.89 46.86 5.03
2320 6677 1.028330 AGGTGCATGCAATGGTCGAG 61.028 55.000 24.58 0.00 46.86 4.04
2321 6678 0.608856 AAGGTGCATGCAATGGTCGA 60.609 50.000 24.58 0.00 46.86 4.20
2322 6679 0.244450 AAAGGTGCATGCAATGGTCG 59.756 50.000 24.58 0.00 46.86 4.79
2323 6680 1.001181 ACAAAGGTGCATGCAATGGTC 59.999 47.619 24.58 9.53 46.86 4.02
2325 6682 1.801771 CAACAAAGGTGCATGCAATGG 59.198 47.619 24.58 11.93 46.86 3.16
2327 6684 1.515081 GCAACAAAGGTGCATGCAAT 58.485 45.000 24.58 11.76 39.49 3.56
2329 6686 1.069427 GGCAACAAAGGTGCATGCA 59.931 52.632 18.46 18.46 40.76 3.96
2330 6687 3.955775 GGCAACAAAGGTGCATGC 58.044 55.556 11.82 11.82 39.16 4.06
2342 6699 0.894835 ATCGGTGGGAAAATGGCAAC 59.105 50.000 0.00 0.00 0.00 4.17
2344 6701 2.516227 TAATCGGTGGGAAAATGGCA 57.484 45.000 0.00 0.00 0.00 4.92
2346 6703 7.049799 ACAATAATAATCGGTGGGAAAATGG 57.950 36.000 0.00 0.00 0.00 3.16
2369 6856 9.427127 GCTCTTCATCGAAGAACAAAATTATAC 57.573 33.333 7.76 0.00 46.18 1.47
2371 6858 7.121168 TGGCTCTTCATCGAAGAACAAAATTAT 59.879 33.333 7.76 0.00 46.18 1.28
2379 6866 3.238108 TCTGGCTCTTCATCGAAGAAC 57.762 47.619 7.76 3.63 46.18 3.01
2381 6868 4.211125 ACTATCTGGCTCTTCATCGAAGA 58.789 43.478 6.29 6.29 45.01 2.87
2382 6869 4.582701 ACTATCTGGCTCTTCATCGAAG 57.417 45.455 0.00 0.00 40.65 3.79
2385 6872 6.266168 AGATTACTATCTGGCTCTTCATCG 57.734 41.667 0.00 0.00 39.66 3.84
2395 6882 5.712446 TGGCACTAGCTAGATTACTATCTGG 59.288 44.000 27.45 0.00 41.07 3.86
2398 6885 7.164230 ACATGGCACTAGCTAGATTACTATC 57.836 40.000 27.45 7.89 41.70 2.08
2399 6886 7.147983 GCTACATGGCACTAGCTAGATTACTAT 60.148 40.741 27.45 12.58 41.70 2.12
2400 6887 6.151312 GCTACATGGCACTAGCTAGATTACTA 59.849 42.308 27.45 10.94 41.70 1.82
2401 6888 5.047660 GCTACATGGCACTAGCTAGATTACT 60.048 44.000 27.45 0.89 41.70 2.24
2402 6889 5.164954 GCTACATGGCACTAGCTAGATTAC 58.835 45.833 27.45 13.74 41.70 1.89
2403 6890 4.832823 TGCTACATGGCACTAGCTAGATTA 59.167 41.667 27.45 10.45 41.70 1.75
2404 6891 3.643320 TGCTACATGGCACTAGCTAGATT 59.357 43.478 27.45 2.54 41.70 2.40
2405 6892 3.234353 TGCTACATGGCACTAGCTAGAT 58.766 45.455 27.45 7.30 41.70 1.98
2406 6893 2.625314 CTGCTACATGGCACTAGCTAGA 59.375 50.000 27.45 4.95 41.70 2.43
2407 6894 2.865670 GCTGCTACATGGCACTAGCTAG 60.866 54.545 19.44 19.44 41.70 3.42
2409 6896 0.179062 GCTGCTACATGGCACTAGCT 60.179 55.000 20.82 0.00 41.70 3.32
2410 6897 0.462581 TGCTGCTACATGGCACTAGC 60.463 55.000 15.85 15.85 37.29 3.42
2411 6898 1.871676 CATGCTGCTACATGGCACTAG 59.128 52.381 10.59 0.00 43.05 2.57
2412 6899 1.957668 CATGCTGCTACATGGCACTA 58.042 50.000 10.59 0.00 43.05 2.74
2420 6907 3.963665 GTGTTTTTCACATGCTGCTACA 58.036 40.909 0.00 0.00 45.51 2.74
2431 6918 6.532302 ACGTTATTTTTCCAGGTGTTTTTCAC 59.468 34.615 0.00 0.00 45.47 3.18
2432 6919 6.631962 ACGTTATTTTTCCAGGTGTTTTTCA 58.368 32.000 0.00 0.00 0.00 2.69
2433 6920 6.075257 CGACGTTATTTTTCCAGGTGTTTTTC 60.075 38.462 0.00 0.00 0.00 2.29
2434 6921 5.744819 CGACGTTATTTTTCCAGGTGTTTTT 59.255 36.000 0.00 0.00 0.00 1.94
2435 6922 5.163632 ACGACGTTATTTTTCCAGGTGTTTT 60.164 36.000 0.00 0.00 0.00 2.43
2436 6923 4.336153 ACGACGTTATTTTTCCAGGTGTTT 59.664 37.500 0.00 0.00 0.00 2.83
2437 6924 3.878699 ACGACGTTATTTTTCCAGGTGTT 59.121 39.130 0.00 0.00 0.00 3.32
2439 6926 3.805823 CACGACGTTATTTTTCCAGGTG 58.194 45.455 0.00 0.00 0.00 4.00
2441 6928 2.413634 GGCACGACGTTATTTTTCCAGG 60.414 50.000 0.00 0.00 0.00 4.45
2442 6929 2.224549 TGGCACGACGTTATTTTTCCAG 59.775 45.455 0.00 0.00 0.00 3.86
2443 6930 2.219458 TGGCACGACGTTATTTTTCCA 58.781 42.857 0.00 0.00 0.00 3.53
2444 6931 2.973419 TGGCACGACGTTATTTTTCC 57.027 45.000 0.00 0.00 0.00 3.13
2445 6932 3.817238 ACATGGCACGACGTTATTTTTC 58.183 40.909 0.00 0.00 0.00 2.29
2446 6933 3.907894 ACATGGCACGACGTTATTTTT 57.092 38.095 0.00 0.00 0.00 1.94
2447 6934 3.998341 ACTACATGGCACGACGTTATTTT 59.002 39.130 0.00 0.00 0.00 1.82
2448 6935 3.592059 ACTACATGGCACGACGTTATTT 58.408 40.909 0.00 0.00 0.00 1.40
2449 6936 3.241067 ACTACATGGCACGACGTTATT 57.759 42.857 0.00 0.00 0.00 1.40
2450 6937 2.953466 ACTACATGGCACGACGTTAT 57.047 45.000 0.00 0.00 0.00 1.89
2451 6938 5.239087 TCATATACTACATGGCACGACGTTA 59.761 40.000 0.00 0.00 0.00 3.18
2452 6939 2.953466 ATACTACATGGCACGACGTT 57.047 45.000 0.00 0.00 0.00 3.99
2453 6940 3.566742 TCATATACTACATGGCACGACGT 59.433 43.478 0.00 0.00 0.00 4.34
2454 6941 3.912563 GTCATATACTACATGGCACGACG 59.087 47.826 0.00 0.00 0.00 5.12
2455 6942 5.122512 AGTCATATACTACATGGCACGAC 57.877 43.478 0.00 0.00 36.36 4.34
2456 6943 5.784578 AAGTCATATACTACATGGCACGA 57.215 39.130 0.00 0.00 37.50 4.35
2457 6944 6.582672 CACTAAGTCATATACTACATGGCACG 59.417 42.308 0.00 0.00 37.50 5.34
2458 6945 6.366332 GCACTAAGTCATATACTACATGGCAC 59.634 42.308 0.00 0.00 37.50 5.01
2459 6946 6.267699 AGCACTAAGTCATATACTACATGGCA 59.732 38.462 0.00 0.00 37.50 4.92
2460 6947 6.692486 AGCACTAAGTCATATACTACATGGC 58.308 40.000 0.00 0.00 37.50 4.40
2461 6948 7.316640 GGAGCACTAAGTCATATACTACATGG 58.683 42.308 0.00 0.00 37.50 3.66
2462 6949 7.039714 TGGGAGCACTAAGTCATATACTACATG 60.040 40.741 0.00 0.00 37.50 3.21
2464 6951 6.370453 TGGGAGCACTAAGTCATATACTACA 58.630 40.000 0.00 0.00 37.50 2.74
2466 6953 7.907841 TTTGGGAGCACTAAGTCATATACTA 57.092 36.000 0.00 0.00 37.50 1.82
2467 6954 6.808321 TTTGGGAGCACTAAGTCATATACT 57.192 37.500 0.00 0.00 41.49 2.12
2468 6955 6.428159 CCATTTGGGAGCACTAAGTCATATAC 59.572 42.308 0.00 0.00 40.01 1.47
2469 6956 6.101150 ACCATTTGGGAGCACTAAGTCATATA 59.899 38.462 0.96 0.00 41.15 0.86
2470 6957 5.103940 ACCATTTGGGAGCACTAAGTCATAT 60.104 40.000 0.96 0.00 41.15 1.78
2471 6958 4.227300 ACCATTTGGGAGCACTAAGTCATA 59.773 41.667 0.96 0.00 41.15 2.15
2472 6959 3.010584 ACCATTTGGGAGCACTAAGTCAT 59.989 43.478 0.96 0.00 41.15 3.06
2474 6961 3.010420 GACCATTTGGGAGCACTAAGTC 58.990 50.000 0.96 0.00 41.15 3.01
2475 6962 2.375174 TGACCATTTGGGAGCACTAAGT 59.625 45.455 0.96 0.00 41.15 2.24
2476 6963 3.071874 TGACCATTTGGGAGCACTAAG 57.928 47.619 0.96 0.00 41.15 2.18
2477 6964 3.266772 AGATGACCATTTGGGAGCACTAA 59.733 43.478 0.96 0.00 41.15 2.24
2478 6965 2.846206 AGATGACCATTTGGGAGCACTA 59.154 45.455 0.96 0.00 41.15 2.74
2480 6967 2.134789 AGATGACCATTTGGGAGCAC 57.865 50.000 0.96 0.00 41.15 4.40
2482 6969 3.091545 TCAAAGATGACCATTTGGGAGC 58.908 45.455 0.96 0.00 41.15 4.70
2483 6970 4.338879 ACTCAAAGATGACCATTTGGGAG 58.661 43.478 4.65 0.00 38.86 4.30
2485 6972 6.604795 AGAATACTCAAAGATGACCATTTGGG 59.395 38.462 0.96 0.00 41.65 4.12


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

AutoCloner maintained by Alex Coulton.