Multiple sequence alignment - TraesCS6D01G387100

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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 TraesCS6D01G387100 chr6D 100.000 3831 0 0 1 3831 464258093 464261923 0.000000e+00 7075.0
1 TraesCS6D01G387100 chr6D 83.648 899 122 19 1 884 464184197 464185085 0.000000e+00 822.0
2 TraesCS6D01G387100 chr6D 97.248 109 2 1 1941 2048 45510040 45510148 2.350000e-42 183.0
3 TraesCS6D01G387100 chr6A 91.334 1731 89 35 2105 3796 610898835 610900543 0.000000e+00 2309.0
4 TraesCS6D01G387100 chr6A 84.181 1966 213 61 6 1943 610896943 610898838 0.000000e+00 1818.0
5 TraesCS6D01G387100 chr6A 84.729 406 44 14 1160 1557 1327272 1327667 1.290000e-104 390.0
6 TraesCS6D01G387100 chr6A 84.422 398 46 10 1167 1557 17430879 17430491 1.000000e-100 377.0
7 TraesCS6D01G387100 chr6A 86.617 269 15 4 1658 1926 17430425 17430178 1.050000e-70 278.0
8 TraesCS6D01G387100 chr6A 86.735 98 8 3 2302 2394 465615704 465615607 1.880000e-18 104.0
9 TraesCS6D01G387100 chr6A 100.000 31 0 0 3801 3831 610901224 610901254 1.490000e-04 58.4
10 TraesCS6D01G387100 chr6B 84.371 1414 129 53 2435 3796 708020473 708021846 0.000000e+00 1303.0
11 TraesCS6D01G387100 chr6B 83.882 608 51 25 932 1506 708019195 708019788 1.570000e-148 536.0
12 TraesCS6D01G387100 chr6B 90.347 259 21 2 1688 1943 708020029 708020286 1.710000e-88 337.0
13 TraesCS6D01G387100 chr6B 76.129 620 85 35 1160 1744 647769755 647770346 2.270000e-67 267.0
14 TraesCS6D01G387100 chr6B 90.674 193 17 1 2105 2296 708020283 708020475 4.910000e-64 255.0
15 TraesCS6D01G387100 chr6B 88.820 161 18 0 1765 1925 464518715 464518875 8.390000e-47 198.0
16 TraesCS6D01G387100 chr3D 85.432 405 42 11 1167 1563 3896745 3896350 4.610000e-109 405.0
17 TraesCS6D01G387100 chr3D 86.636 217 8 6 1658 1874 3896290 3896095 1.790000e-53 220.0
18 TraesCS6D01G387100 chr3D 98.305 59 0 1 2052 2109 158930488 158930546 6.770000e-18 102.0
19 TraesCS6D01G387100 chr3D 100.000 55 0 0 2052 2106 158936603 158936657 6.770000e-18 102.0
20 TraesCS6D01G387100 chr3D 100.000 55 0 0 2052 2106 589247832 589247886 6.770000e-18 102.0
21 TraesCS6D01G387100 chr4D 99.083 218 2 0 3181 3398 90039155 90038938 3.590000e-105 392.0
22 TraesCS6D01G387100 chr5B 83.784 407 49 12 1167 1563 676286603 676286204 1.680000e-98 370.0
23 TraesCS6D01G387100 chr5B 80.196 409 57 8 1533 1940 699304427 699304042 6.260000e-73 285.0
24 TraesCS6D01G387100 chr5B 86.194 268 16 4 1658 1925 676286144 676285898 1.750000e-68 270.0
25 TraesCS6D01G387100 chr5B 100.000 55 0 0 2052 2106 413612427 413612481 6.770000e-18 102.0
26 TraesCS6D01G387100 chr1B 83.744 406 48 12 1160 1557 683657466 683657861 6.050000e-98 368.0
27 TraesCS6D01G387100 chr1B 83.210 405 52 11 1167 1563 143667263 143666867 1.310000e-94 357.0
28 TraesCS6D01G387100 chr1B 86.992 246 11 6 1658 1903 683657927 683658151 1.370000e-64 257.0
29 TraesCS6D01G387100 chr1A 83.498 406 49 9 1160 1557 66229056 66229451 2.810000e-96 363.0
30 TraesCS6D01G387100 chr1A 85.075 268 19 4 1658 1925 66229517 66229763 1.770000e-63 254.0
31 TraesCS6D01G387100 chr1A 97.248 109 2 1 1941 2048 554459996 554459888 2.350000e-42 183.0
32 TraesCS6D01G387100 chr4A 76.015 813 112 45 1160 1935 724422122 724422888 1.020000e-90 344.0
33 TraesCS6D01G387100 chr4A 86.598 97 6 6 2302 2395 734074225 734074317 2.440000e-17 100.0
34 TraesCS6D01G387100 chr7D 81.418 409 52 8 1533 1940 573298621 573298236 2.870000e-81 313.0
35 TraesCS6D01G387100 chr7D 97.248 109 2 1 1941 2048 77240359 77240251 2.350000e-42 183.0
36 TraesCS6D01G387100 chr7D 88.889 99 6 1 2302 2395 263946345 263946247 2.420000e-22 117.0
37 TraesCS6D01G387100 chr2D 81.095 402 53 19 1160 1557 490507845 490508227 2.240000e-77 300.0
38 TraesCS6D01G387100 chr2D 87.383 214 6 6 1658 1871 490508291 490508483 3.850000e-55 226.0
39 TraesCS6D01G387100 chr2D 97.248 109 2 1 1941 2048 9786672 9786564 2.350000e-42 183.0
40 TraesCS6D01G387100 chr7A 78.960 404 60 10 1535 1937 351155827 351156206 6.350000e-63 252.0
41 TraesCS6D01G387100 chr5D 98.148 108 2 0 1941 2048 120801400 120801293 5.050000e-44 189.0
42 TraesCS6D01G387100 chr5D 97.248 109 2 1 1941 2048 503288841 503288733 2.350000e-42 183.0
43 TraesCS6D01G387100 chr5D 97.248 109 2 1 1941 2048 512408009 512408117 2.350000e-42 183.0
44 TraesCS6D01G387100 chr5D 97.248 109 2 1 1941 2048 512414944 512415052 2.350000e-42 183.0
45 TraesCS6D01G387100 chr7B 79.195 298 38 13 1533 1829 236936296 236936022 6.540000e-43 185.0
46 TraesCS6D01G387100 chr1D 97.248 109 2 1 1941 2048 254418589 254418481 2.350000e-42 183.0
47 TraesCS6D01G387100 chr1D 87.879 99 7 1 2302 2395 394864536 394864438 1.130000e-20 111.0
48 TraesCS6D01G387100 chrUn 100.000 58 0 0 2049 2106 371790031 371790088 1.460000e-19 108.0
49 TraesCS6D01G387100 chrUn 100.000 58 0 0 2049 2106 418328968 418328911 1.460000e-19 108.0
50 TraesCS6D01G387100 chrUn 100.000 58 0 0 2049 2106 443328573 443328516 1.460000e-19 108.0
51 TraesCS6D01G387100 chr5A 100.000 55 0 0 2052 2106 482024393 482024339 6.770000e-18 102.0
52 TraesCS6D01G387100 chr3B 100.000 55 0 0 2052 2106 201555804 201555750 6.770000e-18 102.0
53 TraesCS6D01G387100 chr3B 83.673 98 9 3 2302 2394 547576550 547576455 6.820000e-13 86.1


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 TraesCS6D01G387100 chr6D 464258093 464261923 3830 False 7075.000000 7075 100.000000 1 3831 1 chr6D.!!$F3 3830
1 TraesCS6D01G387100 chr6D 464184197 464185085 888 False 822.000000 822 83.648000 1 884 1 chr6D.!!$F2 883
2 TraesCS6D01G387100 chr6A 610896943 610901254 4311 False 1395.133333 2309 91.838333 6 3831 3 chr6A.!!$F2 3825
3 TraesCS6D01G387100 chr6A 17430178 17430879 701 True 327.500000 377 85.519500 1167 1926 2 chr6A.!!$R2 759
4 TraesCS6D01G387100 chr6B 708019195 708021846 2651 False 607.750000 1303 87.318500 932 3796 4 chr6B.!!$F3 2864
5 TraesCS6D01G387100 chr6B 647769755 647770346 591 False 267.000000 267 76.129000 1160 1744 1 chr6B.!!$F2 584
6 TraesCS6D01G387100 chr3D 3896095 3896745 650 True 312.500000 405 86.034000 1167 1874 2 chr3D.!!$R1 707
7 TraesCS6D01G387100 chr5B 676285898 676286603 705 True 320.000000 370 84.989000 1167 1925 2 chr5B.!!$R2 758
8 TraesCS6D01G387100 chr1B 683657466 683658151 685 False 312.500000 368 85.368000 1160 1903 2 chr1B.!!$F1 743
9 TraesCS6D01G387100 chr1A 66229056 66229763 707 False 308.500000 363 84.286500 1160 1925 2 chr1A.!!$F1 765
10 TraesCS6D01G387100 chr4A 724422122 724422888 766 False 344.000000 344 76.015000 1160 1935 1 chr4A.!!$F1 775
11 TraesCS6D01G387100 chr2D 490507845 490508483 638 False 263.000000 300 84.239000 1160 1871 2 chr2D.!!$F1 711

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
447 450 1.128200 TATGGCGGCACCTCAGTAAT 58.872 50.0 16.34 0.0 40.22 1.89 F
1558 1783 0.534203 TTGCAACCTTGTCGGAGTCC 60.534 55.0 0.00 0.0 36.31 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1940 2189 0.45460 CCTTAGACTTAGACCGCGCA 59.545 55.0 8.75 0.0 0.00 6.09 R
2857 3133 0.26023 TGGGGAGTTGCTGGACAAAA 59.740 50.0 0.00 0.0 40.82 2.44 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
24 25 4.965814 ACCAAATGTATCTGAGATCGCAT 58.034 39.130 0.00 2.43 0.00 4.73
26 27 6.524734 ACCAAATGTATCTGAGATCGCATAA 58.475 36.000 0.00 0.00 0.00 1.90
27 28 7.164122 ACCAAATGTATCTGAGATCGCATAAT 58.836 34.615 0.00 0.00 0.00 1.28
35 36 5.427378 TCTGAGATCGCATAATCAAAACCA 58.573 37.500 0.00 0.00 0.00 3.67
82 83 8.564574 GGCCATAAAGTATCATAATTTTCACGA 58.435 33.333 0.00 0.00 0.00 4.35
93 94 4.871933 AATTTTCACGAGCCCAAAGATT 57.128 36.364 0.00 0.00 0.00 2.40
105 106 3.259123 GCCCAAAGATTTTGTCACTCCAT 59.741 43.478 1.40 0.00 0.00 3.41
114 115 7.262772 AGATTTTGTCACTCCATTAATGCATG 58.737 34.615 10.11 7.55 0.00 4.06
131 132 9.956640 TTAATGCATGAGGAAAAACCAATTTAT 57.043 25.926 0.00 0.00 42.04 1.40
135 136 6.313658 GCATGAGGAAAAACCAATTTATCACC 59.686 38.462 0.00 0.00 42.04 4.02
154 155 2.304761 ACCGGAAAAGCAGGATGACTAA 59.695 45.455 9.46 0.00 39.69 2.24
157 158 3.941483 CGGAAAAGCAGGATGACTAACAT 59.059 43.478 0.00 0.00 39.69 2.71
189 190 7.095102 TGACGTCGATCATATATCTCCGTTAAA 60.095 37.037 11.62 0.00 0.00 1.52
192 193 7.216505 CGTCGATCATATATCTCCGTTAAACAG 59.783 40.741 0.00 0.00 0.00 3.16
193 194 8.021973 GTCGATCATATATCTCCGTTAAACAGT 58.978 37.037 0.00 0.00 0.00 3.55
245 246 5.868454 AGGGAGTTTGATTTTGGATTTTGG 58.132 37.500 0.00 0.00 0.00 3.28
248 249 6.942005 GGGAGTTTGATTTTGGATTTTGGAAT 59.058 34.615 0.00 0.00 0.00 3.01
260 261 5.236047 TGGATTTTGGAATTTTCAAAGCACG 59.764 36.000 3.19 0.00 35.81 5.34
269 270 7.328249 TGGAATTTTCAAAGCACGACATTAATC 59.672 33.333 0.00 0.00 0.00 1.75
272 273 7.795431 TTTTCAAAGCACGACATTAATCATC 57.205 32.000 0.00 0.00 0.00 2.92
419 422 7.534282 TCACAAAAATTAGCTCGCATATTTCA 58.466 30.769 0.00 0.00 0.00 2.69
424 427 8.566008 AAAATTAGCTCGCATATTTCACAATC 57.434 30.769 0.00 0.00 0.00 2.67
432 435 7.061441 GCTCGCATATTTCACAATCAATTATGG 59.939 37.037 0.00 0.00 0.00 2.74
447 450 1.128200 TATGGCGGCACCTCAGTAAT 58.872 50.000 16.34 0.00 40.22 1.89
467 471 7.609146 CAGTAATATGTCCATGTGGCTCATAAT 59.391 37.037 15.22 11.79 36.33 1.28
478 482 9.467258 CCATGTGGCTCATAATATTTGTTTTAG 57.533 33.333 1.15 0.00 34.67 1.85
500 504 6.351327 AGCGTTGTCTTAGAATAATGCTTC 57.649 37.500 16.43 0.00 41.22 3.86
598 605 1.206811 TGGGACCATGTGGATCAGCA 61.207 55.000 5.96 0.00 38.94 4.41
601 608 1.952296 GGACCATGTGGATCAGCATTC 59.048 52.381 5.96 0.00 38.94 2.67
602 609 1.600957 GACCATGTGGATCAGCATTCG 59.399 52.381 5.96 0.00 38.94 3.34
603 610 1.210234 ACCATGTGGATCAGCATTCGA 59.790 47.619 5.96 0.00 38.94 3.71
604 611 1.600957 CCATGTGGATCAGCATTCGAC 59.399 52.381 0.00 0.00 37.39 4.20
623 630 5.981174 TCGACGACGAAGAATGAAATTTTT 58.019 33.333 7.68 0.00 45.74 1.94
702 709 5.625311 CGTTTTGCTGGATAGAACAACTTTC 59.375 40.000 0.00 0.00 0.00 2.62
896 911 9.670719 TGAAAAAGGAACAAATGAAACAAAAAC 57.329 25.926 0.00 0.00 0.00 2.43
897 912 9.670719 GAAAAAGGAACAAATGAAACAAAAACA 57.329 25.926 0.00 0.00 0.00 2.83
993 1011 3.787001 GCGGGAAGGTGGGGAGAG 61.787 72.222 0.00 0.00 0.00 3.20
1022 1049 2.057922 AGAAAACCTCTTCCTGGCTCA 58.942 47.619 0.00 0.00 0.00 4.26
1160 1201 1.305718 GCCACCACTCCCTCTCTCT 60.306 63.158 0.00 0.00 0.00 3.10
1163 1204 1.473258 CACCACTCCCTCTCTCTCTG 58.527 60.000 0.00 0.00 0.00 3.35
1244 1287 3.993736 CCCGATTTGATTTGTTTGGGTTC 59.006 43.478 0.00 0.00 0.00 3.62
1245 1289 4.502259 CCCGATTTGATTTGTTTGGGTTCA 60.502 41.667 0.00 0.00 0.00 3.18
1257 1327 4.339530 TGTTTGGGTTCAAATTGATCGTGA 59.660 37.500 0.00 0.00 43.73 4.35
1258 1328 5.010516 TGTTTGGGTTCAAATTGATCGTGAT 59.989 36.000 0.00 0.00 43.73 3.06
1261 1331 3.859386 GGGTTCAAATTGATCGTGATTGC 59.141 43.478 0.00 0.00 0.00 3.56
1262 1332 4.380867 GGGTTCAAATTGATCGTGATTGCT 60.381 41.667 0.00 0.00 0.00 3.91
1269 1350 2.068519 TGATCGTGATTGCTGTGTGTC 58.931 47.619 0.00 0.00 0.00 3.67
1271 1352 1.783284 TCGTGATTGCTGTGTGTCTC 58.217 50.000 0.00 0.00 0.00 3.36
1275 1356 2.992543 GTGATTGCTGTGTGTCTCTCTC 59.007 50.000 0.00 0.00 0.00 3.20
1419 1515 4.750098 TGCTAGACTGCTTGTTAGTGAAAC 59.250 41.667 0.00 0.00 38.67 2.78
1429 1525 5.751243 TTGTTAGTGAAACCAGCTTCTTC 57.249 39.130 0.00 0.00 37.80 2.87
1434 1530 3.005155 AGTGAAACCAGCTTCTTCATTGC 59.995 43.478 5.44 0.00 37.80 3.56
1463 1565 4.997395 CAGTGGTACTGTTGCTATTTCAGT 59.003 41.667 0.90 0.00 41.19 3.41
1464 1566 5.470098 CAGTGGTACTGTTGCTATTTCAGTT 59.530 40.000 2.52 0.00 41.19 3.16
1465 1567 5.470098 AGTGGTACTGTTGCTATTTCAGTTG 59.530 40.000 2.52 0.00 41.66 3.16
1466 1568 5.468746 GTGGTACTGTTGCTATTTCAGTTGA 59.531 40.000 2.52 0.00 41.66 3.18
1467 1569 5.700832 TGGTACTGTTGCTATTTCAGTTGAG 59.299 40.000 2.52 0.00 41.66 3.02
1468 1570 4.756084 ACTGTTGCTATTTCAGTTGAGC 57.244 40.909 0.00 0.00 39.00 4.26
1558 1783 0.534203 TTGCAACCTTGTCGGAGTCC 60.534 55.000 0.00 0.00 36.31 3.85
1602 1848 6.870971 TTCACCAGTTTAGCTAAATTCGTT 57.129 33.333 21.28 3.75 0.00 3.85
1619 1865 7.930513 AATTCGTTGAAAAGAAGGATGAAAC 57.069 32.000 0.00 0.00 0.00 2.78
1646 1892 1.064060 CGGCCTTTTTATTCTGAGCGG 59.936 52.381 0.00 0.00 0.00 5.52
1653 1899 3.753294 TTTATTCTGAGCGGGAGGATC 57.247 47.619 0.00 0.00 0.00 3.36
1655 1901 1.727062 ATTCTGAGCGGGAGGATCAT 58.273 50.000 0.00 0.00 40.89 2.45
1656 1902 0.755079 TTCTGAGCGGGAGGATCATG 59.245 55.000 0.00 0.00 40.89 3.07
1822 2071 6.037172 CCGTTACTGATTAATTCACTTGGAGG 59.963 42.308 0.00 0.00 0.00 4.30
1849 2098 3.582647 TGCATACTCTTCTCTTCCCAACA 59.417 43.478 0.00 0.00 0.00 3.33
1851 2100 5.003804 GCATACTCTTCTCTTCCCAACAAA 58.996 41.667 0.00 0.00 0.00 2.83
1914 2163 2.041485 TGCATTTCTGGGAATGGTCTCA 59.959 45.455 4.07 0.00 37.47 3.27
1928 2177 6.878389 GGAATGGTCTCAGGATTATCTCATTC 59.122 42.308 0.00 0.00 37.97 2.67
1948 2197 4.114997 CCCAAACCATGCGCGGTC 62.115 66.667 8.83 0.00 38.76 4.79
1949 2198 3.055719 CCAAACCATGCGCGGTCT 61.056 61.111 8.83 0.00 38.76 3.85
1950 2199 1.743623 CCAAACCATGCGCGGTCTA 60.744 57.895 8.83 0.00 38.76 2.59
1951 2200 1.302383 CCAAACCATGCGCGGTCTAA 61.302 55.000 8.83 0.00 38.76 2.10
1952 2201 0.096976 CAAACCATGCGCGGTCTAAG 59.903 55.000 8.83 0.00 38.76 2.18
1953 2202 0.321298 AAACCATGCGCGGTCTAAGT 60.321 50.000 8.83 0.00 38.76 2.24
1954 2203 0.739813 AACCATGCGCGGTCTAAGTC 60.740 55.000 8.83 0.00 38.76 3.01
1955 2204 1.141881 CCATGCGCGGTCTAAGTCT 59.858 57.895 8.83 0.00 0.00 3.24
1956 2205 0.384309 CCATGCGCGGTCTAAGTCTA 59.616 55.000 8.83 0.00 0.00 2.59
1957 2206 1.202371 CCATGCGCGGTCTAAGTCTAA 60.202 52.381 8.83 0.00 0.00 2.10
1958 2207 2.120232 CATGCGCGGTCTAAGTCTAAG 58.880 52.381 8.83 0.00 0.00 2.18
1959 2208 0.454600 TGCGCGGTCTAAGTCTAAGG 59.545 55.000 8.83 0.00 0.00 2.69
1960 2209 0.737219 GCGCGGTCTAAGTCTAAGGA 59.263 55.000 8.83 0.00 0.00 3.36
1961 2210 1.133790 GCGCGGTCTAAGTCTAAGGAA 59.866 52.381 8.83 0.00 0.00 3.36
1962 2211 2.416431 GCGCGGTCTAAGTCTAAGGAAA 60.416 50.000 8.83 0.00 0.00 3.13
1963 2212 3.737355 GCGCGGTCTAAGTCTAAGGAAAT 60.737 47.826 8.83 0.00 0.00 2.17
1964 2213 4.498682 GCGCGGTCTAAGTCTAAGGAAATA 60.499 45.833 8.83 0.00 0.00 1.40
1965 2214 5.585390 CGCGGTCTAAGTCTAAGGAAATAA 58.415 41.667 0.00 0.00 0.00 1.40
1966 2215 6.038356 CGCGGTCTAAGTCTAAGGAAATAAA 58.962 40.000 0.00 0.00 0.00 1.40
1967 2216 6.532657 CGCGGTCTAAGTCTAAGGAAATAAAA 59.467 38.462 0.00 0.00 0.00 1.52
1968 2217 7.063780 CGCGGTCTAAGTCTAAGGAAATAAAAA 59.936 37.037 0.00 0.00 0.00 1.94
1997 2246 8.282124 TCGCTTATACAATTTCTTCTACATCG 57.718 34.615 0.00 0.00 0.00 3.84
1998 2247 8.132995 TCGCTTATACAATTTCTTCTACATCGA 58.867 33.333 0.00 0.00 0.00 3.59
1999 2248 8.752254 CGCTTATACAATTTCTTCTACATCGAA 58.248 33.333 0.00 0.00 0.00 3.71
2027 2276 5.782893 ATATCAGAATAGCGGATAGAGGC 57.217 43.478 0.00 0.00 37.15 4.70
2028 2277 2.876581 TCAGAATAGCGGATAGAGGCA 58.123 47.619 0.00 0.00 0.00 4.75
2029 2278 3.435275 TCAGAATAGCGGATAGAGGCAT 58.565 45.455 0.00 0.00 0.00 4.40
2030 2279 3.445450 TCAGAATAGCGGATAGAGGCATC 59.555 47.826 0.00 0.00 0.00 3.91
2031 2280 3.194329 CAGAATAGCGGATAGAGGCATCA 59.806 47.826 0.00 0.00 0.00 3.07
2032 2281 4.029520 AGAATAGCGGATAGAGGCATCAT 58.970 43.478 0.00 0.00 0.00 2.45
2033 2282 4.469227 AGAATAGCGGATAGAGGCATCATT 59.531 41.667 0.00 0.00 0.00 2.57
2034 2283 5.658634 AGAATAGCGGATAGAGGCATCATTA 59.341 40.000 0.00 0.00 0.00 1.90
2035 2284 5.939764 ATAGCGGATAGAGGCATCATTAA 57.060 39.130 0.00 0.00 0.00 1.40
2036 2285 4.623932 AGCGGATAGAGGCATCATTAAA 57.376 40.909 0.00 0.00 0.00 1.52
2037 2286 4.573900 AGCGGATAGAGGCATCATTAAAG 58.426 43.478 0.00 0.00 0.00 1.85
2038 2287 3.686726 GCGGATAGAGGCATCATTAAAGG 59.313 47.826 0.00 0.00 0.00 3.11
2039 2288 4.563580 GCGGATAGAGGCATCATTAAAGGA 60.564 45.833 0.00 0.00 0.00 3.36
2040 2289 5.738909 CGGATAGAGGCATCATTAAAGGAT 58.261 41.667 0.00 0.00 0.00 3.24
2041 2290 6.176183 CGGATAGAGGCATCATTAAAGGATT 58.824 40.000 0.00 0.00 0.00 3.01
2042 2291 6.314896 CGGATAGAGGCATCATTAAAGGATTC 59.685 42.308 0.00 0.00 0.00 2.52
2043 2292 7.170965 GGATAGAGGCATCATTAAAGGATTCA 58.829 38.462 0.00 0.00 0.00 2.57
2044 2293 7.336427 GGATAGAGGCATCATTAAAGGATTCAG 59.664 40.741 0.00 0.00 0.00 3.02
2045 2294 5.383476 AGAGGCATCATTAAAGGATTCAGG 58.617 41.667 0.00 0.00 0.00 3.86
2046 2295 5.103771 AGAGGCATCATTAAAGGATTCAGGT 60.104 40.000 0.00 0.00 0.00 4.00
2047 2296 5.136105 AGGCATCATTAAAGGATTCAGGTC 58.864 41.667 0.00 0.00 0.00 3.85
2048 2297 4.279420 GGCATCATTAAAGGATTCAGGTCC 59.721 45.833 0.00 0.00 38.62 4.46
2049 2298 4.889409 GCATCATTAAAGGATTCAGGTCCA 59.111 41.667 0.00 0.00 40.90 4.02
2050 2299 5.537674 GCATCATTAAAGGATTCAGGTCCAT 59.462 40.000 0.00 0.00 40.90 3.41
2051 2300 6.041296 GCATCATTAAAGGATTCAGGTCCATT 59.959 38.462 0.00 0.00 40.90 3.16
2052 2301 7.418254 GCATCATTAAAGGATTCAGGTCCATTT 60.418 37.037 0.00 0.00 40.90 2.32
2053 2302 8.480501 CATCATTAAAGGATTCAGGTCCATTTT 58.519 33.333 0.00 0.00 40.90 1.82
2054 2303 8.434589 TCATTAAAGGATTCAGGTCCATTTTT 57.565 30.769 0.00 0.00 40.90 1.94
2311 2561 3.132111 TCGTAGCCAAGCATTATGAGTCA 59.868 43.478 0.00 0.00 0.00 3.41
2374 2624 1.405121 CCAGGGCCGACTACACTTTAC 60.405 57.143 0.00 0.00 0.00 2.01
2382 2632 3.820777 GACTACACTTTACCGTCGACT 57.179 47.619 14.70 0.00 0.00 4.18
2389 2639 5.181748 ACACTTTACCGTCGACTAGTCTAT 58.818 41.667 20.34 4.24 0.00 1.98
2405 2655 2.359531 GTCTATGAGTCCCTCAGAACGG 59.640 54.545 0.08 0.00 44.08 4.44
2420 2670 2.492484 AGAACGGCTCTTTGACTCGTAT 59.508 45.455 0.00 0.00 33.52 3.06
2421 2671 3.693085 AGAACGGCTCTTTGACTCGTATA 59.307 43.478 0.00 0.00 33.52 1.47
2432 2682 6.647895 TCTTTGACTCGTATAAACCTTGGTTC 59.352 38.462 5.43 0.00 0.00 3.62
2433 2683 4.824289 TGACTCGTATAAACCTTGGTTCC 58.176 43.478 5.43 0.00 0.00 3.62
2489 2744 3.254060 CTTGCTACATCTGTGCTAACGT 58.746 45.455 0.00 0.00 0.00 3.99
2529 2788 3.790091 TCTTCAGATTGATGGAAGCGAG 58.210 45.455 0.00 0.00 38.29 5.03
2592 2851 1.803555 GTGAAGACAAAGCTCTCAGCC 59.196 52.381 0.00 0.00 43.77 4.85
2640 2899 0.598562 TGGAGCTCGACAACTGACTC 59.401 55.000 7.83 0.00 0.00 3.36
2741 3002 1.589196 GGTCCATGTAGTCGAGCGC 60.589 63.158 0.00 0.00 0.00 5.92
2784 3056 3.195661 GGTATTTCTGATCTCGCGGTTT 58.804 45.455 6.13 0.00 0.00 3.27
2789 3061 1.135373 TCTGATCTCGCGGTTTCTGAC 60.135 52.381 6.13 0.00 0.00 3.51
2790 3062 0.888619 TGATCTCGCGGTTTCTGACT 59.111 50.000 6.13 0.00 0.00 3.41
2857 3133 7.852263 AGATAGTATGTGTTCTTGCCTAGTTT 58.148 34.615 0.00 0.00 0.00 2.66
2858 3134 8.322091 AGATAGTATGTGTTCTTGCCTAGTTTT 58.678 33.333 0.00 0.00 0.00 2.43
2859 3135 8.863872 ATAGTATGTGTTCTTGCCTAGTTTTT 57.136 30.769 0.00 0.00 0.00 1.94
2879 3155 0.482446 TGTCCAGCAACTCCCCATTT 59.518 50.000 0.00 0.00 0.00 2.32
2929 3205 6.725364 AGGTTCCAATATGTCTCTGAATGTT 58.275 36.000 0.00 0.00 0.00 2.71
3218 3514 1.467920 GACCCTTTCTTCCCATGCAG 58.532 55.000 0.00 0.00 0.00 4.41
3253 3552 8.371571 AGATTTTCTTTTATTGCTGGATCCTT 57.628 30.769 14.23 0.00 0.00 3.36
3303 3669 3.956744 ACTTATGAGCTTTTGGACCCTC 58.043 45.455 0.00 0.00 0.00 4.30
3319 3685 3.942115 GACCCTCTCCAGCAAAAAGATAC 59.058 47.826 0.00 0.00 0.00 2.24
3320 3686 3.330701 ACCCTCTCCAGCAAAAAGATACA 59.669 43.478 0.00 0.00 0.00 2.29
3321 3687 3.944015 CCCTCTCCAGCAAAAAGATACAG 59.056 47.826 0.00 0.00 0.00 2.74
3323 3689 5.338381 CCCTCTCCAGCAAAAAGATACAGTA 60.338 44.000 0.00 0.00 0.00 2.74
3324 3690 6.352516 CCTCTCCAGCAAAAAGATACAGTAT 58.647 40.000 0.00 0.00 0.00 2.12
3325 3691 6.259608 CCTCTCCAGCAAAAAGATACAGTATG 59.740 42.308 0.00 0.00 46.00 2.39
3326 3692 6.946340 TCTCCAGCAAAAAGATACAGTATGA 58.054 36.000 0.00 0.00 39.69 2.15
3347 3713 2.990066 AATTCGCTCCTTGGGACTAG 57.010 50.000 0.00 0.00 37.36 2.57
3350 3716 0.039180 TCGCTCCTTGGGACTAGTGA 59.961 55.000 0.00 0.00 32.41 3.41
3373 3739 7.495606 GTGAATCTTTTGGATGTCCTTTTTGTT 59.504 33.333 0.09 0.00 34.45 2.83
3411 3777 6.674694 TGGAAAACATGGTTGATTTTTGTG 57.325 33.333 0.00 0.00 29.03 3.33
3424 3790 6.347270 TGATTTTTGTGTGTGCTGAAAATG 57.653 33.333 0.00 0.00 32.00 2.32
3469 3839 4.398988 GCATTTTGTGATGTGACTATGGGA 59.601 41.667 0.00 0.00 0.00 4.37
3568 3938 2.765807 CGGGGATCCTCTGTGCCT 60.766 66.667 10.68 0.00 0.00 4.75
3572 3942 1.142748 GGATCCTCTGTGCCTGTCG 59.857 63.158 3.84 0.00 0.00 4.35
3575 3945 1.938657 ATCCTCTGTGCCTGTCGTCG 61.939 60.000 0.00 0.00 0.00 5.12
3611 3984 2.250031 TGGCTGCCACTTGAATTGAAT 58.750 42.857 19.30 0.00 0.00 2.57
3669 4047 6.630444 AGCATCACAAATTCAGGCTTATAG 57.370 37.500 0.00 0.00 0.00 1.31
3724 4103 8.669946 TTCATGTAAAGACATTGACACACTTA 57.330 30.769 0.00 0.00 44.18 2.24
3738 4117 1.315690 CACTTATCGTAGCCCCGAGA 58.684 55.000 1.72 0.00 40.68 4.04
3739 4118 1.679680 CACTTATCGTAGCCCCGAGAA 59.320 52.381 3.19 3.19 40.68 2.87
3766 4145 6.139672 GACAAATTATGTTTGTCGCCTTTG 57.860 37.500 17.31 0.00 45.63 2.77
3772 4151 1.133407 TGTTTGTCGCCTTTGTTGGTC 59.867 47.619 0.00 0.00 0.00 4.02
3784 4163 1.822506 TGTTGGTCACACGTGGAAAA 58.177 45.000 21.57 9.34 0.00 2.29
3786 4165 1.064952 GTTGGTCACACGTGGAAAAGG 59.935 52.381 21.57 2.02 0.00 3.11
3787 4166 0.253610 TGGTCACACGTGGAAAAGGT 59.746 50.000 21.57 0.00 0.00 3.50
3793 4172 2.755836 CACGTGGAAAAGGTGTCAAG 57.244 50.000 7.95 0.00 39.36 3.02
3794 4173 2.014128 CACGTGGAAAAGGTGTCAAGT 58.986 47.619 7.95 0.00 39.36 3.16
3795 4174 2.014128 ACGTGGAAAAGGTGTCAAGTG 58.986 47.619 0.00 0.00 0.00 3.16
3796 4175 2.285083 CGTGGAAAAGGTGTCAAGTGA 58.715 47.619 0.00 0.00 0.00 3.41
3797 4176 2.878406 CGTGGAAAAGGTGTCAAGTGAT 59.122 45.455 0.00 0.00 0.00 3.06
3798 4177 3.315191 CGTGGAAAAGGTGTCAAGTGATT 59.685 43.478 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.057533 TGGTTTTGATTATGCGATCTCAGAT 58.942 36.000 0.00 0.00 0.00 2.90
64 65 5.680619 TGGGCTCGTGAAAATTATGATACT 58.319 37.500 0.00 0.00 0.00 2.12
82 83 2.893489 GGAGTGACAAAATCTTTGGGCT 59.107 45.455 4.30 0.00 0.00 5.19
93 94 5.125900 CCTCATGCATTAATGGAGTGACAAA 59.874 40.000 17.02 0.00 0.00 2.83
105 106 9.956640 ATAAATTGGTTTTTCCTCATGCATTAA 57.043 25.926 0.00 0.00 37.07 1.40
114 115 5.184287 TCCGGTGATAAATTGGTTTTTCCTC 59.816 40.000 0.00 0.00 37.07 3.71
131 132 0.690192 TCATCCTGCTTTTCCGGTGA 59.310 50.000 0.00 0.00 0.00 4.02
135 136 3.334691 TGTTAGTCATCCTGCTTTTCCG 58.665 45.455 0.00 0.00 0.00 4.30
157 158 9.569167 GGAGATATATGATCGACGTCATTTTAA 57.431 33.333 17.16 0.00 39.45 1.52
224 225 7.984422 ATTCCAAAATCCAAAATCAAACTCC 57.016 32.000 0.00 0.00 0.00 3.85
236 237 5.236047 CGTGCTTTGAAAATTCCAAAATCCA 59.764 36.000 7.20 3.71 33.68 3.41
237 238 5.465056 TCGTGCTTTGAAAATTCCAAAATCC 59.535 36.000 7.20 1.88 33.68 3.01
238 239 6.019156 TGTCGTGCTTTGAAAATTCCAAAATC 60.019 34.615 7.20 4.15 33.68 2.17
245 246 8.226543 TGATTAATGTCGTGCTTTGAAAATTC 57.773 30.769 0.00 0.00 0.00 2.17
248 249 7.592938 AGATGATTAATGTCGTGCTTTGAAAA 58.407 30.769 0.00 0.00 0.00 2.29
252 253 8.894409 TTTTAGATGATTAATGTCGTGCTTTG 57.106 30.769 0.00 0.00 0.00 2.77
365 368 8.231837 GCAAATAAAAAGTCGGTGAACTACATA 58.768 33.333 0.00 0.00 0.00 2.29
370 373 5.508200 TGCAAATAAAAAGTCGGTGAACT 57.492 34.783 0.00 0.00 0.00 3.01
376 379 6.761731 TTGTGATTGCAAATAAAAAGTCGG 57.238 33.333 1.71 0.00 0.00 4.79
419 422 1.408702 GGTGCCGCCATAATTGATTGT 59.591 47.619 0.00 0.00 37.17 2.71
424 427 0.664761 CTGAGGTGCCGCCATAATTG 59.335 55.000 0.00 0.00 40.61 2.32
432 435 2.135933 GACATATTACTGAGGTGCCGC 58.864 52.381 0.00 0.00 0.00 6.53
447 450 7.944000 ACAAATATTATGAGCCACATGGACATA 59.056 33.333 0.87 7.92 39.77 2.29
478 482 6.188175 CAGAAGCATTATTCTAAGACAACGC 58.812 40.000 0.00 0.00 37.43 4.84
559 566 5.474532 TCCCAAAGAAGAATGTTCATGACAG 59.525 40.000 0.00 0.00 42.62 3.51
640 647 6.903883 ATAGTTGCCGATGTTTACTTGTAG 57.096 37.500 0.00 0.00 0.00 2.74
655 662 6.862711 GGAACTATGGTAAGAATAGTTGCC 57.137 41.667 12.27 9.80 46.10 4.52
656 663 6.047231 ACGGAACTATGGTAAGAATAGTTGC 58.953 40.000 12.27 13.37 46.10 4.17
887 902 9.490379 TTGGTACACAAGTATTTGTTTTTGTTT 57.510 25.926 0.08 0.00 45.01 2.83
890 905 8.105135 CGTTTGGTACACAAGTATTTGTTTTTG 58.895 33.333 0.08 0.00 45.01 2.44
896 911 4.849883 TGCGTTTGGTACACAAGTATTTG 58.150 39.130 0.00 0.00 40.82 2.32
897 912 5.502153 TTGCGTTTGGTACACAAGTATTT 57.498 34.783 0.00 0.00 40.82 1.40
900 915 4.155462 TGTTTTGCGTTTGGTACACAAGTA 59.845 37.500 0.00 0.00 40.82 2.24
905 920 2.849473 CTGTGTTTTGCGTTTGGTACAC 59.151 45.455 0.00 0.00 39.29 2.90
910 925 1.199624 GCTCTGTGTTTTGCGTTTGG 58.800 50.000 0.00 0.00 0.00 3.28
1022 1049 1.301293 GCAGAGGCAAACCCTAGCT 59.699 57.895 0.00 0.00 46.60 3.32
1069 1101 4.407694 TTCGACATCGCCGCGTCA 62.408 61.111 13.39 0.00 39.60 4.35
1073 1105 1.076533 TTCTTCTTCGACATCGCCGC 61.077 55.000 0.00 0.00 39.60 6.53
1075 1107 1.656095 CTGTTCTTCTTCGACATCGCC 59.344 52.381 0.00 0.00 39.60 5.54
1160 1201 1.283613 GACAGGGAGAGGAGAGACAGA 59.716 57.143 0.00 0.00 0.00 3.41
1163 1204 1.005450 AGTGACAGGGAGAGGAGAGAC 59.995 57.143 0.00 0.00 0.00 3.36
1244 1287 4.322539 CACACAGCAATCACGATCAATTTG 59.677 41.667 0.00 0.00 0.00 2.32
1245 1289 4.022935 ACACACAGCAATCACGATCAATTT 60.023 37.500 0.00 0.00 0.00 1.82
1257 1327 1.973515 TGGAGAGAGACACACAGCAAT 59.026 47.619 0.00 0.00 0.00 3.56
1258 1328 1.342496 CTGGAGAGAGACACACAGCAA 59.658 52.381 0.00 0.00 0.00 3.91
1261 1331 0.894141 CCCTGGAGAGAGACACACAG 59.106 60.000 0.00 0.00 0.00 3.66
1262 1332 0.542938 CCCCTGGAGAGAGACACACA 60.543 60.000 0.00 0.00 0.00 3.72
1275 1356 1.500783 TTGGCCTTCTTCTCCCCTGG 61.501 60.000 3.32 0.00 0.00 4.45
1358 1452 2.364842 AGCGTCAGAGCAGGGGAT 60.365 61.111 0.00 0.00 40.15 3.85
1368 1462 1.787281 CGAGTCGAGTAACAGCGTCAG 60.787 57.143 6.73 0.00 0.00 3.51
1442 1538 5.468746 TCAACTGAAATAGCAACAGTACCAC 59.531 40.000 0.00 0.00 42.81 4.16
1445 1541 5.179368 TGCTCAACTGAAATAGCAACAGTAC 59.821 40.000 0.00 0.00 42.81 2.73
1458 1560 4.773013 TGATATGCTCATGCTCAACTGAA 58.227 39.130 0.00 0.00 40.48 3.02
1491 1686 0.537188 AACCAGAGCTCCATGTACCG 59.463 55.000 10.93 0.00 0.00 4.02
1521 1716 2.611292 GCAACCTCACATAGCAAGCTAG 59.389 50.000 7.91 3.09 31.45 3.42
1558 1783 2.684001 TCCCCAGCATACAAAGTACG 57.316 50.000 0.00 0.00 0.00 3.67
1565 1811 1.638070 TGGTGAATTCCCCAGCATACA 59.362 47.619 5.44 0.00 37.15 2.29
1568 1814 3.602104 CTGGTGAATTCCCCAGCAT 57.398 52.632 21.89 0.00 41.65 3.79
1586 1832 8.902735 CCTTCTTTTCAACGAATTTAGCTAAAC 58.097 33.333 20.85 8.72 0.00 2.01
1602 1848 4.578516 TCGCAAGTTTCATCCTTCTTTTCA 59.421 37.500 0.00 0.00 39.48 2.69
1619 1865 2.161609 AGAATAAAAAGGCCGTCGCAAG 59.838 45.455 0.00 0.00 36.38 4.01
1646 1892 2.122768 AGAGTCCAACCATGATCCTCC 58.877 52.381 0.00 0.00 0.00 4.30
1770 2019 6.231211 TCCAAGTGAATTAGTCCTTCTGAAC 58.769 40.000 0.00 0.00 0.00 3.18
1822 2071 4.036144 GGGAAGAGAAGAGTATGCAAATGC 59.964 45.833 0.00 0.00 42.50 3.56
1849 2098 4.446371 CTCTCAGTCAGGTCACACTTTTT 58.554 43.478 0.00 0.00 0.00 1.94
1851 2100 2.366916 CCTCTCAGTCAGGTCACACTTT 59.633 50.000 0.00 0.00 0.00 2.66
1896 2145 3.192944 TCCTGAGACCATTCCCAGAAAT 58.807 45.455 0.00 0.00 0.00 2.17
1939 2188 1.067212 CCTTAGACTTAGACCGCGCAT 59.933 52.381 8.75 0.00 0.00 4.73
1940 2189 0.454600 CCTTAGACTTAGACCGCGCA 59.545 55.000 8.75 0.00 0.00 6.09
1941 2190 0.737219 TCCTTAGACTTAGACCGCGC 59.263 55.000 0.00 0.00 0.00 6.86
1942 2191 3.498927 TTTCCTTAGACTTAGACCGCG 57.501 47.619 0.00 0.00 0.00 6.46
1943 2192 7.838771 TTTTATTTCCTTAGACTTAGACCGC 57.161 36.000 0.00 0.00 0.00 5.68
1971 2220 8.916654 CGATGTAGAAGAAATTGTATAAGCGAT 58.083 33.333 0.00 0.00 0.00 4.58
1972 2221 8.132995 TCGATGTAGAAGAAATTGTATAAGCGA 58.867 33.333 0.00 0.00 0.00 4.93
1973 2222 8.282124 TCGATGTAGAAGAAATTGTATAAGCG 57.718 34.615 0.00 0.00 0.00 4.68
2001 2250 9.015367 GCCTCTATCCGCTATTCTGATATATAA 57.985 37.037 0.00 0.00 0.00 0.98
2002 2251 8.164070 TGCCTCTATCCGCTATTCTGATATATA 58.836 37.037 0.00 0.00 0.00 0.86
2003 2252 7.007116 TGCCTCTATCCGCTATTCTGATATAT 58.993 38.462 0.00 0.00 0.00 0.86
2004 2253 6.365520 TGCCTCTATCCGCTATTCTGATATA 58.634 40.000 0.00 0.00 0.00 0.86
2005 2254 5.204292 TGCCTCTATCCGCTATTCTGATAT 58.796 41.667 0.00 0.00 0.00 1.63
2006 2255 4.600062 TGCCTCTATCCGCTATTCTGATA 58.400 43.478 0.00 0.00 0.00 2.15
2007 2256 3.435275 TGCCTCTATCCGCTATTCTGAT 58.565 45.455 0.00 0.00 0.00 2.90
2008 2257 2.876581 TGCCTCTATCCGCTATTCTGA 58.123 47.619 0.00 0.00 0.00 3.27
2009 2258 3.194329 TGATGCCTCTATCCGCTATTCTG 59.806 47.826 0.00 0.00 0.00 3.02
2010 2259 3.435275 TGATGCCTCTATCCGCTATTCT 58.565 45.455 0.00 0.00 0.00 2.40
2011 2260 3.876274 TGATGCCTCTATCCGCTATTC 57.124 47.619 0.00 0.00 0.00 1.75
2012 2261 4.833478 AATGATGCCTCTATCCGCTATT 57.167 40.909 0.00 0.00 0.00 1.73
2013 2262 5.939764 TTAATGATGCCTCTATCCGCTAT 57.060 39.130 0.00 0.00 0.00 2.97
2014 2263 5.337571 CCTTTAATGATGCCTCTATCCGCTA 60.338 44.000 0.00 0.00 0.00 4.26
2015 2264 4.564406 CCTTTAATGATGCCTCTATCCGCT 60.564 45.833 0.00 0.00 0.00 5.52
2016 2265 3.686726 CCTTTAATGATGCCTCTATCCGC 59.313 47.826 0.00 0.00 0.00 5.54
2017 2266 5.152623 TCCTTTAATGATGCCTCTATCCG 57.847 43.478 0.00 0.00 0.00 4.18
2018 2267 7.170965 TGAATCCTTTAATGATGCCTCTATCC 58.829 38.462 0.00 0.00 0.00 2.59
2019 2268 7.336427 CCTGAATCCTTTAATGATGCCTCTATC 59.664 40.741 0.00 0.00 0.00 2.08
2020 2269 7.173722 CCTGAATCCTTTAATGATGCCTCTAT 58.826 38.462 0.00 0.00 0.00 1.98
2021 2270 6.101734 ACCTGAATCCTTTAATGATGCCTCTA 59.898 38.462 0.00 0.00 0.00 2.43
2022 2271 5.103771 ACCTGAATCCTTTAATGATGCCTCT 60.104 40.000 0.00 0.00 0.00 3.69
2023 2272 5.136105 ACCTGAATCCTTTAATGATGCCTC 58.864 41.667 0.00 0.00 0.00 4.70
2024 2273 5.134725 ACCTGAATCCTTTAATGATGCCT 57.865 39.130 0.00 0.00 0.00 4.75
2025 2274 4.279420 GGACCTGAATCCTTTAATGATGCC 59.721 45.833 0.00 0.00 35.68 4.40
2026 2275 4.889409 TGGACCTGAATCCTTTAATGATGC 59.111 41.667 0.00 0.00 39.75 3.91
2027 2276 7.592885 AATGGACCTGAATCCTTTAATGATG 57.407 36.000 0.00 0.00 39.75 3.07
2028 2277 8.613922 AAAATGGACCTGAATCCTTTAATGAT 57.386 30.769 0.00 0.00 39.75 2.45
2029 2278 8.434589 AAAAATGGACCTGAATCCTTTAATGA 57.565 30.769 0.00 0.00 39.75 2.57
2096 2345 9.373603 CAATTCAAGGAAAATGCATTCTAATCA 57.626 29.630 13.38 0.00 0.00 2.57
2097 2346 8.333186 GCAATTCAAGGAAAATGCATTCTAATC 58.667 33.333 13.38 8.87 37.92 1.75
2098 2347 7.281549 GGCAATTCAAGGAAAATGCATTCTAAT 59.718 33.333 13.38 1.16 38.94 1.73
2099 2348 6.594937 GGCAATTCAAGGAAAATGCATTCTAA 59.405 34.615 13.38 0.00 38.94 2.10
2100 2349 6.070653 AGGCAATTCAAGGAAAATGCATTCTA 60.071 34.615 13.38 0.00 38.94 2.10
2101 2350 4.939439 GGCAATTCAAGGAAAATGCATTCT 59.061 37.500 13.38 0.00 38.94 2.40
2102 2351 4.939439 AGGCAATTCAAGGAAAATGCATTC 59.061 37.500 13.38 1.39 38.94 2.67
2103 2352 4.913784 AGGCAATTCAAGGAAAATGCATT 58.086 34.783 5.99 5.99 38.94 3.56
2374 2624 2.801679 GGACTCATAGACTAGTCGACGG 59.198 54.545 17.07 9.85 42.51 4.79
2405 2655 5.063564 CCAAGGTTTATACGAGTCAAAGAGC 59.936 44.000 0.00 0.00 0.00 4.09
2420 2670 2.351706 AACGCTGGAACCAAGGTTTA 57.648 45.000 5.87 0.00 38.60 2.01
2421 2671 1.136110 CAAACGCTGGAACCAAGGTTT 59.864 47.619 5.87 12.79 38.60 3.27
2432 2682 3.122297 TCAAAATTCAAGCAAACGCTGG 58.878 40.909 0.00 0.00 40.49 4.85
2433 2683 4.682860 AGATCAAAATTCAAGCAAACGCTG 59.317 37.500 0.00 0.00 40.49 5.18
2489 2744 5.301045 TGAAGAGACGGAGAAACAGAACTAA 59.699 40.000 0.00 0.00 0.00 2.24
2529 2788 2.083002 CTGCTGCCCTTCTTCTTCTTC 58.917 52.381 0.00 0.00 0.00 2.87
2640 2899 2.738743 ACAGTTTAGGCCATGGGAATG 58.261 47.619 15.13 0.00 0.00 2.67
2673 2933 5.416083 TCCGACGATTACATCAAAATGACT 58.584 37.500 0.00 0.00 36.67 3.41
2772 3037 1.272781 CAGTCAGAAACCGCGAGATC 58.727 55.000 8.23 1.71 0.00 2.75
2773 3038 0.603569 ACAGTCAGAAACCGCGAGAT 59.396 50.000 8.23 0.00 0.00 2.75
2774 3039 0.318699 CACAGTCAGAAACCGCGAGA 60.319 55.000 8.23 0.00 0.00 4.04
2775 3040 0.597637 ACACAGTCAGAAACCGCGAG 60.598 55.000 8.23 0.00 0.00 5.03
2784 3056 2.766263 GGGTGGATCATACACAGTCAGA 59.234 50.000 1.39 0.00 40.54 3.27
2789 3061 1.069204 CGAGGGGTGGATCATACACAG 59.931 57.143 1.39 0.00 40.54 3.66
2790 3062 1.119684 CGAGGGGTGGATCATACACA 58.880 55.000 1.39 0.00 40.54 3.72
2857 3133 0.260230 TGGGGAGTTGCTGGACAAAA 59.740 50.000 0.00 0.00 40.82 2.44
2858 3134 0.482446 ATGGGGAGTTGCTGGACAAA 59.518 50.000 0.00 0.00 40.82 2.83
2859 3135 0.482446 AATGGGGAGTTGCTGGACAA 59.518 50.000 0.00 0.00 35.33 3.18
2862 3138 1.004745 GAGAAATGGGGAGTTGCTGGA 59.995 52.381 0.00 0.00 0.00 3.86
2879 3155 3.580022 TGCAGGTTGATGAAAGAGAGAGA 59.420 43.478 0.00 0.00 0.00 3.10
2929 3205 2.940410 GTGAGGTTTGTCCGTTCTGAAA 59.060 45.455 0.00 0.00 41.99 2.69
3122 3414 2.909504 ACTAGACTTCTCAGAGGCCA 57.090 50.000 5.01 0.00 0.00 5.36
3192 3484 2.246327 TGGGAAGAAAGGGTCCAAAAGT 59.754 45.455 0.00 0.00 35.44 2.66
3253 3552 6.718454 AGAAATCTTCATCTCTTTTGCTGGAA 59.282 34.615 0.00 0.00 0.00 3.53
3303 3669 7.615582 TTCATACTGTATCTTTTTGCTGGAG 57.384 36.000 0.00 0.00 0.00 3.86
3319 3685 4.201950 CCCAAGGAGCGAATTTTCATACTG 60.202 45.833 0.00 0.00 0.00 2.74
3320 3686 3.947834 CCCAAGGAGCGAATTTTCATACT 59.052 43.478 0.00 0.00 0.00 2.12
3321 3687 3.945285 TCCCAAGGAGCGAATTTTCATAC 59.055 43.478 0.00 0.00 0.00 2.39
3323 3689 2.755103 GTCCCAAGGAGCGAATTTTCAT 59.245 45.455 0.00 0.00 29.39 2.57
3324 3690 2.159382 GTCCCAAGGAGCGAATTTTCA 58.841 47.619 0.00 0.00 29.39 2.69
3325 3691 2.437413 AGTCCCAAGGAGCGAATTTTC 58.563 47.619 0.00 0.00 29.39 2.29
3326 3692 2.586648 AGTCCCAAGGAGCGAATTTT 57.413 45.000 0.00 0.00 29.39 1.82
3347 3713 6.986231 ACAAAAAGGACATCCAAAAGATTCAC 59.014 34.615 0.00 0.00 38.89 3.18
3350 3716 7.563906 TCAACAAAAAGGACATCCAAAAGATT 58.436 30.769 0.00 0.00 38.89 2.40
3373 3739 9.656040 CCATGTTTTCCATCTCAAATAAAATCA 57.344 29.630 0.00 0.00 0.00 2.57
3384 3750 7.442062 ACAAAAATCAACCATGTTTTCCATCTC 59.558 33.333 0.00 0.00 30.15 2.75
3411 3777 6.237384 CGCAAAAGATATCATTTTCAGCACAC 60.237 38.462 5.32 0.00 0.00 3.82
3424 3790 4.556699 GCCATTACCACCGCAAAAGATATC 60.557 45.833 0.00 0.00 0.00 1.63
3469 3839 3.512219 TTATTGGTTGGGTTTCGGAGT 57.488 42.857 0.00 0.00 0.00 3.85
3568 3938 0.936600 TGTAACACTCGTCGACGACA 59.063 50.000 34.97 26.64 44.22 4.35
3572 3942 3.423571 CCATAGTGTAACACTCGTCGAC 58.576 50.000 5.18 5.18 41.21 4.20
3575 3945 3.179830 CAGCCATAGTGTAACACTCGTC 58.820 50.000 0.00 0.00 41.21 4.20
3611 3984 4.071423 GGCGGTAGGGTTTGTTAACTTTA 58.929 43.478 7.22 0.00 34.59 1.85
3701 4079 7.899841 CGATAAGTGTGTCAATGTCTTTACATG 59.100 37.037 0.00 0.00 45.79 3.21
3714 4092 1.479323 GGGGCTACGATAAGTGTGTCA 59.521 52.381 0.00 0.00 0.00 3.58
3717 4095 0.742505 TCGGGGCTACGATAAGTGTG 59.257 55.000 0.00 0.00 38.06 3.82
3724 4103 2.132352 GGGTTCTCGGGGCTACGAT 61.132 63.158 5.41 0.00 42.62 3.73
3765 4144 1.740585 CTTTTCCACGTGTGACCAACA 59.259 47.619 15.65 0.00 36.04 3.33
3766 4145 1.064952 CCTTTTCCACGTGTGACCAAC 59.935 52.381 15.65 0.00 0.00 3.77
3772 4151 1.374560 TGACACCTTTTCCACGTGTG 58.625 50.000 15.65 6.66 40.70 3.82
3784 4163 2.644798 AGCCCTAAATCACTTGACACCT 59.355 45.455 0.00 0.00 0.00 4.00
3786 4165 4.636206 CCTAAGCCCTAAATCACTTGACAC 59.364 45.833 0.00 0.00 0.00 3.67
3787 4166 4.288626 ACCTAAGCCCTAAATCACTTGACA 59.711 41.667 0.00 0.00 0.00 3.58
3788 4167 4.636206 CACCTAAGCCCTAAATCACTTGAC 59.364 45.833 0.00 0.00 0.00 3.18
3789 4168 4.288626 ACACCTAAGCCCTAAATCACTTGA 59.711 41.667 0.00 0.00 0.00 3.02
3790 4169 4.589908 ACACCTAAGCCCTAAATCACTTG 58.410 43.478 0.00 0.00 0.00 3.16
3792 4171 3.200165 GGACACCTAAGCCCTAAATCACT 59.800 47.826 0.00 0.00 0.00 3.41
3793 4172 3.542648 GGACACCTAAGCCCTAAATCAC 58.457 50.000 0.00 0.00 0.00 3.06
3794 4173 2.508300 GGGACACCTAAGCCCTAAATCA 59.492 50.000 0.00 0.00 38.85 2.57
3795 4174 2.158652 GGGGACACCTAAGCCCTAAATC 60.159 54.545 0.00 0.00 41.72 2.17
3796 4175 1.850998 GGGGACACCTAAGCCCTAAAT 59.149 52.381 0.00 0.00 41.72 1.40
3797 4176 1.292085 GGGGACACCTAAGCCCTAAA 58.708 55.000 0.00 0.00 41.72 1.85
3798 4177 3.016745 GGGGACACCTAAGCCCTAA 57.983 57.895 0.00 0.00 41.72 2.69


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

AutoCloner maintained by Alex Coulton.