Multiple sequence alignment - TraesCS3B01G072200

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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 TraesCS3B01G072200 chr3B 100.000 4612 0 0 1 4612 43559890 43555279 0.000000e+00 8517.0
1 TraesCS3B01G072200 chr3B 88.956 1322 106 25 1 1305 43572387 43571089 0.000000e+00 1596.0
2 TraesCS3B01G072200 chr3B 88.880 1322 107 25 1 1305 43566114 43564816 0.000000e+00 1591.0
3 TraesCS3B01G072200 chr3B 85.881 772 74 21 523 1278 43583548 43582796 0.000000e+00 789.0
4 TraesCS3B01G072200 chr3B 94.928 276 14 0 3516 3791 536444663 536444938 2.550000e-117 433.0
5 TraesCS3B01G072200 chr3A 91.589 1819 108 16 2397 4194 36087716 36085922 0.000000e+00 2470.0
6 TraesCS3B01G072200 chr3A 87.365 926 51 27 931 1828 36089058 36088171 0.000000e+00 1002.0
7 TraesCS3B01G072200 chr3A 92.548 416 29 2 4197 4612 36085309 36084896 3.070000e-166 595.0
8 TraesCS3B01G072200 chr3A 81.541 558 70 19 391 929 36089948 36089405 3.300000e-116 429.0
9 TraesCS3B01G072200 chr3D 89.337 1735 129 26 2397 4099 26176073 26174363 0.000000e+00 2128.0
10 TraesCS3B01G072200 chr3D 88.195 1025 83 24 391 1399 26177510 26176508 0.000000e+00 1188.0
11 TraesCS3B01G072200 chr3D 92.982 399 27 1 4196 4594 26173799 26173402 8.600000e-162 580.0
12 TraesCS3B01G072200 chr3D 81.532 222 14 5 2167 2387 26176249 26176054 1.720000e-34 158.0
13 TraesCS3B01G072200 chr7B 95.290 276 13 0 3516 3791 703377785 703378060 5.480000e-119 438.0
14 TraesCS3B01G072200 chr7B 94.286 280 16 0 3516 3795 591874261 591873982 3.300000e-116 429.0
15 TraesCS3B01G072200 chr7B 76.289 582 81 33 2081 2638 591873445 591872897 1.650000e-64 257.0
16 TraesCS3B01G072200 chr7B 83.333 270 36 5 1823 2083 703378229 703378498 1.660000e-59 241.0
17 TraesCS3B01G072200 chr7B 82.955 264 35 6 1829 2083 591873811 591873549 3.590000e-56 230.0
18 TraesCS3B01G072200 chr7D 93.200 250 16 1 143 391 619558638 619558887 2.620000e-97 366.0
19 TraesCS3B01G072200 chr7D 91.379 116 10 0 1 116 619536922 619537037 4.780000e-35 159.0
20 TraesCS3B01G072200 chr7D 96.774 31 1 0 115 145 619548144 619548174 8.000000e-03 52.8
21 TraesCS3B01G072200 chr2B 97.279 147 4 0 3649 3795 730071522 730071376 2.760000e-62 250.0
22 TraesCS3B01G072200 chr2B 82.576 264 37 5 1829 2083 730071205 730070942 1.670000e-54 224.0


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 TraesCS3B01G072200 chr3B 43555279 43559890 4611 True 8517.000000 8517 100.00000 1 4612 1 chr3B.!!$R1 4611
1 TraesCS3B01G072200 chr3B 43571089 43572387 1298 True 1596.000000 1596 88.95600 1 1305 1 chr3B.!!$R3 1304
2 TraesCS3B01G072200 chr3B 43564816 43566114 1298 True 1591.000000 1591 88.88000 1 1305 1 chr3B.!!$R2 1304
3 TraesCS3B01G072200 chr3B 43582796 43583548 752 True 789.000000 789 85.88100 523 1278 1 chr3B.!!$R4 755
4 TraesCS3B01G072200 chr3A 36084896 36089948 5052 True 1124.000000 2470 88.26075 391 4612 4 chr3A.!!$R1 4221
5 TraesCS3B01G072200 chr3D 26173402 26177510 4108 True 1013.500000 2128 88.01150 391 4594 4 chr3D.!!$R1 4203
6 TraesCS3B01G072200 chr7B 703377785 703378498 713 False 339.500000 438 89.31150 1823 3791 2 chr7B.!!$F1 1968
7 TraesCS3B01G072200 chr7B 591872897 591874261 1364 True 305.333333 429 84.51000 1829 3795 3 chr7B.!!$R1 1966
8 TraesCS3B01G072200 chr2B 730070942 730071522 580 True 237.000000 250 89.92750 1829 3795 2 chr2B.!!$R1 1966

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
284 286 0.684805 AGACCCTCTAGAAGGCACCG 60.685 60.0 7.34 0.00 44.71 4.94 F
1831 2257 0.029834 GCTGGTGTCAGTTTGCAGTG 59.970 55.0 0.00 0.00 42.78 3.66 F
1834 2260 0.029834 GGTGTCAGTTTGCAGTGCTG 59.970 55.0 17.60 6.19 0.00 4.41 F
1896 2322 0.305922 GCACATGCGACTATTCAGCC 59.694 55.0 0.00 0.00 0.00 4.85 F
3398 3857 0.313672 TCTTTTTCGCACCATGGCAC 59.686 50.0 13.04 2.59 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2518 0.033228 CCAAATGTTCCGCCTTGCAA 59.967 50.0 0.00 0.0 0.00 4.08 R
2748 3189 0.108019 AAACTCAACCACCGGACTCC 59.892 55.0 9.46 0.0 0.00 3.85 R
3395 3854 0.305922 GCAGTCATAAGATGCCGTGC 59.694 55.0 0.00 0.0 33.81 5.34 R
3440 3899 0.444260 GCTCGCTGCAGTAGGAAAAC 59.556 55.0 16.64 0.0 42.31 2.43 R
4210 6145 0.613777 GGACGTTGAGGTTGATCCCT 59.386 55.0 0.00 0.0 37.62 4.20 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
280 282 0.747852 CCGAAGACCCTCTAGAAGGC 59.252 60.000 7.34 0.00 44.71 4.35
283 285 1.483004 GAAGACCCTCTAGAAGGCACC 59.517 57.143 7.34 0.00 44.71 5.01
284 286 0.684805 AGACCCTCTAGAAGGCACCG 60.685 60.000 7.34 0.00 44.71 4.94
286 288 2.105128 CCTCTAGAAGGCACCGCG 59.895 66.667 0.00 0.00 38.67 6.46
323 325 7.448748 ACATCAAACCTATTAACAAGACCAC 57.551 36.000 0.00 0.00 0.00 4.16
328 330 7.776030 TCAAACCTATTAACAAGACCACAAGAA 59.224 33.333 0.00 0.00 0.00 2.52
333 335 5.473796 TTAACAAGACCACAAGAACGAAC 57.526 39.130 0.00 0.00 0.00 3.95
336 338 2.943033 CAAGACCACAAGAACGAACCTT 59.057 45.455 0.00 0.00 0.00 3.50
357 359 6.071560 ACCTTCGGGGATTTAATTTCAGAAAC 60.072 38.462 0.00 0.00 40.03 2.78
359 361 6.902771 TCGGGGATTTAATTTCAGAAACAA 57.097 33.333 0.00 0.00 0.00 2.83
373 375 3.564225 CAGAAACAAAAGTAACCCGAGCT 59.436 43.478 0.00 0.00 0.00 4.09
379 381 4.514066 ACAAAAGTAACCCGAGCTTTAGTG 59.486 41.667 0.00 0.00 32.81 2.74
451 453 1.470890 TCACATGTCTCATGTCGCGTA 59.529 47.619 5.77 0.00 0.00 4.42
496 498 1.151899 AACCACTGGCCACCTCCTA 60.152 57.895 0.00 0.00 0.00 2.94
595 597 5.183713 TGAAATGCATTGTGGGTCTCTAAAG 59.816 40.000 13.82 0.00 0.00 1.85
606 608 5.189145 GTGGGTCTCTAAAGTATTTCAGGGA 59.811 44.000 0.00 0.00 40.09 4.20
622 624 3.446161 TCAGGGATGTTACGTAGGTTCTG 59.554 47.826 0.00 1.52 0.00 3.02
636 656 6.495181 ACGTAGGTTCTGGAATCATCATCTAT 59.505 38.462 0.00 0.00 0.00 1.98
680 700 7.348815 AGTGTTTCATCCATATCCAGAATCAA 58.651 34.615 0.00 0.00 0.00 2.57
737 757 5.326200 ACCTAGCATGACACACTTACTAC 57.674 43.478 0.00 0.00 0.00 2.73
748 768 5.326069 ACACACTTACTACACTCTGAGGAT 58.674 41.667 9.85 0.00 0.00 3.24
756 776 4.648762 ACTACACTCTGAGGATCTGAATGG 59.351 45.833 9.85 0.00 43.25 3.16
757 777 3.448934 ACACTCTGAGGATCTGAATGGT 58.551 45.455 9.85 0.00 43.25 3.55
799 819 6.386927 TGACCTATCTGACACCCTTGAAATAT 59.613 38.462 0.00 0.00 0.00 1.28
800 820 7.567250 TGACCTATCTGACACCCTTGAAATATA 59.433 37.037 0.00 0.00 0.00 0.86
804 824 9.265901 CTATCTGACACCCTTGAAATATAGTTG 57.734 37.037 0.00 0.00 0.00 3.16
808 828 7.685481 TGACACCCTTGAAATATAGTTGAAGA 58.315 34.615 12.76 0.00 0.00 2.87
820 840 2.755650 AGTTGAAGAACCTACTGTGCG 58.244 47.619 0.00 0.00 31.81 5.34
821 841 2.102588 AGTTGAAGAACCTACTGTGCGT 59.897 45.455 0.00 0.00 31.81 5.24
833 853 0.895530 CTGTGCGTTTCCCTCCTAGA 59.104 55.000 0.00 0.00 0.00 2.43
929 956 2.511829 TCTCTCGCCTCCTCGTCG 60.512 66.667 0.00 0.00 0.00 5.12
958 1331 0.938192 AAACCCAAAACCCCTCCTCA 59.062 50.000 0.00 0.00 0.00 3.86
988 1364 2.395353 CCCCCATTCCCTTCTCCCC 61.395 68.421 0.00 0.00 0.00 4.81
992 1368 1.356494 CCATTCCCTTCTCCCCCTCC 61.356 65.000 0.00 0.00 0.00 4.30
1281 1666 4.720902 TACCTCGCCACCGACGGA 62.721 66.667 23.38 0.00 38.82 4.69
1292 1677 3.760035 CGACGGACAGGTGAGGGG 61.760 72.222 0.00 0.00 0.00 4.79
1355 1748 1.258427 CGCGTTGTACGGTCGATTTA 58.742 50.000 0.00 0.00 42.82 1.40
1367 1761 2.005537 CGATTTATTGCTGCGCGGC 61.006 57.895 34.00 34.00 0.00 6.53
1385 1779 1.153086 CAGAGGAATCCTTGCCGGG 60.153 63.158 2.09 0.00 31.76 5.73
1420 1815 5.592587 TTTTTCATGGGGTAGGAGAGAAA 57.407 39.130 0.00 0.00 0.00 2.52
1423 1818 1.141858 CATGGGGTAGGAGAGAAAGCC 59.858 57.143 0.00 0.00 0.00 4.35
1480 1882 0.461548 GCGTGGATGATGACTCTGGA 59.538 55.000 0.00 0.00 0.00 3.86
1482 1884 2.752121 CGTGGATGATGACTCTGGATG 58.248 52.381 0.00 0.00 0.00 3.51
1487 1889 5.479724 GTGGATGATGACTCTGGATGATAGA 59.520 44.000 0.00 0.00 0.00 1.98
1508 1910 5.613329 AGATGTTTTACCGGTAGTTGTTCA 58.387 37.500 15.20 9.82 0.00 3.18
1570 1972 1.367840 GTATACCAGGAGCTGCCCG 59.632 63.158 0.00 0.00 37.37 6.13
1596 1998 7.548097 TCTGTAAGAGTGAATTACTGATGGTC 58.452 38.462 0.00 0.00 38.67 4.02
1597 1999 7.178451 TCTGTAAGAGTGAATTACTGATGGTCA 59.822 37.037 0.00 0.00 38.67 4.02
1643 2067 8.644374 TTTTGGTATCCACTGTAATTTAGCTT 57.356 30.769 0.00 0.00 30.78 3.74
1671 2095 8.684386 TTTCCTGTGTTCTAATGTACATTCAA 57.316 30.769 24.00 15.07 32.50 2.69
1683 2107 7.718272 AATGTACATTCAATTATGCATTGCC 57.282 32.000 15.47 0.00 42.06 4.52
1684 2108 6.218108 TGTACATTCAATTATGCATTGCCA 57.782 33.333 3.54 0.00 42.06 4.92
1685 2109 6.274579 TGTACATTCAATTATGCATTGCCAG 58.725 36.000 3.54 0.00 42.06 4.85
1686 2110 4.124238 ACATTCAATTATGCATTGCCAGC 58.876 39.130 3.54 0.00 42.06 4.85
1694 2120 1.548081 TGCATTGCCAGCATGTAAGT 58.452 45.000 6.12 0.00 37.02 2.24
1697 2123 2.353011 GCATTGCCAGCATGTAAGTTGT 60.353 45.455 0.00 0.00 0.00 3.32
1700 2126 0.109132 GCCAGCATGTAAGTTGTGCC 60.109 55.000 0.00 0.00 39.62 5.01
1702 2128 1.068333 CCAGCATGTAAGTTGTGCCAC 60.068 52.381 0.00 0.00 39.62 5.01
1709 2135 2.084546 GTAAGTTGTGCCACCATCCTC 58.915 52.381 0.00 0.00 0.00 3.71
1711 2137 0.773644 AGTTGTGCCACCATCCTCTT 59.226 50.000 0.00 0.00 0.00 2.85
1712 2138 1.985159 AGTTGTGCCACCATCCTCTTA 59.015 47.619 0.00 0.00 0.00 2.10
1727 2153 8.567285 CCATCCTCTTATGGTTTATGGATTAC 57.433 38.462 0.00 0.00 41.38 1.89
1728 2154 7.334421 CCATCCTCTTATGGTTTATGGATTACG 59.666 40.741 0.00 0.00 41.38 3.18
1729 2155 6.765403 TCCTCTTATGGTTTATGGATTACGG 58.235 40.000 0.00 0.00 0.00 4.02
1730 2156 6.555738 TCCTCTTATGGTTTATGGATTACGGA 59.444 38.462 0.00 0.00 0.00 4.69
1733 2159 9.938280 CTCTTATGGTTTATGGATTACGGATTA 57.062 33.333 0.00 0.00 0.00 1.75
1755 2181 5.705609 AAGCTTGGTTTATAGTGTTGTGG 57.294 39.130 0.00 0.00 0.00 4.17
1758 2184 6.300703 AGCTTGGTTTATAGTGTTGTGGTAA 58.699 36.000 0.00 0.00 0.00 2.85
1764 2190 8.915036 TGGTTTATAGTGTTGTGGTAAAAACAT 58.085 29.630 0.00 0.00 38.47 2.71
1771 2197 5.971202 GTGTTGTGGTAAAAACATGTCTGAG 59.029 40.000 0.00 0.00 38.47 3.35
1828 2254 2.340210 TTAGCTGGTGTCAGTTTGCA 57.660 45.000 0.00 0.00 42.78 4.08
1829 2255 1.882912 TAGCTGGTGTCAGTTTGCAG 58.117 50.000 0.00 0.00 42.78 4.41
1830 2256 0.107017 AGCTGGTGTCAGTTTGCAGT 60.107 50.000 0.00 0.00 42.78 4.40
1831 2257 0.029834 GCTGGTGTCAGTTTGCAGTG 59.970 55.000 0.00 0.00 42.78 3.66
1832 2258 0.029834 CTGGTGTCAGTTTGCAGTGC 59.970 55.000 8.58 8.58 36.30 4.40
1833 2259 0.394216 TGGTGTCAGTTTGCAGTGCT 60.394 50.000 17.60 0.00 0.00 4.40
1834 2260 0.029834 GGTGTCAGTTTGCAGTGCTG 59.970 55.000 17.60 6.19 0.00 4.41
1835 2261 0.734889 GTGTCAGTTTGCAGTGCTGT 59.265 50.000 17.60 0.00 0.00 4.40
1836 2262 0.734309 TGTCAGTTTGCAGTGCTGTG 59.266 50.000 17.60 8.30 0.00 3.66
1837 2263 0.593263 GTCAGTTTGCAGTGCTGTGC 60.593 55.000 17.60 4.16 44.27 4.57
1838 2264 0.749091 TCAGTTTGCAGTGCTGTGCT 60.749 50.000 17.60 6.46 44.32 4.40
1839 2265 0.946528 CAGTTTGCAGTGCTGTGCTA 59.053 50.000 17.60 2.22 44.32 3.49
1840 2266 1.069432 CAGTTTGCAGTGCTGTGCTAG 60.069 52.381 17.60 0.00 44.32 3.42
1841 2267 1.202687 AGTTTGCAGTGCTGTGCTAGA 60.203 47.619 17.60 0.00 44.32 2.43
1842 2268 1.603802 GTTTGCAGTGCTGTGCTAGAA 59.396 47.619 17.60 0.00 44.32 2.10
1843 2269 1.965935 TTGCAGTGCTGTGCTAGAAA 58.034 45.000 17.60 0.00 44.32 2.52
1844 2270 1.229428 TGCAGTGCTGTGCTAGAAAC 58.771 50.000 17.60 0.00 44.32 2.78
1845 2271 1.229428 GCAGTGCTGTGCTAGAAACA 58.771 50.000 8.18 0.00 40.54 2.83
1846 2272 1.603802 GCAGTGCTGTGCTAGAAACAA 59.396 47.619 8.18 0.00 40.54 2.83
1847 2273 2.350197 GCAGTGCTGTGCTAGAAACAAG 60.350 50.000 8.18 0.00 40.54 3.16
1848 2274 2.874701 CAGTGCTGTGCTAGAAACAAGT 59.125 45.455 0.00 0.00 0.00 3.16
1849 2275 3.059325 CAGTGCTGTGCTAGAAACAAGTC 60.059 47.826 0.00 0.00 0.00 3.01
1850 2276 3.134458 GTGCTGTGCTAGAAACAAGTCT 58.866 45.455 0.00 0.00 0.00 3.24
1851 2277 3.059325 GTGCTGTGCTAGAAACAAGTCTG 60.059 47.826 0.00 0.00 0.00 3.51
1852 2278 3.181466 TGCTGTGCTAGAAACAAGTCTGA 60.181 43.478 0.00 0.00 0.00 3.27
1853 2279 3.809832 GCTGTGCTAGAAACAAGTCTGAA 59.190 43.478 0.00 0.00 0.00 3.02
1854 2280 4.453819 GCTGTGCTAGAAACAAGTCTGAAT 59.546 41.667 0.00 0.00 0.00 2.57
1855 2281 5.639506 GCTGTGCTAGAAACAAGTCTGAATA 59.360 40.000 0.00 0.00 0.00 1.75
1856 2282 6.314896 GCTGTGCTAGAAACAAGTCTGAATAT 59.685 38.462 0.00 0.00 0.00 1.28
1857 2283 7.148340 GCTGTGCTAGAAACAAGTCTGAATATT 60.148 37.037 0.00 0.00 0.00 1.28
1858 2284 8.621532 TGTGCTAGAAACAAGTCTGAATATTT 57.378 30.769 0.00 0.00 0.00 1.40
1859 2285 8.721478 TGTGCTAGAAACAAGTCTGAATATTTC 58.279 33.333 0.00 6.65 0.00 2.17
1860 2286 8.721478 GTGCTAGAAACAAGTCTGAATATTTCA 58.279 33.333 13.68 0.00 38.17 2.69
1861 2287 9.283768 TGCTAGAAACAAGTCTGAATATTTCAA 57.716 29.630 13.68 0.03 39.58 2.69
1862 2288 9.548208 GCTAGAAACAAGTCTGAATATTTCAAC 57.452 33.333 13.68 3.51 39.58 3.18
1865 2291 8.078596 AGAAACAAGTCTGAATATTTCAACTGC 58.921 33.333 13.68 0.00 39.58 4.40
1866 2292 7.516198 AACAAGTCTGAATATTTCAACTGCT 57.484 32.000 0.00 0.00 39.58 4.24
1867 2293 8.621532 AACAAGTCTGAATATTTCAACTGCTA 57.378 30.769 0.00 0.00 39.58 3.49
1868 2294 8.798859 ACAAGTCTGAATATTTCAACTGCTAT 57.201 30.769 0.00 0.00 39.58 2.97
1869 2295 9.236006 ACAAGTCTGAATATTTCAACTGCTATT 57.764 29.630 0.00 0.00 39.58 1.73
1872 2298 9.678260 AGTCTGAATATTTCAACTGCTATTTCT 57.322 29.630 0.00 0.00 39.58 2.52
1873 2299 9.928236 GTCTGAATATTTCAACTGCTATTTCTC 57.072 33.333 0.00 0.00 39.58 2.87
1874 2300 9.896645 TCTGAATATTTCAACTGCTATTTCTCT 57.103 29.630 0.00 0.00 39.58 3.10
1875 2301 9.932699 CTGAATATTTCAACTGCTATTTCTCTG 57.067 33.333 0.00 0.00 39.58 3.35
1876 2302 9.671279 TGAATATTTCAACTGCTATTTCTCTGA 57.329 29.630 0.00 0.00 36.59 3.27
1878 2304 5.869753 TTTCAACTGCTATTTCTCTGAGC 57.130 39.130 0.00 0.00 36.72 4.26
1879 2305 4.541973 TCAACTGCTATTTCTCTGAGCA 57.458 40.909 0.00 0.00 43.74 4.26
1880 2306 4.248859 TCAACTGCTATTTCTCTGAGCAC 58.751 43.478 0.00 0.00 41.18 4.40
1881 2307 3.969287 ACTGCTATTTCTCTGAGCACA 57.031 42.857 0.00 0.00 41.18 4.57
1882 2308 4.484537 ACTGCTATTTCTCTGAGCACAT 57.515 40.909 0.00 0.00 41.18 3.21
1883 2309 4.190001 ACTGCTATTTCTCTGAGCACATG 58.810 43.478 0.00 0.00 41.18 3.21
1884 2310 2.941064 TGCTATTTCTCTGAGCACATGC 59.059 45.455 0.00 0.00 41.18 4.06
1895 2321 3.814049 GCACATGCGACTATTCAGC 57.186 52.632 0.00 0.00 0.00 4.26
1896 2322 0.305922 GCACATGCGACTATTCAGCC 59.694 55.000 0.00 0.00 0.00 4.85
1897 2323 1.655484 CACATGCGACTATTCAGCCA 58.345 50.000 0.00 0.00 0.00 4.75
1898 2324 2.009051 CACATGCGACTATTCAGCCAA 58.991 47.619 0.00 0.00 0.00 4.52
1899 2325 2.615447 CACATGCGACTATTCAGCCAAT 59.385 45.455 0.00 0.00 0.00 3.16
1900 2326 2.615447 ACATGCGACTATTCAGCCAATG 59.385 45.455 0.00 0.00 0.00 2.82
1901 2327 2.401583 TGCGACTATTCAGCCAATGT 57.598 45.000 0.00 0.00 0.00 2.71
1902 2328 2.710377 TGCGACTATTCAGCCAATGTT 58.290 42.857 0.00 0.00 0.00 2.71
1903 2329 2.419673 TGCGACTATTCAGCCAATGTTG 59.580 45.455 0.00 0.00 0.00 3.33
1915 2341 3.663995 CCAATGTTGGTTTGCTGATCA 57.336 42.857 3.58 0.00 43.43 2.92
1920 2346 6.350361 CCAATGTTGGTTTGCTGATCATTCTA 60.350 38.462 0.00 0.00 43.43 2.10
1963 2389 9.241919 TGTATTTAAATGAGTGTGATTGATGGT 57.758 29.630 11.05 0.00 0.00 3.55
1972 2398 9.631257 ATGAGTGTGATTGATGGTAAATATTGA 57.369 29.630 0.00 0.00 0.00 2.57
1973 2399 9.112725 TGAGTGTGATTGATGGTAAATATTGAG 57.887 33.333 0.00 0.00 0.00 3.02
1974 2400 8.455903 AGTGTGATTGATGGTAAATATTGAGG 57.544 34.615 0.00 0.00 0.00 3.86
1975 2401 7.503566 AGTGTGATTGATGGTAAATATTGAGGG 59.496 37.037 0.00 0.00 0.00 4.30
2021 2453 3.695816 TCGTGTGAGAGCAATATTCGAG 58.304 45.455 0.00 0.00 0.00 4.04
2023 2455 3.452474 GTGTGAGAGCAATATTCGAGCT 58.548 45.455 0.00 0.00 42.17 4.09
2026 2458 4.115516 GTGAGAGCAATATTCGAGCTGAA 58.884 43.478 0.26 0.00 39.02 3.02
2034 2466 6.016777 AGCAATATTCGAGCTGAAATTTAGGG 60.017 38.462 0.00 0.00 40.71 3.53
2042 2474 5.184892 AGCTGAAATTTAGGGTCATCAGT 57.815 39.130 0.00 0.00 37.27 3.41
2056 2488 8.193953 AGGGTCATCAGTTATTGTTTGAAAAT 57.806 30.769 0.00 0.00 0.00 1.82
2074 2506 6.303054 TGAAAATCCTGAAATGACTGTGGTA 58.697 36.000 0.00 0.00 0.00 3.25
2075 2507 6.947733 TGAAAATCCTGAAATGACTGTGGTAT 59.052 34.615 0.00 0.00 0.00 2.73
2094 2526 7.066525 TGTGGTATATACTACTTTTTGCAAGGC 59.933 37.037 24.52 0.69 38.35 4.35
2096 2528 5.751243 ATATACTACTTTTTGCAAGGCGG 57.249 39.130 0.00 0.00 0.00 6.13
2116 2548 4.394610 GCGGAACATTTGGCCATAAAATTT 59.605 37.500 6.09 1.30 0.00 1.82
2148 2580 5.043189 GCTACTTAGCGTCAAATTTTGGT 57.957 39.130 9.18 0.67 39.82 3.67
2149 2581 5.086727 GCTACTTAGCGTCAAATTTTGGTC 58.913 41.667 9.18 2.99 39.82 4.02
2159 2591 4.857037 GTCAAATTTTGGTCTTGCGGATAC 59.143 41.667 9.18 0.00 0.00 2.24
2162 2594 4.701956 ATTTTGGTCTTGCGGATACTTG 57.298 40.909 0.00 0.00 0.00 3.16
2165 2597 1.095807 GGTCTTGCGGATACTTGGGC 61.096 60.000 0.00 0.00 0.00 5.36
2175 2607 3.243569 CGGATACTTGGGCTTCTACTGAG 60.244 52.174 0.00 0.00 0.00 3.35
2184 2616 3.181464 GGGCTTCTACTGAGTATTGGTCC 60.181 52.174 0.00 0.00 0.00 4.46
2202 2634 1.899814 TCCGTCTGACATTTACCTGCT 59.100 47.619 8.73 0.00 0.00 4.24
2206 2638 3.935203 CGTCTGACATTTACCTGCTTGAT 59.065 43.478 8.73 0.00 0.00 2.57
2227 2659 7.199167 TGATTGAGAGGGAGATTTGTTATCA 57.801 36.000 0.00 0.00 0.00 2.15
2229 2661 6.874278 TTGAGAGGGAGATTTGTTATCAGA 57.126 37.500 0.00 0.00 0.00 3.27
2277 2718 2.097466 GGAATTGTGGTGATACCTTGCG 59.903 50.000 0.00 0.00 39.58 4.85
2289 2730 2.401766 CCTTGCGTGGATGACTGGC 61.402 63.158 0.00 0.00 0.00 4.85
2308 2749 5.484290 ACTGGCTGAAGGTGTTTACTAGTAT 59.516 40.000 2.79 0.00 0.00 2.12
2311 2752 6.877322 TGGCTGAAGGTGTTTACTAGTATTTC 59.123 38.462 2.79 2.99 0.00 2.17
2346 2787 3.368539 CGTGCGTTGCTAATTTACCACTA 59.631 43.478 0.00 0.00 0.00 2.74
2347 2788 4.033587 CGTGCGTTGCTAATTTACCACTAT 59.966 41.667 0.00 0.00 0.00 2.12
2371 2812 1.795286 GCCAGTGTCGAGAGTTTTCAG 59.205 52.381 0.00 0.00 0.00 3.02
2373 2814 2.546795 CCAGTGTCGAGAGTTTTCAGCT 60.547 50.000 0.00 0.00 0.00 4.24
2374 2815 3.126831 CAGTGTCGAGAGTTTTCAGCTT 58.873 45.455 0.00 0.00 0.00 3.74
2375 2816 3.557595 CAGTGTCGAGAGTTTTCAGCTTT 59.442 43.478 0.00 0.00 0.00 3.51
2376 2817 4.745125 CAGTGTCGAGAGTTTTCAGCTTTA 59.255 41.667 0.00 0.00 0.00 1.85
2377 2818 4.745620 AGTGTCGAGAGTTTTCAGCTTTAC 59.254 41.667 0.00 0.00 0.00 2.01
2378 2819 4.745620 GTGTCGAGAGTTTTCAGCTTTACT 59.254 41.667 0.00 0.00 0.00 2.24
2380 2821 3.741344 TCGAGAGTTTTCAGCTTTACTGC 59.259 43.478 0.00 0.00 46.76 4.40
2381 2822 3.743396 CGAGAGTTTTCAGCTTTACTGCT 59.257 43.478 0.00 0.00 46.76 4.24
2382 2823 4.212214 CGAGAGTTTTCAGCTTTACTGCTT 59.788 41.667 0.00 0.00 46.76 3.91
2383 2824 5.277538 CGAGAGTTTTCAGCTTTACTGCTTT 60.278 40.000 0.00 0.00 46.76 3.51
2384 2825 6.456795 AGAGTTTTCAGCTTTACTGCTTTT 57.543 33.333 0.00 0.00 46.76 2.27
2385 2826 6.867550 AGAGTTTTCAGCTTTACTGCTTTTT 58.132 32.000 0.00 0.00 46.76 1.94
2473 2914 2.036475 CAGTTAGTCAGACTGCCAGTGT 59.964 50.000 13.84 0.00 38.20 3.55
2487 2928 2.823984 CCAGTGTTTCTTTGCATGCAA 58.176 42.857 28.80 28.80 0.00 4.08
2500 2941 6.319405 TCTTTGCATGCAAGTCACATATGTAT 59.681 34.615 30.25 0.00 37.24 2.29
2629 3070 5.379827 GTTTTATGTTGCTTCTGACGGTAC 58.620 41.667 0.00 0.00 0.00 3.34
2651 3092 5.748592 ACTGTGCTAAAAACGAATCTGAAC 58.251 37.500 0.00 0.00 0.00 3.18
2707 3148 4.514441 CCATTCAGCTGATATCAGTTCACC 59.486 45.833 28.92 14.97 45.45 4.02
2801 3243 9.454859 TTGGTTTCAAATTTCAATTACTTTGGT 57.545 25.926 0.00 0.00 35.92 3.67
2833 3276 3.181497 CGGGACAGCAATATGAAAACTGG 60.181 47.826 0.00 0.00 32.60 4.00
2849 3292 9.807649 ATGAAAACTGGCATTTAGATTCATTAC 57.192 29.630 9.07 0.00 34.66 1.89
2881 3325 7.201530 CCTGAAAATCCTGAAACGACTGTATAC 60.202 40.741 0.00 0.00 0.00 1.47
2892 3336 7.274904 TGAAACGACTGTATACATGCTACTTTC 59.725 37.037 5.91 9.20 0.00 2.62
2895 3339 6.127703 ACGACTGTATACATGCTACTTTCTGT 60.128 38.462 5.91 0.00 0.00 3.41
2900 3344 8.420374 TGTATACATGCTACTTTCTGTAAAGC 57.580 34.615 0.08 0.00 45.06 3.51
2918 3375 6.819649 TGTAAAGCGTAGGCATACAATTAACT 59.180 34.615 18.04 0.00 43.41 2.24
2929 3386 6.528072 GGCATACAATTAACTTCAGTTCTTGC 59.472 38.462 11.89 0.00 39.31 4.01
2971 3429 6.088616 GCTGTTTAGCTCAATTCATTTGTCAC 59.911 38.462 0.00 0.00 46.57 3.67
3003 3461 4.284746 CAGGAACCTACTCCAGAAGACTTT 59.715 45.833 0.00 0.00 38.02 2.66
3018 3476 5.536538 AGAAGACTTTCCCTTTGAAATGGTC 59.463 40.000 0.00 0.00 41.96 4.02
3099 3557 2.954318 GGTCATTGTCAGCATGCCTAAT 59.046 45.455 15.66 7.25 34.76 1.73
3100 3558 4.136796 GGTCATTGTCAGCATGCCTAATA 58.863 43.478 15.66 0.00 34.76 0.98
3137 3595 3.265791 AGTTTGATGAAGATGACGAGGC 58.734 45.455 0.00 0.00 0.00 4.70
3144 3602 0.387202 AAGATGACGAGGCCGATGAG 59.613 55.000 0.00 0.00 39.50 2.90
3182 3640 2.099921 ACGAAGACGATGAAGATGAGGG 59.900 50.000 0.00 0.00 42.66 4.30
3187 3645 1.958205 GATGAAGATGAGGGCGGCG 60.958 63.158 0.51 0.51 0.00 6.46
3192 3650 1.690219 AAGATGAGGGCGGCGAAGAT 61.690 55.000 12.98 0.00 0.00 2.40
3195 3653 2.356433 GAGGGCGGCGAAGATAGC 60.356 66.667 12.98 0.00 0.00 2.97
3202 3660 1.493950 CGGCGAAGATAGCAGCCTTG 61.494 60.000 0.00 0.00 46.85 3.61
3266 3724 3.052082 CACCTGCACAGCCTTCCG 61.052 66.667 0.00 0.00 0.00 4.30
3313 3771 5.114780 TGATGATAGCAGAGAAAACAGAGC 58.885 41.667 0.00 0.00 0.00 4.09
3327 3785 1.207570 ACAGAGCCTGATGCAGAGAAG 59.792 52.381 8.91 0.00 44.83 2.85
3339 3797 2.174639 TGCAGAGAAGTTCCCCTTTGAA 59.825 45.455 0.00 0.00 32.03 2.69
3348 3806 1.071314 TCCCCTTTGAAGGCCCTGAA 61.071 55.000 0.00 0.00 45.10 3.02
3362 3820 3.065371 GGCCCTGAATTCACGTAAGAATG 59.935 47.826 3.38 0.00 38.21 2.67
3394 3853 1.401931 CCTGCTCTTTTTCGCACCATG 60.402 52.381 0.00 0.00 31.95 3.66
3395 3854 0.597568 TGCTCTTTTTCGCACCATGG 59.402 50.000 11.19 11.19 0.00 3.66
3396 3855 0.733909 GCTCTTTTTCGCACCATGGC 60.734 55.000 13.04 0.00 0.00 4.40
3397 3856 0.597568 CTCTTTTTCGCACCATGGCA 59.402 50.000 13.04 0.00 0.00 4.92
3398 3857 0.313672 TCTTTTTCGCACCATGGCAC 59.686 50.000 13.04 2.59 0.00 5.01
3426 3885 1.399714 ATGACTGCCCATTGCTGATG 58.600 50.000 0.00 0.00 41.11 3.07
3440 3899 1.746516 GCTGATGGCTCTTCCCTCTTG 60.747 57.143 0.00 0.00 38.06 3.02
3467 3926 3.306595 CTGCAGCGAGCTTCCTCCA 62.307 63.158 0.00 0.00 45.94 3.86
3503 3962 2.498167 CTGTTCAAGTTCCTGGAGGTG 58.502 52.381 0.00 0.00 36.34 4.00
3524 3983 2.027024 GGTGTGACGCTGACGACA 59.973 61.111 0.00 0.00 43.93 4.35
3542 4001 1.333619 ACAACCAACTTCATGCACGAC 59.666 47.619 0.00 0.00 0.00 4.34
3635 4094 1.251251 GTTGAACAGATGGCCTTGCT 58.749 50.000 3.32 0.00 0.00 3.91
3761 4224 1.759445 GTCCTGAATCAGCAGCTAGGA 59.241 52.381 6.76 6.76 34.56 2.94
3947 5212 1.676967 CAGAGTTTGCTCCCCTGGC 60.677 63.158 0.00 0.00 42.59 4.85
4139 5452 1.082104 CGCGTTCCAACTCAAAGCC 60.082 57.895 0.00 0.00 0.00 4.35
4156 5469 1.525923 CCCTGTGATCTGGAGCTGG 59.474 63.158 0.00 0.00 35.11 4.85
4157 5470 0.979709 CCCTGTGATCTGGAGCTGGA 60.980 60.000 0.00 0.00 35.11 3.86
4158 5471 0.907486 CCTGTGATCTGGAGCTGGAA 59.093 55.000 0.00 0.00 35.11 3.53
4179 5492 8.263218 CTGGAACATTTTGTGATGATGGAACAG 61.263 40.741 0.00 0.00 39.91 3.16
4256 6191 2.281517 CTACGTCTGACCTGATCGAGT 58.718 52.381 1.55 0.00 0.00 4.18
4267 6202 2.607038 CCTGATCGAGTGTTCGTTGTCA 60.607 50.000 0.00 1.02 46.72 3.58
4319 6254 1.460689 ACCTCCAACAACCTCCGGA 60.461 57.895 2.93 2.93 0.00 5.14
4330 6265 4.468689 CTCCGGAAAGCGGGGTCC 62.469 72.222 5.23 0.00 35.36 4.46
4368 6303 2.187685 CTCCATGCTGCGTGCCTA 59.812 61.111 16.26 3.33 42.00 3.93
4436 6371 0.828762 AGCCATTGGTGCAGCTGAAA 60.829 50.000 20.43 5.95 33.41 2.69
4500 6435 0.465460 GTCAACCAACTCCAGTGGCA 60.465 55.000 3.51 0.00 0.00 4.92
4529 6464 4.343526 AGCGGTGATGACTCAGATCTTATT 59.656 41.667 0.00 0.00 30.18 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
158 159 3.820467 TCCATGTAGCTTTTGGTGTTCAG 59.180 43.478 0.00 0.00 0.00 3.02
280 282 5.460748 TGATGTTACTAACAATATCGCGGTG 59.539 40.000 6.13 2.10 45.86 4.94
283 285 6.844279 GGTTTGATGTTACTAACAATATCGCG 59.156 38.462 0.00 0.00 45.86 5.87
284 286 7.916552 AGGTTTGATGTTACTAACAATATCGC 58.083 34.615 5.73 0.00 45.86 4.58
314 316 2.093128 AGGTTCGTTCTTGTGGTCTTGT 60.093 45.455 0.00 0.00 0.00 3.16
319 321 1.578583 CGAAGGTTCGTTCTTGTGGT 58.421 50.000 3.91 0.00 45.09 4.16
336 338 6.902771 TTGTTTCTGAAATTAAATCCCCGA 57.097 33.333 6.06 0.00 0.00 5.14
338 340 8.902540 ACTTTTGTTTCTGAAATTAAATCCCC 57.097 30.769 6.06 0.00 0.00 4.81
348 350 5.449451 GCTCGGGTTACTTTTGTTTCTGAAA 60.449 40.000 0.00 0.00 0.00 2.69
357 359 4.083484 CCACTAAAGCTCGGGTTACTTTTG 60.083 45.833 0.00 0.00 35.38 2.44
359 361 3.325716 TCCACTAAAGCTCGGGTTACTTT 59.674 43.478 0.00 0.00 37.40 2.66
368 370 0.103208 ATCCGCTCCACTAAAGCTCG 59.897 55.000 0.00 0.00 37.62 5.03
373 375 2.176045 TGACTCATCCGCTCCACTAAA 58.824 47.619 0.00 0.00 0.00 1.85
379 381 0.596083 CACGATGACTCATCCGCTCC 60.596 60.000 12.58 0.00 37.57 4.70
451 453 3.694043 AAAAACAAGTTGGCAGGTGTT 57.306 38.095 7.96 6.68 35.77 3.32
496 498 0.393077 AGTGAGTACGCAAAGGCAGT 59.607 50.000 0.00 0.00 41.24 4.40
555 557 9.507280 AATGCATTTCACTCGTTTCTTAATATG 57.493 29.630 5.99 0.00 0.00 1.78
575 577 4.307032 ACTTTAGAGACCCACAATGCAT 57.693 40.909 0.00 0.00 0.00 3.96
595 597 5.910614 ACCTACGTAACATCCCTGAAATAC 58.089 41.667 0.00 0.00 0.00 1.89
606 608 5.670792 TGATTCCAGAACCTACGTAACAT 57.329 39.130 0.00 0.00 0.00 2.71
680 700 7.775561 GGTCCTTGGACTACTTTGATATTGAAT 59.224 37.037 17.99 0.00 0.00 2.57
700 720 7.015389 GTCATGCTAGGTAAAGTATAGGTCCTT 59.985 40.741 0.00 0.00 0.00 3.36
737 757 3.450096 TCACCATTCAGATCCTCAGAGTG 59.550 47.826 0.00 0.00 0.00 3.51
782 802 7.824289 TCTTCAACTATATTTCAAGGGTGTCAG 59.176 37.037 0.00 0.00 0.00 3.51
799 819 3.319972 ACGCACAGTAGGTTCTTCAACTA 59.680 43.478 0.00 0.00 32.50 2.24
800 820 2.102588 ACGCACAGTAGGTTCTTCAACT 59.897 45.455 0.00 0.00 32.50 3.16
804 824 2.479275 GGAAACGCACAGTAGGTTCTTC 59.521 50.000 6.10 0.00 0.00 2.87
808 828 0.763035 AGGGAAACGCACAGTAGGTT 59.237 50.000 0.00 0.00 0.00 3.50
910 937 1.153329 GACGAGGAGGCGAGAGAGA 60.153 63.158 0.00 0.00 34.83 3.10
929 956 4.262721 GGGGTTTTGGGTTTGGATTAAGAC 60.263 45.833 0.00 0.00 0.00 3.01
958 1331 0.354199 AATGGGGGAGGGGATAAGGT 59.646 55.000 0.00 0.00 0.00 3.50
1281 1666 2.930562 GCACTCCCCCTCACCTGT 60.931 66.667 0.00 0.00 0.00 4.00
1367 1761 1.153086 CCCGGCAAGGATTCCTCTG 60.153 63.158 5.48 7.93 45.00 3.35
1385 1779 5.772169 CCCCATGAAAAATCCCTCTCTAATC 59.228 44.000 0.00 0.00 0.00 1.75
1420 1815 3.502211 CGAACAAAATTCCAGTACAGGCT 59.498 43.478 0.00 0.00 0.00 4.58
1423 1818 4.755123 ACTCCGAACAAAATTCCAGTACAG 59.245 41.667 0.00 0.00 0.00 2.74
1480 1882 7.562135 ACAACTACCGGTAAAACATCTATCAT 58.438 34.615 16.65 0.00 0.00 2.45
1482 1884 7.546667 TGAACAACTACCGGTAAAACATCTATC 59.453 37.037 16.65 6.17 0.00 2.08
1487 1889 5.370679 ACTGAACAACTACCGGTAAAACAT 58.629 37.500 16.65 2.08 0.00 2.71
1508 1910 1.204146 ACGCATGGTCCATTCCTACT 58.796 50.000 0.00 0.00 0.00 2.57
1570 1972 7.324178 ACCATCAGTAATTCACTCTTACAGAC 58.676 38.462 0.00 0.00 34.26 3.51
1594 1996 3.411415 GCACCATCATGCTTAACTGAC 57.589 47.619 0.00 0.00 42.62 3.51
1643 2067 5.616270 TGTACATTAGAACACAGGAAAGCA 58.384 37.500 0.00 0.00 0.00 3.91
1675 2099 1.548081 ACTTACATGCTGGCAATGCA 58.452 45.000 7.79 3.75 44.95 3.96
1680 2104 0.597568 GCACAACTTACATGCTGGCA 59.402 50.000 0.00 0.00 36.40 4.92
1681 2105 0.109132 GGCACAACTTACATGCTGGC 60.109 55.000 0.00 0.00 39.38 4.85
1683 2107 1.068333 GGTGGCACAACTTACATGCTG 60.068 52.381 20.82 0.00 46.61 4.41
1684 2108 1.247567 GGTGGCACAACTTACATGCT 58.752 50.000 20.82 0.00 46.61 3.79
1685 2109 3.792716 GGTGGCACAACTTACATGC 57.207 52.632 20.82 0.00 46.61 4.06
1694 2120 2.357050 CCATAAGAGGATGGTGGCACAA 60.357 50.000 20.82 9.03 44.16 3.33
1711 2137 8.380099 AGCTTAATCCGTAATCCATAAACCATA 58.620 33.333 0.00 0.00 0.00 2.74
1712 2138 7.231467 AGCTTAATCCGTAATCCATAAACCAT 58.769 34.615 0.00 0.00 0.00 3.55
1716 2142 7.057894 ACCAAGCTTAATCCGTAATCCATAAA 58.942 34.615 0.00 0.00 0.00 1.40
1719 2145 5.048846 ACCAAGCTTAATCCGTAATCCAT 57.951 39.130 0.00 0.00 0.00 3.41
1720 2146 4.497291 ACCAAGCTTAATCCGTAATCCA 57.503 40.909 0.00 0.00 0.00 3.41
1721 2147 5.830000 AAACCAAGCTTAATCCGTAATCC 57.170 39.130 0.00 0.00 0.00 3.01
1722 2148 9.269453 ACTATAAACCAAGCTTAATCCGTAATC 57.731 33.333 0.00 0.00 0.00 1.75
1723 2149 9.052759 CACTATAAACCAAGCTTAATCCGTAAT 57.947 33.333 0.00 0.00 0.00 1.89
1724 2150 8.042515 ACACTATAAACCAAGCTTAATCCGTAA 58.957 33.333 0.00 0.00 0.00 3.18
1725 2151 7.558604 ACACTATAAACCAAGCTTAATCCGTA 58.441 34.615 0.00 0.00 0.00 4.02
1726 2152 6.412214 ACACTATAAACCAAGCTTAATCCGT 58.588 36.000 0.00 0.00 0.00 4.69
1727 2153 6.920569 ACACTATAAACCAAGCTTAATCCG 57.079 37.500 0.00 0.00 0.00 4.18
1728 2154 7.968405 CACAACACTATAAACCAAGCTTAATCC 59.032 37.037 0.00 0.00 0.00 3.01
1729 2155 7.968405 CCACAACACTATAAACCAAGCTTAATC 59.032 37.037 0.00 0.00 0.00 1.75
1730 2156 7.450323 ACCACAACACTATAAACCAAGCTTAAT 59.550 33.333 0.00 0.00 0.00 1.40
1733 2159 5.137551 ACCACAACACTATAAACCAAGCTT 58.862 37.500 0.00 0.00 0.00 3.74
1758 2184 7.013655 AGCAGTTCAAATACTCAGACATGTTTT 59.986 33.333 0.00 0.00 0.00 2.43
1764 2190 8.097038 AGAAATAGCAGTTCAAATACTCAGACA 58.903 33.333 0.00 0.00 0.00 3.41
1771 2197 7.065085 TGCTCAGAGAAATAGCAGTTCAAATAC 59.935 37.037 0.00 0.00 41.15 1.89
1810 2236 1.140852 ACTGCAAACTGACACCAGCTA 59.859 47.619 0.00 0.00 44.16 3.32
1821 2247 1.202687 TCTAGCACAGCACTGCAAACT 60.203 47.619 3.30 0.00 39.86 2.66
1828 2254 3.134458 GACTTGTTTCTAGCACAGCACT 58.866 45.455 0.00 0.00 0.00 4.40
1829 2255 3.059325 CAGACTTGTTTCTAGCACAGCAC 60.059 47.826 0.00 0.00 0.00 4.40
1830 2256 3.133691 CAGACTTGTTTCTAGCACAGCA 58.866 45.455 0.00 0.00 0.00 4.41
1831 2257 3.393800 TCAGACTTGTTTCTAGCACAGC 58.606 45.455 0.00 0.00 0.00 4.40
1832 2258 7.840342 ATATTCAGACTTGTTTCTAGCACAG 57.160 36.000 0.00 0.00 0.00 3.66
1833 2259 8.621532 AAATATTCAGACTTGTTTCTAGCACA 57.378 30.769 0.00 0.00 0.00 4.57
1834 2260 8.721478 TGAAATATTCAGACTTGTTTCTAGCAC 58.279 33.333 0.00 0.00 34.08 4.40
1835 2261 8.846943 TGAAATATTCAGACTTGTTTCTAGCA 57.153 30.769 0.00 0.00 34.08 3.49
1836 2262 9.548208 GTTGAAATATTCAGACTTGTTTCTAGC 57.452 33.333 0.00 0.00 41.38 3.42
1839 2265 8.078596 GCAGTTGAAATATTCAGACTTGTTTCT 58.921 33.333 0.00 0.00 41.38 2.52
1840 2266 8.078596 AGCAGTTGAAATATTCAGACTTGTTTC 58.921 33.333 0.00 0.00 41.38 2.78
1841 2267 7.945134 AGCAGTTGAAATATTCAGACTTGTTT 58.055 30.769 0.00 0.00 41.38 2.83
1842 2268 7.516198 AGCAGTTGAAATATTCAGACTTGTT 57.484 32.000 0.00 0.00 41.38 2.83
1843 2269 8.798859 ATAGCAGTTGAAATATTCAGACTTGT 57.201 30.769 0.00 0.00 41.38 3.16
1846 2272 9.678260 AGAAATAGCAGTTGAAATATTCAGACT 57.322 29.630 0.00 0.00 41.38 3.24
1847 2273 9.928236 GAGAAATAGCAGTTGAAATATTCAGAC 57.072 33.333 0.00 0.00 41.38 3.51
1848 2274 9.896645 AGAGAAATAGCAGTTGAAATATTCAGA 57.103 29.630 0.00 0.00 41.38 3.27
1849 2275 9.932699 CAGAGAAATAGCAGTTGAAATATTCAG 57.067 33.333 0.00 0.00 41.38 3.02
1850 2276 9.671279 TCAGAGAAATAGCAGTTGAAATATTCA 57.329 29.630 0.00 0.00 38.04 2.57
1852 2278 8.619546 GCTCAGAGAAATAGCAGTTGAAATATT 58.380 33.333 0.00 0.00 36.26 1.28
1853 2279 7.772292 TGCTCAGAGAAATAGCAGTTGAAATAT 59.228 33.333 0.00 0.00 41.15 1.28
1854 2280 7.065085 GTGCTCAGAGAAATAGCAGTTGAAATA 59.935 37.037 0.00 0.00 46.26 1.40
1855 2281 5.942236 TGCTCAGAGAAATAGCAGTTGAAAT 59.058 36.000 0.00 0.00 41.15 2.17
1856 2282 5.180117 GTGCTCAGAGAAATAGCAGTTGAAA 59.820 40.000 0.00 0.00 46.26 2.69
1857 2283 4.692625 GTGCTCAGAGAAATAGCAGTTGAA 59.307 41.667 0.00 0.00 46.26 2.69
1858 2284 4.248859 GTGCTCAGAGAAATAGCAGTTGA 58.751 43.478 0.00 0.00 46.26 3.18
1859 2285 3.999001 TGTGCTCAGAGAAATAGCAGTTG 59.001 43.478 0.00 0.00 46.26 3.16
1860 2286 4.277515 TGTGCTCAGAGAAATAGCAGTT 57.722 40.909 0.00 0.00 46.26 3.16
1861 2287 3.969287 TGTGCTCAGAGAAATAGCAGT 57.031 42.857 0.00 0.00 46.26 4.40
1862 2288 3.002451 GCATGTGCTCAGAGAAATAGCAG 59.998 47.826 0.00 0.00 46.26 4.24
1863 2289 2.941064 GCATGTGCTCAGAGAAATAGCA 59.059 45.455 0.00 0.00 43.66 3.49
1864 2290 2.033065 CGCATGTGCTCAGAGAAATAGC 60.033 50.000 0.00 0.00 39.32 2.97
1865 2291 3.244814 GTCGCATGTGCTCAGAGAAATAG 59.755 47.826 0.00 0.00 39.32 1.73
1866 2292 3.118992 AGTCGCATGTGCTCAGAGAAATA 60.119 43.478 0.00 0.00 39.32 1.40
1867 2293 2.005451 GTCGCATGTGCTCAGAGAAAT 58.995 47.619 0.00 0.00 39.32 2.17
1868 2294 1.001293 AGTCGCATGTGCTCAGAGAAA 59.999 47.619 0.00 0.00 39.32 2.52
1869 2295 0.605083 AGTCGCATGTGCTCAGAGAA 59.395 50.000 0.00 0.00 39.32 2.87
1870 2296 1.463674 TAGTCGCATGTGCTCAGAGA 58.536 50.000 0.00 0.00 39.32 3.10
1871 2297 2.505628 ATAGTCGCATGTGCTCAGAG 57.494 50.000 0.00 0.00 39.32 3.35
1872 2298 2.166254 TGAATAGTCGCATGTGCTCAGA 59.834 45.455 0.00 0.00 39.32 3.27
1873 2299 2.538861 CTGAATAGTCGCATGTGCTCAG 59.461 50.000 0.00 4.63 39.32 3.35
1874 2300 2.543641 CTGAATAGTCGCATGTGCTCA 58.456 47.619 0.00 0.00 39.32 4.26
1875 2301 1.260033 GCTGAATAGTCGCATGTGCTC 59.740 52.381 0.00 0.00 39.32 4.26
1876 2302 1.293924 GCTGAATAGTCGCATGTGCT 58.706 50.000 0.00 4.98 39.32 4.40
1877 2303 0.305922 GGCTGAATAGTCGCATGTGC 59.694 55.000 0.00 0.00 37.78 4.57
1878 2304 1.655484 TGGCTGAATAGTCGCATGTG 58.345 50.000 0.00 0.00 0.00 3.21
1879 2305 2.401583 TTGGCTGAATAGTCGCATGT 57.598 45.000 8.71 0.00 0.00 3.21
1880 2306 2.615447 ACATTGGCTGAATAGTCGCATG 59.385 45.455 8.71 7.26 0.00 4.06
1881 2307 2.923121 ACATTGGCTGAATAGTCGCAT 58.077 42.857 8.71 0.00 0.00 4.73
1882 2308 2.401583 ACATTGGCTGAATAGTCGCA 57.598 45.000 8.71 0.00 0.00 5.10
1883 2309 2.223340 CCAACATTGGCTGAATAGTCGC 60.223 50.000 0.00 0.00 42.21 5.19
1884 2310 3.680642 CCAACATTGGCTGAATAGTCG 57.319 47.619 0.00 0.00 42.21 4.18
1896 2322 5.475719 AGAATGATCAGCAAACCAACATTG 58.524 37.500 0.09 0.00 0.00 2.82
1897 2323 5.733620 AGAATGATCAGCAAACCAACATT 57.266 34.783 0.09 0.00 0.00 2.71
1898 2324 6.839124 TTAGAATGATCAGCAAACCAACAT 57.161 33.333 0.09 0.00 0.00 2.71
1899 2325 6.433716 TCATTAGAATGATCAGCAAACCAACA 59.566 34.615 0.09 0.00 40.32 3.33
1900 2326 6.855836 TCATTAGAATGATCAGCAAACCAAC 58.144 36.000 0.09 0.00 40.32 3.77
1953 2379 8.837099 AAACCCTCAATATTTACCATCAATCA 57.163 30.769 0.00 0.00 0.00 2.57
1954 2380 9.533253 CAAAACCCTCAATATTTACCATCAATC 57.467 33.333 0.00 0.00 0.00 2.67
1959 2385 8.875168 TGAAACAAAACCCTCAATATTTACCAT 58.125 29.630 0.00 0.00 0.00 3.55
1960 2386 8.251383 TGAAACAAAACCCTCAATATTTACCA 57.749 30.769 0.00 0.00 0.00 3.25
1961 2387 9.549078 TTTGAAACAAAACCCTCAATATTTACC 57.451 29.630 0.00 0.00 0.00 2.85
1967 2393 9.672673 TCAAAATTTGAAACAAAACCCTCAATA 57.327 25.926 5.87 0.00 36.59 1.90
1968 2394 8.572855 TCAAAATTTGAAACAAAACCCTCAAT 57.427 26.923 5.87 0.00 36.59 2.57
1969 2395 7.986085 TCAAAATTTGAAACAAAACCCTCAA 57.014 28.000 5.87 0.00 36.59 3.02
1970 2396 7.986085 TTCAAAATTTGAAACAAAACCCTCA 57.014 28.000 17.69 0.00 45.94 3.86
1998 2424 4.682787 TCGAATATTGCTCTCACACGAAT 58.317 39.130 0.00 0.00 0.00 3.34
2001 2433 2.217393 GCTCGAATATTGCTCTCACACG 59.783 50.000 0.00 0.00 0.00 4.49
2004 2436 3.711086 TCAGCTCGAATATTGCTCTCAC 58.289 45.455 0.00 0.00 34.51 3.51
2021 2453 5.904362 AACTGATGACCCTAAATTTCAGC 57.096 39.130 0.00 0.00 35.20 4.26
2023 2455 8.877864 ACAATAACTGATGACCCTAAATTTCA 57.122 30.769 0.00 0.00 0.00 2.69
2026 2458 9.308000 TCAAACAATAACTGATGACCCTAAATT 57.692 29.630 0.00 0.00 0.00 1.82
2034 2466 9.132521 CAGGATTTTCAAACAATAACTGATGAC 57.867 33.333 0.00 0.00 0.00 3.06
2056 2488 7.914427 AGTATATACCACAGTCATTTCAGGA 57.086 36.000 9.32 0.00 0.00 3.86
2063 2495 9.326413 GCAAAAAGTAGTATATACCACAGTCAT 57.674 33.333 12.99 0.00 0.00 3.06
2074 2506 5.433526 TCCGCCTTGCAAAAAGTAGTATAT 58.566 37.500 0.00 0.00 0.00 0.86
2075 2507 4.834534 TCCGCCTTGCAAAAAGTAGTATA 58.165 39.130 0.00 0.00 0.00 1.47
2086 2518 0.033228 CCAAATGTTCCGCCTTGCAA 59.967 50.000 0.00 0.00 0.00 4.08
2094 2526 6.493449 AAAATTTTATGGCCAAATGTTCCG 57.507 33.333 10.96 0.00 0.00 4.30
2096 2528 9.824534 CAAGTAAAATTTTATGGCCAAATGTTC 57.175 29.630 10.96 1.73 0.00 3.18
2116 2548 4.397103 TGACGCTAAGTAGCTAGCAAGTAA 59.603 41.667 18.83 0.00 46.85 2.24
2134 2566 1.451651 CGCAAGACCAAAATTTGACGC 59.548 47.619 7.37 1.69 43.02 5.19
2137 2569 4.764823 AGTATCCGCAAGACCAAAATTTGA 59.235 37.500 7.37 0.00 43.02 2.69
2140 2572 4.082245 CCAAGTATCCGCAAGACCAAAATT 60.082 41.667 0.00 0.00 43.02 1.82
2141 2573 3.443681 CCAAGTATCCGCAAGACCAAAAT 59.556 43.478 0.00 0.00 43.02 1.82
2148 2580 0.618458 AAGCCCAAGTATCCGCAAGA 59.382 50.000 0.00 0.00 43.02 3.02
2149 2581 1.017387 GAAGCCCAAGTATCCGCAAG 58.983 55.000 0.00 0.00 0.00 4.01
2159 2591 4.080863 ACCAATACTCAGTAGAAGCCCAAG 60.081 45.833 0.00 0.00 0.00 3.61
2162 2594 3.181464 GGACCAATACTCAGTAGAAGCCC 60.181 52.174 0.00 0.00 0.00 5.19
2165 2597 4.641094 AGACGGACCAATACTCAGTAGAAG 59.359 45.833 0.00 0.00 0.00 2.85
2175 2607 4.569564 GGTAAATGTCAGACGGACCAATAC 59.430 45.833 3.17 3.97 46.38 1.89
2184 2616 3.325870 TCAAGCAGGTAAATGTCAGACG 58.674 45.455 0.00 0.00 0.00 4.18
2202 2634 7.632861 TGATAACAAATCTCCCTCTCAATCAA 58.367 34.615 0.00 0.00 0.00 2.57
2206 2638 6.669591 TCTCTGATAACAAATCTCCCTCTCAA 59.330 38.462 0.00 0.00 0.00 3.02
2227 2659 9.575783 GAAAAATATCAGTAGAAACGTCTCTCT 57.424 33.333 0.00 0.00 35.12 3.10
2229 2661 9.930693 AAGAAAAATATCAGTAGAAACGTCTCT 57.069 29.630 0.00 0.00 35.12 3.10
2277 2718 0.326264 ACCTTCAGCCAGTCATCCAC 59.674 55.000 0.00 0.00 0.00 4.02
2308 2749 2.223745 GCACGGTCCTACCAAAAGAAA 58.776 47.619 0.00 0.00 38.47 2.52
2311 2752 0.601841 ACGCACGGTCCTACCAAAAG 60.602 55.000 0.00 0.00 38.47 2.27
2346 2787 3.895232 AACTCTCGACACTGGCAATAT 57.105 42.857 0.00 0.00 0.00 1.28
2347 2788 3.678056 AAACTCTCGACACTGGCAATA 57.322 42.857 0.00 0.00 0.00 1.90
2387 2828 9.491675 ACAAGCAATAAAAATGAATTGATGTCA 57.508 25.926 0.00 0.00 35.53 3.58
2391 2832 9.615295 GCAAACAAGCAATAAAAATGAATTGAT 57.385 25.926 0.00 0.00 35.53 2.57
2392 2833 8.074972 GGCAAACAAGCAATAAAAATGAATTGA 58.925 29.630 0.00 0.00 35.53 2.57
2393 2834 7.861372 TGGCAAACAAGCAATAAAAATGAATTG 59.139 29.630 0.00 0.00 36.40 2.32
2394 2835 7.938715 TGGCAAACAAGCAATAAAAATGAATT 58.061 26.923 0.00 0.00 35.83 2.17
2395 2836 7.507733 TGGCAAACAAGCAATAAAAATGAAT 57.492 28.000 0.00 0.00 35.83 2.57
2396 2837 6.932356 TGGCAAACAAGCAATAAAAATGAA 57.068 29.167 0.00 0.00 35.83 2.57
2397 2838 6.568081 GCATGGCAAACAAGCAATAAAAATGA 60.568 34.615 0.00 0.00 43.04 2.57
2398 2839 5.569823 GCATGGCAAACAAGCAATAAAAATG 59.430 36.000 0.00 0.00 43.04 2.32
2399 2840 5.701855 GCATGGCAAACAAGCAATAAAAAT 58.298 33.333 0.00 0.00 43.04 1.82
2400 2841 5.105834 GCATGGCAAACAAGCAATAAAAA 57.894 34.783 0.00 0.00 43.04 1.94
2401 2842 4.745837 GCATGGCAAACAAGCAATAAAA 57.254 36.364 0.00 0.00 43.04 1.52
2473 2914 3.797451 TGTGACTTGCATGCAAAGAAA 57.203 38.095 31.37 15.93 35.33 2.52
2500 2941 6.811253 ACACAAAACCGAGCTAAATCATAA 57.189 33.333 0.00 0.00 0.00 1.90
2519 2960 9.122779 TGATGAATATGCATAAGAATCAACACA 57.877 29.630 11.13 11.20 0.00 3.72
2629 3070 5.747565 TGTTCAGATTCGTTTTTAGCACAG 58.252 37.500 0.00 0.00 0.00 3.66
2651 3092 1.891150 AGAGAAACAGCAGCCCAAATG 59.109 47.619 0.00 0.00 0.00 2.32
2732 3173 5.221641 CCGGACTCCCTCATTCAAATACATA 60.222 44.000 0.00 0.00 0.00 2.29
2736 3177 3.112263 ACCGGACTCCCTCATTCAAATA 58.888 45.455 9.46 0.00 0.00 1.40
2748 3189 0.108019 AAACTCAACCACCGGACTCC 59.892 55.000 9.46 0.00 0.00 3.85
2801 3243 1.971167 GCTGTCCCGCCATGTGAAA 60.971 57.895 0.00 0.00 0.00 2.69
2833 3276 7.975616 TCAGGCAAAAGTAATGAATCTAAATGC 59.024 33.333 0.00 0.00 0.00 3.56
2849 3292 4.445385 CGTTTCAGGATTTTCAGGCAAAAG 59.555 41.667 0.00 0.00 37.40 2.27
2881 3325 4.928661 ACGCTTTACAGAAAGTAGCATG 57.071 40.909 0.00 0.00 43.51 4.06
2892 3336 5.734855 AATTGTATGCCTACGCTTTACAG 57.265 39.130 0.00 0.00 36.40 2.74
2895 3339 7.549842 TGAAGTTAATTGTATGCCTACGCTTTA 59.450 33.333 0.00 0.00 35.36 1.85
2900 3344 6.903883 ACTGAAGTTAATTGTATGCCTACG 57.096 37.500 0.00 0.00 0.00 3.51
2929 3386 6.690194 AAACAGCCTAGATATTTGCAAGAG 57.310 37.500 0.00 0.00 0.00 2.85
2942 3400 6.690194 AATGAATTGAGCTAAACAGCCTAG 57.310 37.500 0.00 0.00 34.90 3.02
2971 3429 4.040461 TGGAGTAGGTTCCTGTCAAAAGAG 59.960 45.833 1.12 0.00 38.12 2.85
3003 3461 3.712016 TCATCGACCATTTCAAAGGGA 57.288 42.857 8.09 0.00 0.00 4.20
3018 3476 1.269988 ACGCTCATCCCATCTTCATCG 60.270 52.381 0.00 0.00 0.00 3.84
3099 3557 3.438131 AACTCAGGATCCCCTTCCATA 57.562 47.619 8.55 0.00 42.02 2.74
3100 3558 2.243221 CAAACTCAGGATCCCCTTCCAT 59.757 50.000 8.55 0.00 42.02 3.41
3137 3595 4.598894 CAGCCGCCTCCTCATCGG 62.599 72.222 0.00 0.00 45.46 4.18
3149 3607 3.121030 CTTCGTCCTTGGCAGCCG 61.121 66.667 7.03 0.00 0.00 5.52
3150 3608 2.035442 GTCTTCGTCCTTGGCAGCC 61.035 63.158 3.66 3.66 0.00 4.85
3165 3623 0.387202 CGCCCTCATCTTCATCGTCT 59.613 55.000 0.00 0.00 0.00 4.18
3182 3640 3.341835 GGCTGCTATCTTCGCCGC 61.342 66.667 0.00 0.00 36.96 6.53
3195 3653 2.408271 TCACCTTCATAGCAAGGCTG 57.592 50.000 0.07 0.17 46.34 4.85
3202 3660 5.510520 CCTTGGAGACTATCACCTTCATAGC 60.511 48.000 0.00 0.00 0.00 2.97
3266 3724 1.576356 GTCAATGGTGATCTCCTCGC 58.424 55.000 14.65 0.00 35.80 5.03
3313 3771 1.407989 GGGGAACTTCTCTGCATCAGG 60.408 57.143 0.00 0.00 31.51 3.86
3327 3785 0.900182 CAGGGCCTTCAAAGGGGAAC 60.900 60.000 1.32 0.00 46.56 3.62
3339 3797 1.906574 TCTTACGTGAATTCAGGGCCT 59.093 47.619 26.86 0.00 36.17 5.19
3348 3806 4.002982 TGAAGCAGCATTCTTACGTGAAT 58.997 39.130 0.00 0.00 37.16 2.57
3362 3820 0.392729 AGAGCAGGATGTGAAGCAGC 60.393 55.000 0.00 0.00 39.31 5.25
3394 3853 0.940126 CAGTCATAAGATGCCGTGCC 59.060 55.000 0.00 0.00 0.00 5.01
3395 3854 0.305922 GCAGTCATAAGATGCCGTGC 59.694 55.000 0.00 0.00 33.81 5.34
3426 3885 2.163509 GGAAAACAAGAGGGAAGAGCC 58.836 52.381 0.00 0.00 0.00 4.70
3434 3893 2.485814 GCTGCAGTAGGAAAACAAGAGG 59.514 50.000 16.64 0.00 0.00 3.69
3440 3899 0.444260 GCTCGCTGCAGTAGGAAAAC 59.556 55.000 16.64 0.00 42.31 2.43
3467 3926 1.898574 CAGGCCCTTCTGCACGTTT 60.899 57.895 0.00 0.00 0.00 3.60
3524 3983 1.967319 AGTCGTGCATGAAGTTGGTT 58.033 45.000 10.93 0.00 0.00 3.67
3542 4001 3.201290 GGTCTGCTTGGTGATCATGTAG 58.799 50.000 0.00 0.00 35.57 2.74
3600 4059 2.248248 TCAACCTCACTACTGGACCAG 58.752 52.381 20.45 20.45 37.52 4.00
3635 4094 0.599991 ATTTGCTGTCGAGTCACGCA 60.600 50.000 0.00 0.59 42.26 5.24
3761 4224 6.813152 CCAAAACACAAATGAAACTCACTCTT 59.187 34.615 0.00 0.00 0.00 2.85
3823 5024 4.843220 AGGAAGTCTTGTTTCATTGCTG 57.157 40.909 0.00 0.00 0.00 4.41
4119 5432 1.574428 CTTTGAGTTGGAACGCGGG 59.426 57.895 12.47 0.00 0.00 6.13
4120 5433 1.082104 GCTTTGAGTTGGAACGCGG 60.082 57.895 12.47 0.00 0.00 6.46
4139 5452 0.907486 TTCCAGCTCCAGATCACAGG 59.093 55.000 0.00 0.00 0.00 4.00
4156 5469 6.680810 TCTGTTCCATCATCACAAAATGTTC 58.319 36.000 0.00 0.00 0.00 3.18
4157 5470 6.266103 ACTCTGTTCCATCATCACAAAATGTT 59.734 34.615 0.00 0.00 0.00 2.71
4158 5471 5.771666 ACTCTGTTCCATCATCACAAAATGT 59.228 36.000 0.00 0.00 0.00 2.71
4179 5492 1.801025 CGCCCAACCAACACAAAACTC 60.801 52.381 0.00 0.00 0.00 3.01
4204 6139 0.620556 TGAGGTTGATCCCTTCCTGC 59.379 55.000 0.00 0.00 34.03 4.85
4206 6141 1.279271 CGTTGAGGTTGATCCCTTCCT 59.721 52.381 0.00 0.00 34.03 3.36
4210 6145 0.613777 GGACGTTGAGGTTGATCCCT 59.386 55.000 0.00 0.00 37.62 4.20
4213 6148 1.683790 CGCGGACGTTGAGGTTGATC 61.684 60.000 0.00 0.00 33.53 2.92
4233 6168 1.015109 GATCAGGTCAGACGTAGCGA 58.985 55.000 0.00 0.00 0.00 4.93
4256 6191 1.761244 CGCAGCACTGACAACGAACA 61.761 55.000 0.81 0.00 0.00 3.18
4319 6254 2.669240 GTAGCTGGACCCCGCTTT 59.331 61.111 10.16 0.00 35.69 3.51
4411 6346 3.058160 GCACCAATGGCTGACGCT 61.058 61.111 0.00 0.00 36.09 5.07
4529 6464 1.371337 GCTGGCTGTTGATGATGCGA 61.371 55.000 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.