Multiple sequence alignment - TraesCS2D01G039400

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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 TraesCS2D01G039400 chr2D 100.000 3989 0 0 1 3989 14397714 14393726 0.000000e+00 7367
1 TraesCS2D01G039400 chr2A 89.827 1848 164 11 12 1839 16670471 16668628 0.000000e+00 2350
2 TraesCS2D01G039400 chr2A 92.981 1154 66 4 1852 3004 16668645 16667506 0.000000e+00 1668
3 TraesCS2D01G039400 chr2A 89.559 431 23 4 3129 3559 16667082 16666674 9.820000e-146 527
4 TraesCS2D01G039400 chr2A 87.692 455 30 11 3557 3989 16666612 16666162 1.280000e-139 507
5 TraesCS2D01G039400 chr2B 93.730 1276 66 10 1855 3124 26292241 26290974 0.000000e+00 1901
6 TraesCS2D01G039400 chr2B 86.739 1282 151 8 569 1839 26293500 26292227 0.000000e+00 1408
7 TraesCS2D01G039400 chr2B 94.253 348 12 4 12 353 26293845 26293500 3.530000e-145 525
8 TraesCS2D01G039400 chr2B 84.652 417 46 14 3583 3989 26290121 26289713 2.230000e-107 399
9 TraesCS2D01G039400 chr2B 84.043 376 44 5 3202 3570 26290581 26290215 8.200000e-92 348
10 TraesCS2D01G039400 chr6D 74.532 267 66 2 2378 2643 308938188 308937923 9.060000e-22 115
11 TraesCS2D01G039400 chr6B 71.026 497 134 10 2152 2643 476429119 476428628 1.170000e-20 111
12 TraesCS2D01G039400 chr6A 70.825 497 135 10 2152 2643 445644414 445643923 5.450000e-19 106


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 TraesCS2D01G039400 chr2D 14393726 14397714 3988 True 7367.0 7367 100.00000 1 3989 1 chr2D.!!$R1 3988
1 TraesCS2D01G039400 chr2A 16666162 16670471 4309 True 1263.0 2350 90.01475 12 3989 4 chr2A.!!$R1 3977
2 TraesCS2D01G039400 chr2B 26289713 26293845 4132 True 916.2 1901 88.68340 12 3989 5 chr2B.!!$R1 3977

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
455 467 0.189574 TTTTTGGTGCCCTGATCCCA 59.810 50.0 0.0 0.0 0.00 4.37 F
1767 1792 0.032217 TCAATCCAAATGGGGAGGCC 60.032 55.0 0.0 0.0 41.08 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1854 0.109597 CAATTGAACCTGCGAGCCAC 60.110 55.0 0.00 0.00 0.0 5.01 R
3289 3656 0.173255 CGGCCCTGCAGTAAAATTGG 59.827 55.0 13.81 5.74 0.0 3.16 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 6.538021 CCAAACATCCAACAAATTTTGACTCA 59.462 34.615 15.81 0.00 0.00 3.41
40 41 6.469782 ACATCCAACAAATTTTGACTCACT 57.530 33.333 15.81 0.00 0.00 3.41
170 171 4.383861 CAGTCTGGCGGCTCAGCA 62.384 66.667 11.43 0.00 39.27 4.41
234 235 3.192001 GCATTTCAGGACATCAAGAGCAA 59.808 43.478 0.00 0.00 0.00 3.91
241 246 2.354259 GACATCAAGAGCAAGGGACAG 58.646 52.381 0.00 0.00 0.00 3.51
250 255 1.967535 CAAGGGACAGCAGAGACGA 59.032 57.895 0.00 0.00 0.00 4.20
362 373 3.760738 TGTGCAATTGGTGGTTCATCTA 58.239 40.909 7.72 0.00 0.00 1.98
380 391 3.774528 CTAGGCTGGTGGCGAGCA 61.775 66.667 0.00 0.00 44.18 4.26
395 406 4.458989 TGGCGAGCAAAAACATATCTTCTT 59.541 37.500 0.00 0.00 0.00 2.52
416 427 1.215173 CCATTTATCCACCCAGAGCCA 59.785 52.381 0.00 0.00 0.00 4.75
423 434 1.197430 CCACCCAGAGCCAGAGACTT 61.197 60.000 0.00 0.00 0.00 3.01
427 438 0.248843 CCAGAGCCAGAGACTTGACC 59.751 60.000 0.00 0.00 0.00 4.02
442 453 5.009854 ACTTGACCAGTCAACATTTTTGG 57.990 39.130 9.12 0.64 43.90 3.28
443 454 4.466015 ACTTGACCAGTCAACATTTTTGGT 59.534 37.500 9.12 1.23 43.90 3.67
448 459 2.102925 CAGTCAACATTTTTGGTGCCCT 59.897 45.455 0.00 0.00 0.00 5.19
449 460 2.102925 AGTCAACATTTTTGGTGCCCTG 59.897 45.455 0.00 0.00 0.00 4.45
450 461 2.102252 GTCAACATTTTTGGTGCCCTGA 59.898 45.455 0.00 0.00 0.00 3.86
451 462 2.971330 TCAACATTTTTGGTGCCCTGAT 59.029 40.909 0.00 0.00 0.00 2.90
452 463 3.006752 TCAACATTTTTGGTGCCCTGATC 59.993 43.478 0.00 0.00 0.00 2.92
455 467 0.189574 TTTTTGGTGCCCTGATCCCA 59.810 50.000 0.00 0.00 0.00 4.37
465 477 0.846693 CCTGATCCCAAGGGTAAGGG 59.153 60.000 4.80 0.00 46.90 3.95
519 531 5.048504 ACTGCATAGTGTTCAGTTGGAATTG 60.049 40.000 0.00 0.00 37.78 2.32
525 537 4.218417 AGTGTTCAGTTGGAATTGTATGCC 59.782 41.667 0.00 0.00 37.93 4.40
530 542 4.832266 TCAGTTGGAATTGTATGCCAAACT 59.168 37.500 0.63 0.00 42.77 2.66
540 552 2.206576 ATGCCAAACTTGTCCCTCTC 57.793 50.000 0.00 0.00 0.00 3.20
562 574 7.612677 TCTCTTGAAGAGTATGTCCCTTTTAC 58.387 38.462 20.59 0.00 42.83 2.01
563 575 6.708285 TCTTGAAGAGTATGTCCCTTTTACC 58.292 40.000 0.00 0.00 0.00 2.85
661 674 4.855715 TTTTTGTGTGTGTTCCTGACAA 57.144 36.364 0.00 0.00 40.65 3.18
699 712 4.583871 AGCTATCTCTGGAAACAAAGTGG 58.416 43.478 0.00 0.00 42.06 4.00
893 907 0.837272 AGGACCCACCATATTGACCG 59.163 55.000 0.00 0.00 42.04 4.79
904 918 4.162812 CCATATTGACCGAAAACCAAACG 58.837 43.478 0.00 0.00 0.00 3.60
908 922 1.397692 TGACCGAAAACCAAACGTGAC 59.602 47.619 0.00 0.00 0.00 3.67
910 924 2.018515 ACCGAAAACCAAACGTGACAT 58.981 42.857 0.00 0.00 0.00 3.06
920 934 3.056821 CCAAACGTGACATAGACTCTGGA 60.057 47.826 0.00 0.00 0.00 3.86
922 936 5.171476 CAAACGTGACATAGACTCTGGAAT 58.829 41.667 0.00 0.00 0.00 3.01
925 939 5.892568 ACGTGACATAGACTCTGGAATTAC 58.107 41.667 0.00 0.00 0.00 1.89
930 944 7.276658 GTGACATAGACTCTGGAATTACTTGTG 59.723 40.741 0.00 0.00 0.00 3.33
1053 1078 4.410400 CTCACCCCAACCTCCGCC 62.410 72.222 0.00 0.00 0.00 6.13
1059 1084 1.766461 CCCAACCTCCGCCTCCTAT 60.766 63.158 0.00 0.00 0.00 2.57
1060 1085 1.447643 CCAACCTCCGCCTCCTATG 59.552 63.158 0.00 0.00 0.00 2.23
1092 1117 0.458669 TCGCCTATGACGGTTTCTCC 59.541 55.000 0.00 0.00 0.00 3.71
1093 1118 0.529992 CGCCTATGACGGTTTCTCCC 60.530 60.000 0.00 0.00 0.00 4.30
1097 1122 2.213499 CTATGACGGTTTCTCCCATGC 58.787 52.381 0.00 0.00 0.00 4.06
1106 1131 1.284111 TTCTCCCATGCCATGCTCCT 61.284 55.000 0.00 0.00 0.00 3.69
1107 1132 1.229359 CTCCCATGCCATGCTCCTT 59.771 57.895 0.00 0.00 0.00 3.36
1108 1133 0.475475 CTCCCATGCCATGCTCCTTA 59.525 55.000 0.00 0.00 0.00 2.69
1132 1157 1.725641 TGGTGTAGCTTCAATCGCAG 58.274 50.000 0.00 0.00 0.00 5.18
1178 1203 1.544825 GCTGCCCAGAGTGTAGGACA 61.545 60.000 0.00 0.00 0.00 4.02
1192 1217 1.538047 AGGACACGCTTACTACGGAA 58.462 50.000 0.00 0.00 34.00 4.30
1215 1240 3.532542 CCGGTTTGACTCTATTTCCTCC 58.467 50.000 0.00 0.00 0.00 4.30
1221 1246 5.941555 TTGACTCTATTTCCTCCTTCTCC 57.058 43.478 0.00 0.00 0.00 3.71
1230 1255 1.978580 TCCTCCTTCTCCACAACCTTC 59.021 52.381 0.00 0.00 0.00 3.46
1237 1262 1.483004 TCTCCACAACCTTCGTGTTCA 59.517 47.619 0.00 0.00 32.26 3.18
1248 1273 2.672961 TCGTGTTCATCATCACTCCC 57.327 50.000 0.00 0.00 33.07 4.30
1249 1274 2.179427 TCGTGTTCATCATCACTCCCT 58.821 47.619 0.00 0.00 33.07 4.20
1264 1289 7.286546 TCATCACTCCCTCTTACTCTGATTTAG 59.713 40.741 0.00 0.00 0.00 1.85
1296 1321 1.737793 CTTGCCTTTACGATTTCCGCT 59.262 47.619 0.00 0.00 43.32 5.52
1299 1324 2.273557 GCCTTTACGATTTCCGCTACA 58.726 47.619 0.00 0.00 43.32 2.74
1300 1325 2.284417 GCCTTTACGATTTCCGCTACAG 59.716 50.000 0.00 0.00 43.32 2.74
1302 1327 2.658373 TTACGATTTCCGCTACAGCA 57.342 45.000 1.61 0.00 43.32 4.41
1323 1348 4.530875 CAGACTCTTTATTGGATGCCCTT 58.469 43.478 0.00 0.00 0.00 3.95
1351 1376 3.264193 TCAGTACATGGGCATCTTCAACT 59.736 43.478 0.00 0.00 0.00 3.16
1352 1377 3.624861 CAGTACATGGGCATCTTCAACTC 59.375 47.826 0.00 0.00 0.00 3.01
1354 1379 2.996631 ACATGGGCATCTTCAACTCTC 58.003 47.619 0.00 0.00 0.00 3.20
1360 1385 3.569701 GGGCATCTTCAACTCTCAAAACA 59.430 43.478 0.00 0.00 0.00 2.83
1389 1414 4.771590 TGTCACAAATCATCTCTTTGCC 57.228 40.909 0.00 0.00 37.15 4.52
1392 1417 3.436704 TCACAAATCATCTCTTTGCCGTC 59.563 43.478 0.00 0.00 37.15 4.79
1409 1434 1.772182 GTCGAGCTTGATACCATCCG 58.228 55.000 7.00 0.00 0.00 4.18
1412 1437 2.429250 TCGAGCTTGATACCATCCGAAA 59.571 45.455 0.00 0.00 0.00 3.46
1415 1440 4.623167 CGAGCTTGATACCATCCGAAATAG 59.377 45.833 0.00 0.00 0.00 1.73
1416 1441 4.319177 AGCTTGATACCATCCGAAATAGC 58.681 43.478 0.00 0.00 0.00 2.97
1419 1444 4.594123 TGATACCATCCGAAATAGCGAA 57.406 40.909 0.00 0.00 0.00 4.70
1422 1447 5.995282 TGATACCATCCGAAATAGCGAATTT 59.005 36.000 0.35 0.35 40.59 1.82
1432 1457 6.086222 CGAAATAGCGAATTTGGGGATATTG 58.914 40.000 5.00 0.00 37.93 1.90
1440 1465 6.350445 GCGAATTTGGGGATATTGATGCTAAT 60.350 38.462 0.00 0.00 0.00 1.73
1458 1483 5.007921 TGCTAATCATGTTGGAATCGATGTG 59.992 40.000 0.00 0.00 0.00 3.21
1470 1495 2.163818 TCGATGTGAACACCTTGGTC 57.836 50.000 2.46 0.00 33.88 4.02
1479 1504 4.691216 GTGAACACCTTGGTCTCTATCAAC 59.309 45.833 0.00 0.00 34.53 3.18
1507 1532 1.837439 CTGCTGGATACTACACCCCAA 59.163 52.381 0.00 0.00 37.61 4.12
1521 1546 1.595093 CCCCAAATGGCACGTTCTCC 61.595 60.000 0.00 0.00 0.00 3.71
1528 1553 2.430367 GCACGTTCTCCCCCTTGT 59.570 61.111 0.00 0.00 0.00 3.16
1618 1643 6.100668 GTCAGTTTAGCACCTTACTTAGAGG 58.899 44.000 0.00 0.00 40.24 3.69
1666 1691 5.422012 TCCAGCACTGTCAATCTTACATCTA 59.578 40.000 0.00 0.00 0.00 1.98
1729 1754 2.026636 GGCACCCTAAGTTCCATACACA 60.027 50.000 0.00 0.00 31.04 3.72
1737 1762 6.772716 CCCTAAGTTCCATACACAGCATTATT 59.227 38.462 0.00 0.00 0.00 1.40
1767 1792 0.032217 TCAATCCAAATGGGGAGGCC 60.032 55.000 0.00 0.00 41.08 5.19
1787 1812 3.188667 GCCAAACCACTTAACTACTCAGC 59.811 47.826 0.00 0.00 0.00 4.26
1788 1813 4.385825 CCAAACCACTTAACTACTCAGCA 58.614 43.478 0.00 0.00 0.00 4.41
1796 1821 5.349817 CACTTAACTACTCAGCATTGTCTGG 59.650 44.000 7.82 3.25 34.91 3.86
1823 1848 2.293677 CAGGATGTTCGACGGAATGA 57.706 50.000 0.00 0.00 34.05 2.57
1824 1849 2.826428 CAGGATGTTCGACGGAATGAT 58.174 47.619 0.00 0.00 34.05 2.45
1825 1850 2.797156 CAGGATGTTCGACGGAATGATC 59.203 50.000 0.00 0.00 34.05 2.92
1826 1851 2.430694 AGGATGTTCGACGGAATGATCA 59.569 45.455 0.00 0.00 34.05 2.92
1827 1852 3.118775 AGGATGTTCGACGGAATGATCAA 60.119 43.478 0.00 0.00 34.05 2.57
1828 1853 3.621268 GGATGTTCGACGGAATGATCAAA 59.379 43.478 0.00 0.00 34.05 2.69
1829 1854 4.260375 GGATGTTCGACGGAATGATCAAAG 60.260 45.833 0.00 0.00 34.05 2.77
1830 1855 3.659786 TGTTCGACGGAATGATCAAAGT 58.340 40.909 0.00 0.00 34.05 2.66
1831 1856 3.431912 TGTTCGACGGAATGATCAAAGTG 59.568 43.478 0.00 0.00 34.05 3.16
1832 1857 2.616960 TCGACGGAATGATCAAAGTGG 58.383 47.619 0.00 0.00 0.00 4.00
1833 1858 1.062587 CGACGGAATGATCAAAGTGGC 59.937 52.381 0.00 0.00 0.00 5.01
1834 1859 2.359900 GACGGAATGATCAAAGTGGCT 58.640 47.619 0.00 0.00 0.00 4.75
1835 1860 2.352960 GACGGAATGATCAAAGTGGCTC 59.647 50.000 0.00 0.00 0.00 4.70
1836 1861 1.328680 CGGAATGATCAAAGTGGCTCG 59.671 52.381 0.00 0.00 0.00 5.03
1837 1862 1.064654 GGAATGATCAAAGTGGCTCGC 59.935 52.381 0.00 0.00 0.00 5.03
1838 1863 1.739466 GAATGATCAAAGTGGCTCGCA 59.261 47.619 0.00 0.00 0.00 5.10
1839 1864 1.376543 ATGATCAAAGTGGCTCGCAG 58.623 50.000 0.00 0.00 0.00 5.18
1840 1865 0.674581 TGATCAAAGTGGCTCGCAGG 60.675 55.000 0.00 0.00 0.00 4.85
1841 1866 0.674895 GATCAAAGTGGCTCGCAGGT 60.675 55.000 0.00 0.00 0.00 4.00
1842 1867 0.250901 ATCAAAGTGGCTCGCAGGTT 60.251 50.000 0.00 0.00 0.00 3.50
1843 1868 0.884704 TCAAAGTGGCTCGCAGGTTC 60.885 55.000 0.00 0.00 0.00 3.62
1844 1869 1.148273 AAAGTGGCTCGCAGGTTCA 59.852 52.632 0.00 0.00 0.00 3.18
1845 1870 0.465460 AAAGTGGCTCGCAGGTTCAA 60.465 50.000 0.00 0.00 0.00 2.69
1846 1871 0.250901 AAGTGGCTCGCAGGTTCAAT 60.251 50.000 0.00 0.00 0.00 2.57
1847 1872 0.250901 AGTGGCTCGCAGGTTCAATT 60.251 50.000 0.00 0.00 0.00 2.32
1848 1873 0.109597 GTGGCTCGCAGGTTCAATTG 60.110 55.000 0.00 0.00 0.00 2.32
1849 1874 1.243342 TGGCTCGCAGGTTCAATTGG 61.243 55.000 5.42 0.00 0.00 3.16
1850 1875 1.508088 GCTCGCAGGTTCAATTGGG 59.492 57.895 5.42 0.00 0.00 4.12
1861 1886 3.383761 GTTCAATTGGGTGCTCAAAGTG 58.616 45.455 5.42 0.00 0.00 3.16
1866 1891 2.328099 GGGTGCTCAAAGTGGCTCG 61.328 63.158 0.00 0.00 0.00 5.03
1873 1898 2.831333 CTCAAAGTGGCTCGCATATCT 58.169 47.619 0.00 0.00 0.00 1.98
1876 1901 2.522836 AAGTGGCTCGCATATCTCTG 57.477 50.000 0.00 0.00 0.00 3.35
1877 1902 0.678395 AGTGGCTCGCATATCTCTGG 59.322 55.000 0.00 0.00 0.00 3.86
1885 1910 1.691976 CGCATATCTCTGGGGGTGTTA 59.308 52.381 0.00 0.00 0.00 2.41
1889 1914 5.246307 GCATATCTCTGGGGGTGTTATTAC 58.754 45.833 0.00 0.00 0.00 1.89
1891 1916 6.690460 GCATATCTCTGGGGGTGTTATTACAA 60.690 42.308 0.00 0.00 35.69 2.41
1977 2002 1.986882 AGGCAAGGAAAAGTGGTGAG 58.013 50.000 0.00 0.00 0.00 3.51
2013 2038 4.130118 GTGGGTCATCATCCTTCACATAC 58.870 47.826 0.00 0.00 0.00 2.39
2066 2091 1.704628 TGACAGGATGCTTCTTGGGAA 59.295 47.619 14.91 0.00 42.53 3.97
2085 2110 4.264217 GGGAAAGGAGGATTTGGAAAGGTA 60.264 45.833 0.00 0.00 0.00 3.08
2105 2130 4.703093 GGTATACAAAGGGCTGCTACAAAA 59.297 41.667 5.01 0.00 0.00 2.44
2139 2164 1.861542 TTGCCATCAAGCGGGTTTCG 61.862 55.000 0.00 0.00 42.76 3.46
2318 2343 3.763097 TTTGCATGGTCAAGATAAGCG 57.237 42.857 0.00 0.00 0.00 4.68
2325 2350 2.094182 TGGTCAAGATAAGCGGACTGTC 60.094 50.000 0.00 0.00 0.00 3.51
2332 2357 0.892358 TAAGCGGACTGTCGACTGGT 60.892 55.000 23.96 18.36 0.00 4.00
2337 2362 1.499049 GGACTGTCGACTGGTTTCAC 58.501 55.000 23.96 8.26 0.00 3.18
2466 2491 7.933396 TCGATAATGAAATGAACGGTAGACTA 58.067 34.615 0.00 0.00 0.00 2.59
2520 2545 0.036164 GTACAGATGCCCACACCACA 59.964 55.000 0.00 0.00 0.00 4.17
2550 2575 1.379843 CACCTGGGGGTACATTGCC 60.380 63.158 0.00 0.00 45.41 4.52
2667 2692 3.285484 ACAGGTGAATGATTCTGATGGC 58.715 45.455 6.73 0.00 0.00 4.40
2796 2821 9.207082 GAGTTAGTACTAAAGCTTGGCTTGCTG 62.207 44.444 16.82 2.57 40.60 4.41
2802 2827 2.266627 GCTTGGCTTGCTGTGCTCT 61.267 57.895 0.00 0.00 0.00 4.09
2813 2838 0.247736 CTGTGCTCTCACCCAGTACC 59.752 60.000 0.00 0.00 42.46 3.34
2884 2909 1.843851 TGCTACTCCCGGATTTCCAAT 59.156 47.619 0.73 0.00 35.14 3.16
3000 3026 5.942236 TGGAGGAAGATGATGCATATTTAGC 59.058 40.000 0.00 0.00 0.00 3.09
3015 3041 9.573166 TGCATATTTAGCTATATGGTTTCTTGT 57.427 29.630 15.25 0.00 38.41 3.16
3080 3112 5.276678 CCACATAAAGGATTAGTTACACGCG 60.277 44.000 3.53 3.53 0.00 6.01
3090 3122 1.328374 AGTTACACGCGTGAAAACCAC 59.672 47.619 42.94 26.25 42.30 4.16
3124 3156 9.310716 GTTGTATGAACTAAGGGTACAGATAAC 57.689 37.037 0.00 0.00 0.00 1.89
3125 3157 8.834004 TGTATGAACTAAGGGTACAGATAACT 57.166 34.615 0.00 0.00 0.00 2.24
3151 3518 5.468540 TGAATTATCCTCCCTGTCATACG 57.531 43.478 0.00 0.00 0.00 3.06
3265 3632 6.690194 AATGACATTCAGATGGAAGCTTAC 57.310 37.500 0.11 0.11 39.30 2.34
3267 3634 4.937620 TGACATTCAGATGGAAGCTTACAC 59.062 41.667 15.19 8.31 39.30 2.90
3268 3635 5.171339 ACATTCAGATGGAAGCTTACACT 57.829 39.130 15.19 10.60 39.30 3.55
3291 3658 3.157518 TCTGCAAGACTGTACCCCA 57.842 52.632 0.00 0.00 38.67 4.96
3292 3659 1.429930 TCTGCAAGACTGTACCCCAA 58.570 50.000 0.00 0.00 38.67 4.12
3293 3660 1.985159 TCTGCAAGACTGTACCCCAAT 59.015 47.619 0.00 0.00 38.67 3.16
3294 3661 2.375174 TCTGCAAGACTGTACCCCAATT 59.625 45.455 0.00 0.00 38.67 2.32
3295 3662 3.157087 CTGCAAGACTGTACCCCAATTT 58.843 45.455 0.00 0.00 34.07 1.82
3296 3663 3.571590 TGCAAGACTGTACCCCAATTTT 58.428 40.909 0.00 0.00 0.00 1.82
3342 3709 0.035317 TTCTGCACTGTAGGCTGGTG 59.965 55.000 0.00 5.01 0.00 4.17
3352 3719 2.092968 TGTAGGCTGGTGAATCATGTCC 60.093 50.000 0.00 0.00 0.00 4.02
3376 3743 8.047310 TCCTGTAAGAATTCTTAAATCCTCACC 58.953 37.037 25.73 12.79 39.84 4.02
3395 3762 5.098663 TCACCCCAAGACCTATTTAAGAGT 58.901 41.667 0.00 0.00 0.00 3.24
3396 3763 5.550403 TCACCCCAAGACCTATTTAAGAGTT 59.450 40.000 0.00 0.00 0.00 3.01
3397 3764 6.731919 TCACCCCAAGACCTATTTAAGAGTTA 59.268 38.462 0.00 0.00 0.00 2.24
3398 3765 7.238096 TCACCCCAAGACCTATTTAAGAGTTAA 59.762 37.037 0.00 0.00 0.00 2.01
3399 3766 7.553044 CACCCCAAGACCTATTTAAGAGTTAAG 59.447 40.741 0.00 0.00 0.00 1.85
3400 3767 7.460082 ACCCCAAGACCTATTTAAGAGTTAAGA 59.540 37.037 0.00 0.00 0.00 2.10
3437 3804 3.090532 GGCCACTAGGGGGTCCAG 61.091 72.222 14.41 0.00 37.04 3.86
3470 3837 5.235850 TCAGTGGGTTACTTGCATTCTAA 57.764 39.130 0.00 0.00 37.60 2.10
3540 3914 3.864583 TGACACTGCAAGCAATTGAAAAC 59.135 39.130 10.34 0.00 37.60 2.43
3541 3915 3.859443 ACACTGCAAGCAATTGAAAACA 58.141 36.364 10.34 0.58 37.60 2.83
3552 3926 4.923281 GCAATTGAAAACATAAGCGTTCCT 59.077 37.500 10.34 0.00 0.00 3.36
3559 3997 3.093717 ACATAAGCGTTCCTCCATACG 57.906 47.619 0.00 0.00 40.55 3.06
3601 4120 2.634815 AGCAGCCAAGATCATACTGG 57.365 50.000 0.00 0.00 0.00 4.00
3668 4187 5.998454 AACAATGAGAGTTCAGACAGTTG 57.002 39.130 0.00 0.00 36.61 3.16
3676 4195 3.034635 AGTTCAGACAGTTGGAGTCAGT 58.965 45.455 0.00 0.00 38.46 3.41
3694 4213 3.387699 TCAGTTCAACACCAGATCTGACA 59.612 43.478 24.62 0.00 37.08 3.58
3710 4229 6.708054 AGATCTGACAAAGTGTCCTAGTTTTG 59.292 38.462 5.96 0.00 46.40 2.44
3711 4230 5.741011 TCTGACAAAGTGTCCTAGTTTTGT 58.259 37.500 5.96 1.51 46.40 2.83
3713 4232 6.657541 TCTGACAAAGTGTCCTAGTTTTGTTT 59.342 34.615 5.96 0.00 46.40 2.83
3716 4235 8.238631 TGACAAAGTGTCCTAGTTTTGTTTTAC 58.761 33.333 5.96 0.00 46.40 2.01
3722 4241 6.471198 GTGTCCTAGTTTTGTTTTACAGCAAC 59.529 38.462 0.00 0.00 0.00 4.17
3726 4245 7.771826 TCCTAGTTTTGTTTTACAGCAACTACT 59.228 33.333 8.48 0.00 35.94 2.57
3737 4256 3.261897 ACAGCAACTACTAACTGGAGCAT 59.738 43.478 0.00 0.00 34.40 3.79
3826 4368 4.677673 AACCGTATATAGTTCCACCACC 57.322 45.455 0.00 0.00 0.00 4.61
3854 4401 1.967319 TCTCTGTTCAACCAAGTGCC 58.033 50.000 0.00 0.00 0.00 5.01
3875 4422 6.918569 GTGCCAACTGACTGTATATAGTGTAG 59.081 42.308 6.89 7.70 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.187694 GGATGTTTGGTTTTTGAAGTGCA 58.812 39.130 0.00 0.00 0.00 4.57
1 2 4.187694 TGGATGTTTGGTTTTTGAAGTGC 58.812 39.130 0.00 0.00 0.00 4.40
3 4 5.799213 TGTTGGATGTTTGGTTTTTGAAGT 58.201 33.333 0.00 0.00 0.00 3.01
4 5 6.734104 TTGTTGGATGTTTGGTTTTTGAAG 57.266 33.333 0.00 0.00 0.00 3.02
5 6 7.693969 ATTTGTTGGATGTTTGGTTTTTGAA 57.306 28.000 0.00 0.00 0.00 2.69
6 7 7.693969 AATTTGTTGGATGTTTGGTTTTTGA 57.306 28.000 0.00 0.00 0.00 2.69
7 8 8.645487 CAAAATTTGTTGGATGTTTGGTTTTTG 58.355 29.630 0.00 0.00 0.00 2.44
8 9 8.579863 TCAAAATTTGTTGGATGTTTGGTTTTT 58.420 25.926 5.56 0.00 0.00 1.94
9 10 8.026026 GTCAAAATTTGTTGGATGTTTGGTTTT 58.974 29.630 5.56 0.00 0.00 2.43
10 11 7.392953 AGTCAAAATTTGTTGGATGTTTGGTTT 59.607 29.630 5.56 0.00 0.00 3.27
11 12 6.883756 AGTCAAAATTTGTTGGATGTTTGGTT 59.116 30.769 5.56 0.00 0.00 3.67
12 13 6.413892 AGTCAAAATTTGTTGGATGTTTGGT 58.586 32.000 5.56 0.00 0.00 3.67
13 14 6.538021 TGAGTCAAAATTTGTTGGATGTTTGG 59.462 34.615 5.56 0.00 0.00 3.28
14 15 7.278424 AGTGAGTCAAAATTTGTTGGATGTTTG 59.722 33.333 5.56 0.00 0.00 2.93
15 16 7.330262 AGTGAGTCAAAATTTGTTGGATGTTT 58.670 30.769 5.56 0.00 0.00 2.83
16 17 6.877236 AGTGAGTCAAAATTTGTTGGATGTT 58.123 32.000 5.56 0.00 0.00 2.71
170 171 3.332485 ACCAACCAACCACCATGTAGTAT 59.668 43.478 0.00 0.00 0.00 2.12
212 213 2.751259 TGCTCTTGATGTCCTGAAATGC 59.249 45.455 0.00 0.00 0.00 3.56
216 217 2.290514 CCCTTGCTCTTGATGTCCTGAA 60.291 50.000 0.00 0.00 0.00 3.02
234 235 0.318762 GTTTCGTCTCTGCTGTCCCT 59.681 55.000 0.00 0.00 0.00 4.20
241 246 1.862806 GGCTGTGTTTCGTCTCTGC 59.137 57.895 0.00 0.00 0.00 4.26
250 255 3.431766 GGTATACATCTCCGGCTGTGTTT 60.432 47.826 12.64 7.46 0.00 2.83
362 373 3.775654 GCTCGCCACCAGCCTAGT 61.776 66.667 0.00 0.00 38.78 2.57
395 406 1.494721 GGCTCTGGGTGGATAAATGGA 59.505 52.381 0.00 0.00 0.00 3.41
402 413 0.980231 GTCTCTGGCTCTGGGTGGAT 60.980 60.000 0.00 0.00 0.00 3.41
407 418 0.248843 GTCAAGTCTCTGGCTCTGGG 59.751 60.000 0.00 0.00 0.00 4.45
423 434 3.430098 GCACCAAAAATGTTGACTGGTCA 60.430 43.478 0.00 0.00 38.34 4.02
442 453 1.279025 TACCCTTGGGATCAGGGCAC 61.279 60.000 15.08 0.00 46.52 5.01
443 454 0.551377 TTACCCTTGGGATCAGGGCA 60.551 55.000 15.08 1.26 46.52 5.36
448 459 0.551377 TGCCCTTACCCTTGGGATCA 60.551 55.000 13.39 0.00 46.15 2.92
449 460 0.106669 GTGCCCTTACCCTTGGGATC 60.107 60.000 13.39 0.00 46.15 3.36
450 461 0.849094 TGTGCCCTTACCCTTGGGAT 60.849 55.000 13.39 0.00 46.15 3.85
451 462 0.849094 ATGTGCCCTTACCCTTGGGA 60.849 55.000 13.39 0.00 46.15 4.37
452 463 0.395724 GATGTGCCCTTACCCTTGGG 60.396 60.000 3.77 3.77 46.00 4.12
455 467 1.072266 TGTGATGTGCCCTTACCCTT 58.928 50.000 0.00 0.00 0.00 3.95
465 477 2.988010 TCCAGTAGGATGTGATGTGC 57.012 50.000 0.00 0.00 39.61 4.57
519 531 3.010420 GAGAGGGACAAGTTTGGCATAC 58.990 50.000 0.00 0.00 38.18 2.39
525 537 4.708177 TCTTCAAGAGAGGGACAAGTTTG 58.292 43.478 0.00 0.00 0.00 2.93
540 552 6.595716 CAGGTAAAAGGGACATACTCTTCAAG 59.404 42.308 0.00 0.00 38.52 3.02
709 722 3.426191 CGTTTGTCTCAATGCACCAAATG 59.574 43.478 0.00 0.00 0.00 2.32
774 787 2.096417 CCGACTTTTCCACTAAAGCACG 60.096 50.000 0.00 0.00 38.42 5.34
893 907 5.465724 AGAGTCTATGTCACGTTTGGTTTTC 59.534 40.000 0.00 0.00 0.00 2.29
904 918 7.276658 CACAAGTAATTCCAGAGTCTATGTCAC 59.723 40.741 0.00 0.00 0.00 3.67
908 922 6.344500 AGCACAAGTAATTCCAGAGTCTATG 58.656 40.000 0.00 0.00 0.00 2.23
910 924 6.360370 AAGCACAAGTAATTCCAGAGTCTA 57.640 37.500 0.00 0.00 0.00 2.59
920 934 6.923508 GCCAAAGAACTTAAGCACAAGTAATT 59.076 34.615 1.29 0.47 37.78 1.40
922 936 5.358442 TGCCAAAGAACTTAAGCACAAGTAA 59.642 36.000 1.29 0.00 37.78 2.24
925 939 4.044426 GTGCCAAAGAACTTAAGCACAAG 58.956 43.478 23.96 0.00 44.40 3.16
930 944 3.052745 GCAAGTGCCAAAGAACTTAAGC 58.947 45.455 1.29 0.00 34.90 3.09
1053 1078 0.469917 ACCCATCGTTGGCATAGGAG 59.530 55.000 7.02 0.00 42.15 3.69
1071 1096 1.925185 GAGAAACCGTCATAGGCGAAC 59.075 52.381 0.00 0.00 33.69 3.95
1075 1100 0.539986 TGGGAGAAACCGTCATAGGC 59.460 55.000 0.00 0.00 40.11 3.93
1080 1105 1.002624 GGCATGGGAGAAACCGTCA 60.003 57.895 0.00 0.00 40.11 4.35
1092 1117 2.589720 TCAATAAGGAGCATGGCATGG 58.410 47.619 27.48 10.64 0.00 3.66
1093 1118 3.056821 CCATCAATAAGGAGCATGGCATG 60.057 47.826 22.99 22.99 0.00 4.06
1097 1122 3.559069 ACACCATCAATAAGGAGCATGG 58.441 45.455 0.00 0.00 40.05 3.66
1106 1131 5.007626 GCGATTGAAGCTACACCATCAATAA 59.992 40.000 8.64 0.00 41.29 1.40
1107 1132 4.511454 GCGATTGAAGCTACACCATCAATA 59.489 41.667 8.64 0.00 41.29 1.90
1108 1133 3.313526 GCGATTGAAGCTACACCATCAAT 59.686 43.478 8.45 8.45 43.25 2.57
1132 1157 1.580815 GTTAGCATGAGAGCTCTGCC 58.419 55.000 23.91 8.39 45.26 4.85
1184 1209 0.320160 GTCAAACCGGCTTCCGTAGT 60.320 55.000 0.00 0.00 46.80 2.73
1187 1212 1.301479 GAGTCAAACCGGCTTCCGT 60.301 57.895 0.00 0.00 46.80 4.69
1192 1217 2.572104 AGGAAATAGAGTCAAACCGGCT 59.428 45.455 0.00 0.00 0.00 5.52
1215 1240 2.240493 ACACGAAGGTTGTGGAGAAG 57.760 50.000 0.00 0.00 41.64 2.85
1221 1246 3.498018 TGATGATGAACACGAAGGTTGTG 59.502 43.478 0.00 0.00 42.99 3.33
1230 1255 2.167281 AGAGGGAGTGATGATGAACACG 59.833 50.000 0.00 0.00 41.22 4.49
1237 1262 5.136068 TCAGAGTAAGAGGGAGTGATGAT 57.864 43.478 0.00 0.00 0.00 2.45
1248 1273 4.920640 TCCGCCTAAATCAGAGTAAGAG 57.079 45.455 0.00 0.00 0.00 2.85
1249 1274 6.071334 CCATATCCGCCTAAATCAGAGTAAGA 60.071 42.308 0.00 0.00 0.00 2.10
1264 1289 2.983725 AAGGCAAGCCCATATCCGCC 62.984 60.000 7.62 0.00 39.90 6.13
1296 1321 5.118990 GCATCCAATAAAGAGTCTGCTGTA 58.881 41.667 0.00 0.00 0.00 2.74
1299 1324 3.549794 GGCATCCAATAAAGAGTCTGCT 58.450 45.455 0.00 0.00 0.00 4.24
1300 1325 2.620585 GGGCATCCAATAAAGAGTCTGC 59.379 50.000 0.00 0.00 0.00 4.26
1302 1327 4.385754 GGAAGGGCATCCAATAAAGAGTCT 60.386 45.833 3.88 0.00 39.42 3.24
1323 1348 0.613572 TGCCCATGTACTGAGACGGA 60.614 55.000 0.00 0.00 0.00 4.69
1360 1385 6.586344 AGAGATGATTTGTGACATTACCGAT 58.414 36.000 0.00 0.00 0.00 4.18
1379 1404 0.247736 AAGCTCGACGGCAAAGAGAT 59.752 50.000 10.28 0.00 34.13 2.75
1380 1405 0.667487 CAAGCTCGACGGCAAAGAGA 60.667 55.000 10.28 0.00 34.13 3.10
1389 1414 1.772182 GGATGGTATCAAGCTCGACG 58.228 55.000 0.00 0.00 0.00 5.12
1392 1417 2.509052 TTCGGATGGTATCAAGCTCG 57.491 50.000 0.00 0.00 0.00 5.03
1409 1434 7.214467 TCAATATCCCCAAATTCGCTATTTC 57.786 36.000 0.00 0.00 34.19 2.17
1412 1437 5.126061 GCATCAATATCCCCAAATTCGCTAT 59.874 40.000 0.00 0.00 0.00 2.97
1415 1440 3.256631 AGCATCAATATCCCCAAATTCGC 59.743 43.478 0.00 0.00 0.00 4.70
1416 1441 6.573664 TTAGCATCAATATCCCCAAATTCG 57.426 37.500 0.00 0.00 0.00 3.34
1419 1444 7.676893 ACATGATTAGCATCAATATCCCCAAAT 59.323 33.333 0.00 0.00 42.93 2.32
1422 1447 6.143551 ACATGATTAGCATCAATATCCCCA 57.856 37.500 0.00 0.00 42.93 4.96
1432 1457 5.929697 TCGATTCCAACATGATTAGCATC 57.070 39.130 0.00 0.00 34.15 3.91
1440 1465 4.154015 GTGTTCACATCGATTCCAACATGA 59.846 41.667 13.27 0.65 0.00 3.07
1458 1483 5.153950 AGTTGATAGAGACCAAGGTGTTC 57.846 43.478 0.00 0.00 0.00 3.18
1470 1495 2.499289 AGCAGTGTGGGAGTTGATAGAG 59.501 50.000 0.00 0.00 0.00 2.43
1479 1504 1.198713 AGTATCCAGCAGTGTGGGAG 58.801 55.000 10.12 0.00 38.26 4.30
1507 1532 1.789576 AAGGGGGAGAACGTGCCATT 61.790 55.000 0.00 0.00 38.84 3.16
1618 1643 4.087892 TGGGCGCTGAGGCTTCTC 62.088 66.667 7.64 0.00 45.89 2.87
1666 1691 4.207165 ACATATACCGAGCTTGGCAAAAT 58.793 39.130 20.81 10.86 0.00 1.82
1714 1739 7.642669 CCAATAATGCTGTGTATGGAACTTAG 58.357 38.462 0.00 0.00 0.00 2.18
1729 1754 3.700538 TGAAACTCCAGCCAATAATGCT 58.299 40.909 0.00 0.00 40.41 3.79
1737 1762 2.673775 TTGGATTGAAACTCCAGCCA 57.326 45.000 0.00 0.00 43.46 4.75
1767 1792 6.017109 ACAATGCTGAGTAGTTAAGTGGTTTG 60.017 38.462 0.00 0.00 0.00 2.93
1787 1812 6.586344 ACATCCTGTATAACTCCAGACAATG 58.414 40.000 0.00 0.00 0.00 2.82
1788 1813 6.814954 ACATCCTGTATAACTCCAGACAAT 57.185 37.500 0.00 0.00 0.00 2.71
1796 1821 4.036027 TCCGTCGAACATCCTGTATAACTC 59.964 45.833 0.00 0.00 0.00 3.01
1818 1843 1.739466 TGCGAGCCACTTTGATCATTC 59.261 47.619 0.00 0.00 0.00 2.67
1819 1844 1.741706 CTGCGAGCCACTTTGATCATT 59.258 47.619 0.00 0.00 0.00 2.57
1821 1846 0.674581 CCTGCGAGCCACTTTGATCA 60.675 55.000 0.00 0.00 0.00 2.92
1822 1847 0.674895 ACCTGCGAGCCACTTTGATC 60.675 55.000 0.00 0.00 0.00 2.92
1823 1848 0.250901 AACCTGCGAGCCACTTTGAT 60.251 50.000 0.00 0.00 0.00 2.57
1824 1849 0.884704 GAACCTGCGAGCCACTTTGA 60.885 55.000 0.00 0.00 0.00 2.69
1825 1850 1.165907 TGAACCTGCGAGCCACTTTG 61.166 55.000 0.00 0.00 0.00 2.77
1826 1851 0.465460 TTGAACCTGCGAGCCACTTT 60.465 50.000 0.00 0.00 0.00 2.66
1827 1852 0.250901 ATTGAACCTGCGAGCCACTT 60.251 50.000 0.00 0.00 0.00 3.16
1828 1853 0.250901 AATTGAACCTGCGAGCCACT 60.251 50.000 0.00 0.00 0.00 4.00
1829 1854 0.109597 CAATTGAACCTGCGAGCCAC 60.110 55.000 0.00 0.00 0.00 5.01
1830 1855 1.243342 CCAATTGAACCTGCGAGCCA 61.243 55.000 7.12 0.00 0.00 4.75
1831 1856 1.508088 CCAATTGAACCTGCGAGCC 59.492 57.895 7.12 0.00 0.00 4.70
1832 1857 1.244019 ACCCAATTGAACCTGCGAGC 61.244 55.000 7.12 0.00 0.00 5.03
1833 1858 0.523072 CACCCAATTGAACCTGCGAG 59.477 55.000 7.12 0.00 0.00 5.03
1834 1859 1.523154 GCACCCAATTGAACCTGCGA 61.523 55.000 7.12 0.00 0.00 5.10
1835 1860 1.080569 GCACCCAATTGAACCTGCG 60.081 57.895 7.12 0.00 0.00 5.18
1836 1861 0.244721 GAGCACCCAATTGAACCTGC 59.755 55.000 7.12 7.64 0.00 4.85
1837 1862 1.619654 TGAGCACCCAATTGAACCTG 58.380 50.000 7.12 0.00 0.00 4.00
1838 1863 2.380064 TTGAGCACCCAATTGAACCT 57.620 45.000 7.12 0.00 0.00 3.50
1839 1864 2.365293 ACTTTGAGCACCCAATTGAACC 59.635 45.455 7.12 0.00 0.00 3.62
1840 1865 3.383761 CACTTTGAGCACCCAATTGAAC 58.616 45.455 7.12 0.00 0.00 3.18
1841 1866 2.364970 CCACTTTGAGCACCCAATTGAA 59.635 45.455 7.12 0.00 0.00 2.69
1842 1867 1.962807 CCACTTTGAGCACCCAATTGA 59.037 47.619 7.12 0.00 0.00 2.57
1843 1868 1.606224 GCCACTTTGAGCACCCAATTG 60.606 52.381 0.00 0.00 0.00 2.32
1844 1869 0.681175 GCCACTTTGAGCACCCAATT 59.319 50.000 0.00 0.00 0.00 2.32
1845 1870 0.178953 AGCCACTTTGAGCACCCAAT 60.179 50.000 0.00 0.00 0.00 3.16
1846 1871 0.823356 GAGCCACTTTGAGCACCCAA 60.823 55.000 0.00 0.00 0.00 4.12
1847 1872 1.228245 GAGCCACTTTGAGCACCCA 60.228 57.895 0.00 0.00 0.00 4.51
1848 1873 2.328099 CGAGCCACTTTGAGCACCC 61.328 63.158 0.00 0.00 0.00 4.61
1849 1874 2.970974 GCGAGCCACTTTGAGCACC 61.971 63.158 0.00 0.00 0.00 5.01
1850 1875 1.580845 ATGCGAGCCACTTTGAGCAC 61.581 55.000 0.00 0.00 37.44 4.40
1861 1886 1.294780 CCCCAGAGATATGCGAGCC 59.705 63.158 0.00 0.00 0.00 4.70
1866 1891 4.373156 AATAACACCCCCAGAGATATGC 57.627 45.455 0.00 0.00 0.00 3.14
1873 1898 3.653836 ACTGTTGTAATAACACCCCCAGA 59.346 43.478 0.00 0.00 34.61 3.86
1876 1901 4.146564 ACAACTGTTGTAATAACACCCCC 58.853 43.478 23.62 0.00 43.27 5.40
1877 1902 5.777850 AACAACTGTTGTAATAACACCCC 57.222 39.130 24.93 0.00 44.59 4.95
1885 1910 8.559536 CACTGACAGAATAACAACTGTTGTAAT 58.440 33.333 24.93 13.88 45.54 1.89
1889 1914 6.363577 ACACTGACAGAATAACAACTGTTG 57.636 37.500 18.44 18.44 45.54 3.33
1977 2002 1.743394 GACCCACAATCGATTTCCCAC 59.257 52.381 8.21 0.00 0.00 4.61
2013 2038 1.226211 CGCAGCGGCAAGATCTTTG 60.226 57.895 7.00 2.31 41.24 2.77
2066 2091 6.652205 TGTATACCTTTCCAAATCCTCCTT 57.348 37.500 0.00 0.00 0.00 3.36
2085 2110 4.407365 AGTTTTGTAGCAGCCCTTTGTAT 58.593 39.130 0.00 0.00 0.00 2.29
2139 2164 1.676967 CCCCTGCTTTGACTCTGGC 60.677 63.158 0.00 0.00 0.00 4.85
2318 2343 1.202486 TGTGAAACCAGTCGACAGTCC 60.202 52.381 19.50 10.43 34.36 3.85
2325 2350 3.559655 TGTTGAATCTGTGAAACCAGTCG 59.440 43.478 0.00 0.00 34.36 4.18
2332 2357 9.638239 GCCTTTTATAATGTTGAATCTGTGAAA 57.362 29.630 0.00 0.00 0.00 2.69
2337 2362 8.545420 GCAATGCCTTTTATAATGTTGAATCTG 58.455 33.333 0.00 0.00 0.00 2.90
2445 2470 7.123098 TCACCTAGTCTACCGTTCATTTCATTA 59.877 37.037 0.00 0.00 0.00 1.90
2466 2491 2.158475 TCTTGCCAGACCAAAATCACCT 60.158 45.455 0.00 0.00 0.00 4.00
2520 2545 1.909781 CCAGGTGCCAGCCAAATGT 60.910 57.895 0.00 0.00 0.00 2.71
2719 2744 1.621814 TGGGTCTACCGTTTTGAGGAG 59.378 52.381 0.00 0.00 44.64 3.69
2726 2751 6.536447 TCTTCTAATTTTGGGTCTACCGTTT 58.464 36.000 0.00 0.00 44.64 3.60
2796 2821 0.685097 TTGGTACTGGGTGAGAGCAC 59.315 55.000 0.00 0.00 44.39 4.40
2802 2827 1.899814 CTAGCACTTGGTACTGGGTGA 59.100 52.381 13.64 0.00 32.12 4.02
2813 2838 0.384309 CATGCATGGCCTAGCACTTG 59.616 55.000 22.05 14.76 44.49 3.16
3032 3058 9.647918 TGGAGAATTCTACAACAGAGTATATCT 57.352 33.333 18.39 0.00 34.08 1.98
3033 3059 9.685828 GTGGAGAATTCTACAACAGAGTATATC 57.314 37.037 22.15 1.51 38.80 1.63
3034 3060 9.201989 TGTGGAGAATTCTACAACAGAGTATAT 57.798 33.333 22.15 0.00 41.21 0.86
3035 3061 8.589701 TGTGGAGAATTCTACAACAGAGTATA 57.410 34.615 22.15 0.00 41.21 1.47
3041 3073 7.824289 TCCTTTATGTGGAGAATTCTACAACAG 59.176 37.037 22.15 12.47 46.12 3.16
3054 3086 6.018994 GCGTGTAACTAATCCTTTATGTGGAG 60.019 42.308 0.00 0.00 33.35 3.86
3055 3087 5.813672 GCGTGTAACTAATCCTTTATGTGGA 59.186 40.000 0.00 0.00 34.09 4.02
3056 3088 5.276678 CGCGTGTAACTAATCCTTTATGTGG 60.277 44.000 0.00 0.00 31.75 4.17
3080 3112 5.662211 ACAACACTATACGTGGTTTTCAC 57.338 39.130 0.00 0.00 41.99 3.18
3090 3122 7.486647 ACCCTTAGTTCATACAACACTATACG 58.513 38.462 0.00 0.00 0.00 3.06
3124 3156 6.425210 TGACAGGGAGGATAATTCATACAG 57.575 41.667 0.00 0.00 0.00 2.74
3125 3157 7.309805 CGTATGACAGGGAGGATAATTCATACA 60.310 40.741 15.45 0.00 42.03 2.29
3260 3627 4.991687 AGTCTTGCAGAAGTTAGTGTAAGC 59.008 41.667 9.45 6.39 36.61 3.09
3265 3632 4.686554 GGTACAGTCTTGCAGAAGTTAGTG 59.313 45.833 0.00 0.00 0.00 2.74
3267 3634 4.246458 GGGTACAGTCTTGCAGAAGTTAG 58.754 47.826 0.00 0.00 0.00 2.34
3268 3635 3.007614 GGGGTACAGTCTTGCAGAAGTTA 59.992 47.826 0.00 0.00 0.00 2.24
3289 3656 0.173255 CGGCCCTGCAGTAAAATTGG 59.827 55.000 13.81 5.74 0.00 3.16
3290 3657 1.133025 CTCGGCCCTGCAGTAAAATTG 59.867 52.381 13.81 0.00 0.00 2.32
3291 3658 1.271926 ACTCGGCCCTGCAGTAAAATT 60.272 47.619 13.81 0.00 0.00 1.82
3292 3659 0.328258 ACTCGGCCCTGCAGTAAAAT 59.672 50.000 13.81 0.00 0.00 1.82
3293 3660 0.321298 GACTCGGCCCTGCAGTAAAA 60.321 55.000 13.81 0.00 0.00 1.52
3294 3661 1.295423 GACTCGGCCCTGCAGTAAA 59.705 57.895 13.81 0.00 0.00 2.01
3295 3662 1.888436 CTGACTCGGCCCTGCAGTAA 61.888 60.000 13.81 0.00 0.00 2.24
3296 3663 2.283604 TGACTCGGCCCTGCAGTA 60.284 61.111 13.81 0.00 0.00 2.74
3352 3719 7.283354 GGGGTGAGGATTTAAGAATTCTTACAG 59.717 40.741 24.34 0.00 38.50 2.74
3376 3743 7.769507 GGTCTTAACTCTTAAATAGGTCTTGGG 59.230 40.741 0.00 0.00 0.00 4.12
3395 3762 6.050432 TGCTCAAACTAAGAAACGGTCTTAA 58.950 36.000 10.82 0.00 46.05 1.85
3396 3763 5.603596 TGCTCAAACTAAGAAACGGTCTTA 58.396 37.500 9.64 9.64 45.18 2.10
3398 3765 4.058817 CTGCTCAAACTAAGAAACGGTCT 58.941 43.478 0.00 0.00 38.69 3.85
3399 3766 3.186613 CCTGCTCAAACTAAGAAACGGTC 59.813 47.826 0.00 0.00 0.00 4.79
3400 3767 3.139077 CCTGCTCAAACTAAGAAACGGT 58.861 45.455 0.00 0.00 0.00 4.83
3411 3778 0.678048 CCCTAGTGGCCTGCTCAAAC 60.678 60.000 3.32 0.00 0.00 2.93
3437 3804 3.550437 AACCCACTGATCACAGATAGC 57.450 47.619 0.00 0.00 46.03 2.97
3470 3837 1.352352 AGGGCTTGCAGTGTCAGTAAT 59.648 47.619 0.00 0.00 0.00 1.89
3540 3914 2.794910 CACGTATGGAGGAACGCTTATG 59.205 50.000 0.00 0.00 42.74 1.90
3541 3915 2.691526 TCACGTATGGAGGAACGCTTAT 59.308 45.455 0.00 0.00 42.74 1.73
3559 3997 6.032460 GCTTAAATGCGAACTGTGTTAATCAC 59.968 38.462 0.00 2.41 46.31 3.06
3571 4009 2.095263 TCTTGGCTGCTTAAATGCGAAC 60.095 45.455 0.00 0.00 35.36 3.95
3575 4013 3.788333 TGATCTTGGCTGCTTAAATGC 57.212 42.857 0.00 0.00 0.00 3.56
3668 4187 2.910688 TCTGGTGTTGAACTGACTCC 57.089 50.000 0.00 0.00 0.00 3.85
3676 4195 4.576053 CACTTTGTCAGATCTGGTGTTGAA 59.424 41.667 22.42 8.35 0.00 2.69
3694 4213 7.094118 TGCTGTAAAACAAAACTAGGACACTTT 60.094 33.333 0.00 0.00 0.00 2.66
3710 4229 6.347483 GCTCCAGTTAGTAGTTGCTGTAAAAC 60.347 42.308 0.00 0.00 0.00 2.43
3711 4230 5.699458 GCTCCAGTTAGTAGTTGCTGTAAAA 59.301 40.000 0.00 0.00 0.00 1.52
3713 4232 4.282449 TGCTCCAGTTAGTAGTTGCTGTAA 59.718 41.667 0.00 0.00 0.00 2.41
3716 4235 3.319137 TGCTCCAGTTAGTAGTTGCTG 57.681 47.619 0.00 0.00 0.00 4.41
3722 4241 8.807118 TCTATTATCCAATGCTCCAGTTAGTAG 58.193 37.037 0.00 0.00 0.00 2.57
3726 4245 7.618019 AGTCTATTATCCAATGCTCCAGTTA 57.382 36.000 0.00 0.00 0.00 2.24
3808 4330 4.675976 TTGGGTGGTGGAACTATATACG 57.324 45.455 0.00 0.00 36.74 3.06
3813 4335 5.253096 AGATTAGTTTGGGTGGTGGAACTAT 59.747 40.000 0.00 0.00 35.31 2.12
3826 4368 6.263168 ACTTGGTTGAACAGAGATTAGTTTGG 59.737 38.462 0.00 0.00 0.00 3.28
3854 4401 7.851472 CGACACTACACTATATACAGTCAGTTG 59.149 40.741 0.00 0.00 0.00 3.16
3875 4422 3.508762 ACGAATTGTCTGGATACGACAC 58.491 45.455 2.62 0.00 45.20 3.67
3923 4470 4.451150 CTAGCCCGCCAGCAACGA 62.451 66.667 0.00 0.00 34.23 3.85
3948 4495 1.289830 TCGTTCCTCCCCTCCTTGATA 59.710 52.381 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.