Multiple sequence alignment - TraesCS3A01G203400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3A01G203400 chr3A 100.000 2339 0 0 1 2339 352452330 352449992 0.000000e+00 4320.0
1 TraesCS3A01G203400 chr3A 88.235 51 3 3 1867 1914 281770149 281770199 9.030000e-05 58.4
2 TraesCS3A01G203400 chr3D 94.204 1363 73 6 1 1360 213677774 213676415 0.000000e+00 2074.0
3 TraesCS3A01G203400 chr3D 85.631 1371 187 9 1 1364 177015451 177014084 0.000000e+00 1432.0
4 TraesCS3A01G203400 chr3D 85.474 1370 186 10 1 1362 339845395 339844031 0.000000e+00 1415.0
5 TraesCS3A01G203400 chr3D 91.156 588 42 6 1524 2108 271481225 271480645 0.000000e+00 789.0
6 TraesCS3A01G203400 chr3D 91.667 120 9 1 1362 1481 271481353 271481235 5.170000e-37 165.0
7 TraesCS3A01G203400 chr3D 77.328 247 46 7 1884 2121 437395313 437395068 1.130000e-28 137.0
8 TraesCS3A01G203400 chr1A 91.954 1305 98 6 65 1364 455015485 455014183 0.000000e+00 1821.0
9 TraesCS3A01G203400 chr1A 79.902 204 27 13 1941 2138 232042224 232042419 1.130000e-28 137.0
10 TraesCS3A01G203400 chr7B 89.067 1372 137 12 1 1364 511470549 511469183 0.000000e+00 1690.0
11 TraesCS3A01G203400 chr1D 85.559 1378 181 16 1 1364 286395880 286397253 0.000000e+00 1426.0
12 TraesCS3A01G203400 chr1D 85.193 1371 195 8 1 1364 176360141 176361510 0.000000e+00 1400.0
13 TraesCS3A01G203400 chr6D 85.496 1372 190 9 1 1364 462399755 462398385 0.000000e+00 1423.0
14 TraesCS3A01G203400 chr6D 85.058 1372 193 11 1 1364 452072054 452070687 0.000000e+00 1387.0
15 TraesCS3A01G203400 chr6D 74.375 480 89 26 1673 2138 272113107 272112648 8.590000e-40 174.0
16 TraesCS3A01G203400 chr6D 80.928 194 25 12 1953 2138 294451052 294450863 2.420000e-30 143.0
17 TraesCS3A01G203400 chr6D 80.769 182 25 10 1953 2127 294451485 294451307 1.460000e-27 134.0
18 TraesCS3A01G203400 chr6D 79.275 193 38 2 1937 2127 368767988 368767796 1.460000e-27 134.0
19 TraesCS3A01G203400 chr2B 78.000 350 66 10 1957 2299 233745651 233745996 2.360000e-50 209.0
20 TraesCS3A01G203400 chr3B 79.024 205 24 16 1948 2144 373680636 373680443 3.160000e-24 122.0
21 TraesCS3A01G203400 chr5B 100.000 30 0 0 1714 1743 607819625 607819596 3.250000e-04 56.5


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 TraesCS3A01G203400 chr3A 352449992 352452330 2338 True 4320 4320 100.0000 1 2339 1 chr3A.!!$R1 2338
1 TraesCS3A01G203400 chr3D 213676415 213677774 1359 True 2074 2074 94.2040 1 1360 1 chr3D.!!$R2 1359
2 TraesCS3A01G203400 chr3D 177014084 177015451 1367 True 1432 1432 85.6310 1 1364 1 chr3D.!!$R1 1363
3 TraesCS3A01G203400 chr3D 339844031 339845395 1364 True 1415 1415 85.4740 1 1362 1 chr3D.!!$R3 1361
4 TraesCS3A01G203400 chr3D 271480645 271481353 708 True 477 789 91.4115 1362 2108 2 chr3D.!!$R5 746
5 TraesCS3A01G203400 chr1A 455014183 455015485 1302 True 1821 1821 91.9540 65 1364 1 chr1A.!!$R1 1299
6 TraesCS3A01G203400 chr7B 511469183 511470549 1366 True 1690 1690 89.0670 1 1364 1 chr7B.!!$R1 1363
7 TraesCS3A01G203400 chr1D 286395880 286397253 1373 False 1426 1426 85.5590 1 1364 1 chr1D.!!$F2 1363
8 TraesCS3A01G203400 chr1D 176360141 176361510 1369 False 1400 1400 85.1930 1 1364 1 chr1D.!!$F1 1363
9 TraesCS3A01G203400 chr6D 462398385 462399755 1370 True 1423 1423 85.4960 1 1364 1 chr6D.!!$R4 1363
10 TraesCS3A01G203400 chr6D 452070687 452072054 1367 True 1387 1387 85.0580 1 1364 1 chr6D.!!$R3 1363

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
176 177 0.24445 TAGACAAACTACGTGGCCCG 59.756 55.0 11.48 11.48 44.03 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2067 0.034863 ACACAAGGGACACGGTGTTT 60.035 50.0 15.94 2.92 38.68 2.83 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
84 85 5.820947 CCAATAGGAAAGTTGTAACGCCTAT 59.179 40.000 15.02 15.02 40.79 2.57
111 112 5.279156 CGGGACAACTGTTAACTAAGGTAGT 60.279 44.000 7.22 0.00 41.73 2.73
176 177 0.244450 TAGACAAACTACGTGGCCCG 59.756 55.000 11.48 11.48 44.03 6.13
210 211 6.770746 ATGGATTCTTTCAATTCCACTCTG 57.229 37.500 0.00 0.00 0.00 3.35
247 249 5.506982 GCCAGATTTCATTGCTTGGAGTATC 60.507 44.000 0.00 0.00 0.00 2.24
308 310 3.566351 TCGAGTGGGATCATCAGTATGT 58.434 45.455 0.00 0.00 37.40 2.29
309 311 3.960755 TCGAGTGGGATCATCAGTATGTT 59.039 43.478 0.00 0.00 37.40 2.71
363 365 4.021894 CGAACCACAATTAACCCCATTTGA 60.022 41.667 0.00 0.00 0.00 2.69
388 390 9.384764 GAAGTAAGATATGGAAGTTAGCTTGTT 57.615 33.333 0.00 0.00 34.61 2.83
477 479 5.580691 CGCTAACAAACATATGAAGGTCTCA 59.419 40.000 10.38 0.00 38.81 3.27
478 480 6.258727 CGCTAACAAACATATGAAGGTCTCAT 59.741 38.462 10.38 0.00 46.86 2.90
485 487 8.472413 CAAACATATGAAGGTCTCATCCATTTT 58.528 33.333 10.38 0.00 44.05 1.82
494 496 5.254032 AGGTCTCATCCATTTTCCCTACTTT 59.746 40.000 0.00 0.00 0.00 2.66
495 497 5.952347 GGTCTCATCCATTTTCCCTACTTTT 59.048 40.000 0.00 0.00 0.00 2.27
615 618 2.665185 AAAGTCGACCGTGCTGGC 60.665 61.111 13.01 0.00 43.94 4.85
944 955 1.658686 GCGGTCCTGAGAGACGACAT 61.659 60.000 0.00 0.00 37.66 3.06
990 1003 1.478105 GGGAAGATTGACCATTGCACC 59.522 52.381 0.00 0.00 0.00 5.01
1009 1022 1.740585 CCGATGTGTTAATGGCGGAAA 59.259 47.619 0.00 0.00 41.11 3.13
1085 1098 6.312180 CGCCTTATTATTAACTCGGATAACCC 59.688 42.308 0.00 0.00 0.00 4.11
1086 1099 7.163441 GCCTTATTATTAACTCGGATAACCCA 58.837 38.462 0.00 0.00 34.14 4.51
1115 1132 2.923121 TGAAACTATGCAGGATGGAGC 58.077 47.619 0.00 0.00 42.42 4.70
1378 1396 6.623486 TCAAAAGAAATGAATGTCATGCGAT 58.377 32.000 0.00 0.00 37.15 4.58
1380 1398 6.880822 AAAGAAATGAATGTCATGCGATTG 57.119 33.333 0.00 0.00 37.15 2.67
1405 1423 2.416893 GCACTTTAGCTAGTGGAAGCAC 59.583 50.000 16.53 0.73 45.30 4.40
1428 1446 1.581934 CTCGCTTGGTTGTCTTGTGA 58.418 50.000 0.00 0.00 0.00 3.58
1444 1462 7.216494 TGTCTTGTGAGTTGTAATCTTCATGA 58.784 34.615 0.00 0.00 0.00 3.07
1452 1470 5.663106 AGTTGTAATCTTCATGAGCCTAGGA 59.337 40.000 14.75 0.00 0.00 2.94
1458 1476 3.198635 TCTTCATGAGCCTAGGACTTTGG 59.801 47.826 14.75 3.28 0.00 3.28
1459 1477 2.551270 TCATGAGCCTAGGACTTTGGT 58.449 47.619 14.75 0.00 0.00 3.67
1462 1480 1.351017 TGAGCCTAGGACTTTGGTTGG 59.649 52.381 14.75 0.00 0.00 3.77
1482 1500 1.318576 GCCATACATAGTTGTGGGCC 58.681 55.000 0.00 0.00 45.03 5.80
1483 1501 1.133792 GCCATACATAGTTGTGGGCCT 60.134 52.381 4.53 0.00 45.03 5.19
1484 1502 2.105821 GCCATACATAGTTGTGGGCCTA 59.894 50.000 4.53 0.00 45.03 3.93
1485 1503 3.807209 GCCATACATAGTTGTGGGCCTAG 60.807 52.174 4.53 0.00 45.03 3.02
1486 1504 3.403038 CATACATAGTTGTGGGCCTAGC 58.597 50.000 4.53 0.00 36.53 3.42
1487 1505 1.766496 TACATAGTTGTGGGCCTAGCC 59.234 52.381 4.53 0.00 41.76 3.93
1506 1524 2.910579 CGGAGGTGTTCCCCTATCA 58.089 57.895 0.00 0.00 43.63 2.15
1507 1525 1.200519 CGGAGGTGTTCCCCTATCAA 58.799 55.000 0.00 0.00 43.63 2.57
1508 1526 1.768870 CGGAGGTGTTCCCCTATCAAT 59.231 52.381 0.00 0.00 43.63 2.57
1509 1527 2.969950 CGGAGGTGTTCCCCTATCAATA 59.030 50.000 0.00 0.00 43.63 1.90
1510 1528 3.006967 CGGAGGTGTTCCCCTATCAATAG 59.993 52.174 0.00 0.00 43.63 1.73
1511 1529 3.974642 GGAGGTGTTCCCCTATCAATAGT 59.025 47.826 0.00 0.00 40.37 2.12
1512 1530 4.040584 GGAGGTGTTCCCCTATCAATAGTC 59.959 50.000 0.00 0.00 40.37 2.59
1513 1531 3.974642 AGGTGTTCCCCTATCAATAGTCC 59.025 47.826 0.00 0.00 31.31 3.85
1514 1532 3.072622 GGTGTTCCCCTATCAATAGTCCC 59.927 52.174 0.00 0.00 0.00 4.46
1515 1533 3.072622 GTGTTCCCCTATCAATAGTCCCC 59.927 52.174 0.00 0.00 0.00 4.81
1516 1534 2.302157 GTTCCCCTATCAATAGTCCCCG 59.698 54.545 0.00 0.00 0.00 5.73
1517 1535 1.790779 TCCCCTATCAATAGTCCCCGA 59.209 52.381 0.00 0.00 0.00 5.14
1518 1536 2.180276 CCCCTATCAATAGTCCCCGAG 58.820 57.143 0.00 0.00 0.00 4.63
1519 1537 2.492940 CCCCTATCAATAGTCCCCGAGT 60.493 54.545 0.00 0.00 0.00 4.18
1520 1538 2.826725 CCCTATCAATAGTCCCCGAGTC 59.173 54.545 0.00 0.00 0.00 3.36
1521 1539 2.826725 CCTATCAATAGTCCCCGAGTCC 59.173 54.545 0.00 0.00 0.00 3.85
1522 1540 2.471815 ATCAATAGTCCCCGAGTCCA 57.528 50.000 0.00 0.00 0.00 4.02
1564 1582 1.333177 GACTGCCTCCTCGATGGTAT 58.667 55.000 0.00 0.00 37.07 2.73
1578 1597 3.057526 CGATGGTATATTCCGACTGAGCA 60.058 47.826 0.00 0.00 0.00 4.26
1586 1605 1.006102 CCGACTGAGCACCGAACTT 60.006 57.895 0.00 0.00 0.00 2.66
1606 1625 0.744414 GGAGCGCCATTTGACTGCTA 60.744 55.000 2.29 0.00 35.73 3.49
1623 1642 2.094182 TGCTAACTAAGAGACCTTGGCG 60.094 50.000 0.00 0.00 34.62 5.69
1653 1672 2.111384 GAGCATGTCCCTAGAAGGTGA 58.889 52.381 0.00 0.00 31.93 4.02
1670 1689 2.552743 GGTGAGGTTTGAGCAAGTTACC 59.447 50.000 0.00 0.00 0.00 2.85
1671 1690 3.211045 GTGAGGTTTGAGCAAGTTACCA 58.789 45.455 5.61 0.00 0.00 3.25
1683 1702 3.557054 GCAAGTTACCATGACAGAGTCCA 60.557 47.826 0.00 0.00 0.00 4.02
1684 1703 4.248859 CAAGTTACCATGACAGAGTCCAG 58.751 47.826 0.00 0.00 0.00 3.86
1691 1710 3.494048 CCATGACAGAGTCCAGGATTAGC 60.494 52.174 0.00 0.00 30.47 3.09
1764 1783 3.366052 AAGTTTATCATCGGTGGGCTT 57.634 42.857 0.00 0.00 0.00 4.35
1765 1784 2.919228 AGTTTATCATCGGTGGGCTTC 58.081 47.619 0.00 0.00 0.00 3.86
1766 1785 2.238646 AGTTTATCATCGGTGGGCTTCA 59.761 45.455 0.00 0.00 0.00 3.02
1769 1788 2.442236 ATCATCGGTGGGCTTCATTT 57.558 45.000 0.00 0.00 0.00 2.32
1770 1789 1.462616 TCATCGGTGGGCTTCATTTG 58.537 50.000 0.00 0.00 0.00 2.32
1781 1800 0.107214 CTTCATTTGCCTAGGCCCGA 60.107 55.000 30.81 17.91 41.09 5.14
1788 1807 1.223487 GCCTAGGCCCGAAACATCA 59.777 57.895 24.19 0.00 34.56 3.07
1800 1819 2.098117 CGAAACATCAGGAAGGAATGGC 59.902 50.000 0.00 0.00 0.00 4.40
1813 1832 4.246712 AGGAATGGCATGAAGACTTGAT 57.753 40.909 0.00 0.00 0.00 2.57
1818 1837 6.127647 GGAATGGCATGAAGACTTGATGTAAA 60.128 38.462 14.92 3.29 0.00 2.01
1834 1853 7.482169 TGATGTAAACTCCAAGACATAGAGT 57.518 36.000 0.00 0.00 42.58 3.24
1842 1861 5.889289 ACTCCAAGACATAGAGTTAGTCCTC 59.111 44.000 0.00 0.00 37.60 3.71
1847 1866 2.688958 ACATAGAGTTAGTCCTCGGCAC 59.311 50.000 0.00 0.00 36.56 5.01
1894 1913 6.215031 ACATTATGTAAACCCTAGGTACCCT 58.785 40.000 8.74 0.00 33.12 4.34
1901 1920 0.754587 CCCTAGGTACCCTCGGTGTC 60.755 65.000 8.74 0.00 35.01 3.67
1908 1929 3.956848 AGGTACCCTCGGTGTCTATAAAC 59.043 47.826 8.74 0.00 36.19 2.01
1910 1931 2.823959 ACCCTCGGTGTCTATAAACCA 58.176 47.619 0.00 0.00 36.14 3.67
1924 1945 1.943730 AAACCAAGGTGCCAGGGTCA 61.944 55.000 0.00 0.00 32.01 4.02
1926 1947 0.844661 ACCAAGGTGCCAGGGTCATA 60.845 55.000 0.00 0.00 0.00 2.15
1927 1948 0.107017 CCAAGGTGCCAGGGTCATAG 60.107 60.000 0.00 0.00 0.00 2.23
1928 1949 0.911769 CAAGGTGCCAGGGTCATAGA 59.088 55.000 0.00 0.00 0.00 1.98
1929 1950 1.134280 CAAGGTGCCAGGGTCATAGAG 60.134 57.143 0.00 0.00 0.00 2.43
1930 1951 0.692419 AGGTGCCAGGGTCATAGAGG 60.692 60.000 0.00 0.00 0.00 3.69
2012 2033 6.237901 TCAATACAACAAAGCAGGATGTAGT 58.762 36.000 0.00 0.00 39.31 2.73
2025 2046 5.351740 GCAGGATGTAGTGTTTTACCTCTTC 59.648 44.000 0.00 0.00 39.31 2.87
2036 2057 1.035932 TACCTCTTCGAGAAGGCCCG 61.036 60.000 13.50 0.00 38.88 6.13
2052 2073 0.879090 CCCGAAGTTGGCTAAACACC 59.121 55.000 5.76 0.00 41.61 4.16
2070 2091 0.246635 CCGTGTCCCTTGTGTCCTAG 59.753 60.000 0.00 0.00 0.00 3.02
2097 2118 5.843421 ACCATCTAGCCAAGACTATCAGATT 59.157 40.000 0.00 0.00 36.93 2.40
2103 2124 3.745797 GCCAAGACTATCAGATTGGGACC 60.746 52.174 13.16 0.00 42.04 4.46
2108 2129 2.527057 ACTATCAGATTGGGACCCCCTA 59.473 50.000 8.45 0.00 45.70 3.53
2109 2130 1.821088 ATCAGATTGGGACCCCCTAC 58.179 55.000 8.45 0.00 45.70 3.18
2110 2131 0.327191 TCAGATTGGGACCCCCTACC 60.327 60.000 8.45 0.00 45.70 3.18
2111 2132 1.005690 AGATTGGGACCCCCTACCC 59.994 63.158 8.45 0.00 45.70 3.69
2115 2136 2.457794 GGGACCCCCTACCCAAGA 59.542 66.667 0.00 0.00 44.96 3.02
2116 2137 1.005690 GGGACCCCCTACCCAAGAT 59.994 63.158 0.00 0.00 44.96 2.40
2117 2138 1.060743 GGGACCCCCTACCCAAGATC 61.061 65.000 0.00 0.00 44.96 2.75
2118 2139 1.060743 GGACCCCCTACCCAAGATCC 61.061 65.000 0.00 0.00 0.00 3.36
2119 2140 1.384082 ACCCCCTACCCAAGATCCG 60.384 63.158 0.00 0.00 0.00 4.18
2120 2141 2.819284 CCCCCTACCCAAGATCCGC 61.819 68.421 0.00 0.00 0.00 5.54
2121 2142 2.819284 CCCCTACCCAAGATCCGCC 61.819 68.421 0.00 0.00 0.00 6.13
2122 2143 2.070039 CCCTACCCAAGATCCGCCA 61.070 63.158 0.00 0.00 0.00 5.69
2123 2144 1.447643 CCTACCCAAGATCCGCCAG 59.552 63.158 0.00 0.00 0.00 4.85
2124 2145 1.048724 CCTACCCAAGATCCGCCAGA 61.049 60.000 0.00 0.00 0.00 3.86
2125 2146 1.051812 CTACCCAAGATCCGCCAGAT 58.948 55.000 0.00 0.00 38.17 2.90
2126 2147 1.417890 CTACCCAAGATCCGCCAGATT 59.582 52.381 0.00 0.00 34.42 2.40
2127 2148 0.181350 ACCCAAGATCCGCCAGATTC 59.819 55.000 0.00 0.00 34.42 2.52
2128 2149 0.181114 CCCAAGATCCGCCAGATTCA 59.819 55.000 0.00 0.00 34.42 2.57
2129 2150 1.590932 CCAAGATCCGCCAGATTCAG 58.409 55.000 0.00 0.00 34.42 3.02
2130 2151 1.139654 CCAAGATCCGCCAGATTCAGA 59.860 52.381 0.00 0.00 34.42 3.27
2131 2152 2.224475 CCAAGATCCGCCAGATTCAGAT 60.224 50.000 0.00 0.00 34.42 2.90
2132 2153 3.065655 CAAGATCCGCCAGATTCAGATC 58.934 50.000 0.00 0.00 34.42 2.75
2133 2154 1.622811 AGATCCGCCAGATTCAGATCC 59.377 52.381 0.00 0.00 34.42 3.36
2134 2155 0.319728 ATCCGCCAGATTCAGATCCG 59.680 55.000 0.00 0.00 32.44 4.18
2135 2156 0.755327 TCCGCCAGATTCAGATCCGA 60.755 55.000 0.00 0.00 32.44 4.55
2136 2157 0.598680 CCGCCAGATTCAGATCCGAC 60.599 60.000 0.00 0.00 32.44 4.79
2137 2158 0.103026 CGCCAGATTCAGATCCGACA 59.897 55.000 0.00 0.00 32.44 4.35
2138 2159 1.269988 CGCCAGATTCAGATCCGACAT 60.270 52.381 0.00 0.00 32.44 3.06
2139 2160 2.804572 CGCCAGATTCAGATCCGACATT 60.805 50.000 0.00 0.00 32.44 2.71
2140 2161 2.547211 GCCAGATTCAGATCCGACATTG 59.453 50.000 0.00 0.00 32.44 2.82
2141 2162 3.136763 CCAGATTCAGATCCGACATTGG 58.863 50.000 0.00 0.00 32.44 3.16
2142 2163 3.432749 CCAGATTCAGATCCGACATTGGT 60.433 47.826 0.00 0.00 32.44 3.67
2143 2164 3.558829 CAGATTCAGATCCGACATTGGTG 59.441 47.826 0.00 0.00 32.44 4.17
2144 2165 2.401583 TTCAGATCCGACATTGGTGG 57.598 50.000 0.00 0.00 0.00 4.61
2145 2166 1.567357 TCAGATCCGACATTGGTGGA 58.433 50.000 2.14 2.14 35.96 4.02
2146 2167 2.118679 TCAGATCCGACATTGGTGGAT 58.881 47.619 10.64 10.64 45.02 3.41
2147 2168 2.505407 TCAGATCCGACATTGGTGGATT 59.495 45.455 11.75 2.57 42.46 3.01
2148 2169 3.709141 TCAGATCCGACATTGGTGGATTA 59.291 43.478 11.75 1.67 42.46 1.75
2149 2170 4.347876 TCAGATCCGACATTGGTGGATTAT 59.652 41.667 11.75 3.90 42.46 1.28
2150 2171 5.542251 TCAGATCCGACATTGGTGGATTATA 59.458 40.000 11.75 1.14 42.46 0.98
2151 2172 5.639506 CAGATCCGACATTGGTGGATTATAC 59.360 44.000 11.75 2.18 42.46 1.47
2152 2173 5.306937 AGATCCGACATTGGTGGATTATACA 59.693 40.000 11.75 0.00 42.46 2.29
2153 2174 5.360649 TCCGACATTGGTGGATTATACAA 57.639 39.130 0.00 0.00 0.00 2.41
2154 2175 5.364778 TCCGACATTGGTGGATTATACAAG 58.635 41.667 0.00 0.00 0.00 3.16
2155 2176 5.104693 TCCGACATTGGTGGATTATACAAGT 60.105 40.000 0.00 0.00 0.00 3.16
2156 2177 5.007626 CCGACATTGGTGGATTATACAAGTG 59.992 44.000 0.00 0.00 0.00 3.16
2157 2178 5.504010 CGACATTGGTGGATTATACAAGTGC 60.504 44.000 0.00 0.00 0.00 4.40
2158 2179 4.644685 ACATTGGTGGATTATACAAGTGCC 59.355 41.667 0.00 0.00 0.00 5.01
2159 2180 4.584638 TTGGTGGATTATACAAGTGCCT 57.415 40.909 0.00 0.00 0.00 4.75
2160 2181 4.150897 TGGTGGATTATACAAGTGCCTC 57.849 45.455 0.00 0.00 0.00 4.70
2161 2182 3.780294 TGGTGGATTATACAAGTGCCTCT 59.220 43.478 0.00 0.00 0.00 3.69
2162 2183 4.130118 GGTGGATTATACAAGTGCCTCTG 58.870 47.826 0.00 0.00 0.00 3.35
2163 2184 4.141711 GGTGGATTATACAAGTGCCTCTGA 60.142 45.833 0.00 0.00 0.00 3.27
2164 2185 5.053145 GTGGATTATACAAGTGCCTCTGAG 58.947 45.833 0.00 0.00 0.00 3.35
2165 2186 4.962362 TGGATTATACAAGTGCCTCTGAGA 59.038 41.667 6.17 0.00 0.00 3.27
2166 2187 5.425217 TGGATTATACAAGTGCCTCTGAGAA 59.575 40.000 6.17 0.00 0.00 2.87
2167 2188 6.070251 TGGATTATACAAGTGCCTCTGAGAAA 60.070 38.462 6.17 0.00 0.00 2.52
2168 2189 6.995091 GGATTATACAAGTGCCTCTGAGAAAT 59.005 38.462 6.17 0.00 0.00 2.17
2169 2190 7.172361 GGATTATACAAGTGCCTCTGAGAAATC 59.828 40.741 6.17 0.00 0.00 2.17
2170 2191 5.690464 ATACAAGTGCCTCTGAGAAATCT 57.310 39.130 6.17 0.00 0.00 2.40
2171 2192 6.798427 ATACAAGTGCCTCTGAGAAATCTA 57.202 37.500 6.17 0.00 0.00 1.98
2172 2193 5.489792 ACAAGTGCCTCTGAGAAATCTAA 57.510 39.130 6.17 0.00 0.00 2.10
2173 2194 5.869579 ACAAGTGCCTCTGAGAAATCTAAA 58.130 37.500 6.17 0.00 0.00 1.85
2174 2195 5.703130 ACAAGTGCCTCTGAGAAATCTAAAC 59.297 40.000 6.17 0.00 0.00 2.01
2175 2196 5.753721 AGTGCCTCTGAGAAATCTAAACT 57.246 39.130 6.17 0.00 0.00 2.66
2176 2197 5.486526 AGTGCCTCTGAGAAATCTAAACTG 58.513 41.667 6.17 0.00 0.00 3.16
2177 2198 4.094146 GTGCCTCTGAGAAATCTAAACTGC 59.906 45.833 6.17 0.00 0.00 4.40
2178 2199 4.019860 TGCCTCTGAGAAATCTAAACTGCT 60.020 41.667 6.17 0.00 0.00 4.24
2179 2200 4.570369 GCCTCTGAGAAATCTAAACTGCTC 59.430 45.833 6.17 0.00 0.00 4.26
2180 2201 4.803088 CCTCTGAGAAATCTAAACTGCTCG 59.197 45.833 6.17 0.00 0.00 5.03
2181 2202 5.393569 CCTCTGAGAAATCTAAACTGCTCGA 60.394 44.000 6.17 0.00 0.00 4.04
2182 2203 6.214191 TCTGAGAAATCTAAACTGCTCGAT 57.786 37.500 0.00 0.00 0.00 3.59
2183 2204 6.038985 TCTGAGAAATCTAAACTGCTCGATG 58.961 40.000 0.00 0.00 0.00 3.84
2184 2205 5.111989 TGAGAAATCTAAACTGCTCGATGG 58.888 41.667 0.00 0.00 0.00 3.51
2185 2206 4.446371 AGAAATCTAAACTGCTCGATGGG 58.554 43.478 0.00 0.00 0.00 4.00
2186 2207 3.914426 AATCTAAACTGCTCGATGGGT 57.086 42.857 0.00 0.00 0.00 4.51
2187 2208 2.961526 TCTAAACTGCTCGATGGGTC 57.038 50.000 0.00 0.00 0.00 4.46
2196 2217 3.147595 CGATGGGTCGCCTCCAGA 61.148 66.667 0.00 0.00 41.49 3.86
2197 2218 2.502492 CGATGGGTCGCCTCCAGAT 61.502 63.158 0.00 0.00 41.49 2.90
2198 2219 1.832912 GATGGGTCGCCTCCAGATT 59.167 57.895 0.00 0.00 37.75 2.40
2199 2220 0.533755 GATGGGTCGCCTCCAGATTG 60.534 60.000 0.00 0.00 37.75 2.67
2200 2221 0.982852 ATGGGTCGCCTCCAGATTGA 60.983 55.000 0.00 0.00 37.75 2.57
2201 2222 1.153349 GGGTCGCCTCCAGATTGAC 60.153 63.158 0.00 0.00 0.00 3.18
2202 2223 1.519455 GGTCGCCTCCAGATTGACG 60.519 63.158 0.00 0.00 0.00 4.35
2203 2224 1.511305 GTCGCCTCCAGATTGACGA 59.489 57.895 0.00 0.00 0.00 4.20
2204 2225 0.802607 GTCGCCTCCAGATTGACGAC 60.803 60.000 0.00 0.00 42.36 4.34
2205 2226 1.215382 CGCCTCCAGATTGACGACA 59.785 57.895 0.00 0.00 0.00 4.35
2206 2227 0.803768 CGCCTCCAGATTGACGACAG 60.804 60.000 0.00 0.00 0.00 3.51
2207 2228 1.086634 GCCTCCAGATTGACGACAGC 61.087 60.000 0.00 0.00 0.00 4.40
2208 2229 0.247460 CCTCCAGATTGACGACAGCA 59.753 55.000 0.00 0.00 0.00 4.41
2209 2230 1.134580 CCTCCAGATTGACGACAGCAT 60.135 52.381 0.00 0.00 0.00 3.79
2210 2231 2.200067 CTCCAGATTGACGACAGCATC 58.800 52.381 0.00 0.00 0.00 3.91
2223 2244 4.443857 GCATCGGCTGTAGCATGA 57.556 55.556 6.18 3.54 44.36 3.07
2224 2245 1.937391 GCATCGGCTGTAGCATGAC 59.063 57.895 6.18 0.00 44.36 3.06
2225 2246 1.502163 GCATCGGCTGTAGCATGACC 61.502 60.000 6.18 0.00 44.36 4.02
2226 2247 0.105593 CATCGGCTGTAGCATGACCT 59.894 55.000 6.18 0.00 44.36 3.85
2227 2248 0.390860 ATCGGCTGTAGCATGACCTC 59.609 55.000 6.18 0.00 44.36 3.85
2228 2249 0.684479 TCGGCTGTAGCATGACCTCT 60.684 55.000 6.18 0.00 44.36 3.69
2229 2250 0.176680 CGGCTGTAGCATGACCTCTT 59.823 55.000 6.18 0.00 44.36 2.85
2230 2251 1.406069 CGGCTGTAGCATGACCTCTTT 60.406 52.381 6.18 0.00 44.36 2.52
2231 2252 2.284190 GGCTGTAGCATGACCTCTTTC 58.716 52.381 6.18 0.00 44.36 2.62
2232 2253 2.093235 GGCTGTAGCATGACCTCTTTCT 60.093 50.000 6.18 0.00 44.36 2.52
2233 2254 3.133003 GGCTGTAGCATGACCTCTTTCTA 59.867 47.826 6.18 0.00 44.36 2.10
2234 2255 4.367450 GCTGTAGCATGACCTCTTTCTAG 58.633 47.826 0.00 0.00 41.59 2.43
2235 2256 4.739137 GCTGTAGCATGACCTCTTTCTAGG 60.739 50.000 0.00 0.00 40.82 3.02
2236 2257 4.610333 TGTAGCATGACCTCTTTCTAGGA 58.390 43.478 0.00 0.00 39.15 2.94
2237 2258 4.402793 TGTAGCATGACCTCTTTCTAGGAC 59.597 45.833 0.00 0.00 39.15 3.85
2238 2259 3.445008 AGCATGACCTCTTTCTAGGACA 58.555 45.455 0.00 0.00 43.73 4.02
2239 2260 3.196685 AGCATGACCTCTTTCTAGGACAC 59.803 47.826 0.00 0.00 42.68 3.67
2240 2261 3.680196 GCATGACCTCTTTCTAGGACACC 60.680 52.174 0.00 0.00 42.68 4.16
2241 2262 3.544698 TGACCTCTTTCTAGGACACCT 57.455 47.619 0.00 0.00 39.15 4.00
2242 2263 3.432378 TGACCTCTTTCTAGGACACCTC 58.568 50.000 0.00 0.00 39.15 3.85
2243 2264 3.076182 TGACCTCTTTCTAGGACACCTCT 59.924 47.826 0.00 0.00 39.15 3.69
2244 2265 4.090819 GACCTCTTTCTAGGACACCTCTT 58.909 47.826 0.00 0.00 39.15 2.85
2245 2266 4.494591 ACCTCTTTCTAGGACACCTCTTT 58.505 43.478 0.00 0.00 39.15 2.52
2246 2267 4.284746 ACCTCTTTCTAGGACACCTCTTTG 59.715 45.833 0.00 0.00 39.15 2.77
2247 2268 4.284746 CCTCTTTCTAGGACACCTCTTTGT 59.715 45.833 0.00 0.00 39.15 2.83
2248 2269 5.470047 TCTTTCTAGGACACCTCTTTGTC 57.530 43.478 0.00 0.00 44.53 3.18
2249 2270 5.148502 TCTTTCTAGGACACCTCTTTGTCT 58.851 41.667 3.44 0.00 44.63 3.41
2250 2271 5.602978 TCTTTCTAGGACACCTCTTTGTCTT 59.397 40.000 3.44 0.00 44.63 3.01
2251 2272 5.888982 TTCTAGGACACCTCTTTGTCTTT 57.111 39.130 3.44 0.00 44.63 2.52
2252 2273 6.989155 TTCTAGGACACCTCTTTGTCTTTA 57.011 37.500 3.44 0.00 44.63 1.85
2253 2274 6.989155 TCTAGGACACCTCTTTGTCTTTAA 57.011 37.500 3.44 0.00 44.63 1.52
2254 2275 6.756221 TCTAGGACACCTCTTTGTCTTTAAC 58.244 40.000 3.44 0.00 44.63 2.01
2255 2276 5.367945 AGGACACCTCTTTGTCTTTAACA 57.632 39.130 3.44 0.00 44.63 2.41
2256 2277 5.368989 AGGACACCTCTTTGTCTTTAACAG 58.631 41.667 3.44 0.00 44.63 3.16
2257 2278 4.023963 GGACACCTCTTTGTCTTTAACAGC 60.024 45.833 3.44 0.00 44.63 4.40
2258 2279 4.523083 ACACCTCTTTGTCTTTAACAGCA 58.477 39.130 0.00 0.00 39.58 4.41
2259 2280 5.133221 ACACCTCTTTGTCTTTAACAGCAT 58.867 37.500 0.00 0.00 39.58 3.79
2260 2281 5.594317 ACACCTCTTTGTCTTTAACAGCATT 59.406 36.000 0.00 0.00 39.58 3.56
2261 2282 6.770785 ACACCTCTTTGTCTTTAACAGCATTA 59.229 34.615 0.00 0.00 39.58 1.90
2262 2283 7.078228 CACCTCTTTGTCTTTAACAGCATTAC 58.922 38.462 0.00 0.00 39.58 1.89
2263 2284 6.073222 ACCTCTTTGTCTTTAACAGCATTACG 60.073 38.462 0.00 0.00 39.58 3.18
2264 2285 5.685841 TCTTTGTCTTTAACAGCATTACGC 58.314 37.500 0.00 0.00 39.58 4.42
2279 2300 4.552797 CGCTTTACGCTGATTCGC 57.447 55.556 0.00 0.00 36.13 4.70
2280 2301 1.012234 CGCTTTACGCTGATTCGCC 60.012 57.895 0.00 0.00 36.13 5.54
2281 2302 1.421410 CGCTTTACGCTGATTCGCCT 61.421 55.000 0.00 0.00 36.13 5.52
2282 2303 0.026803 GCTTTACGCTGATTCGCCTG 59.973 55.000 0.00 0.00 35.14 4.85
2283 2304 0.652592 CTTTACGCTGATTCGCCTGG 59.347 55.000 0.00 0.00 0.00 4.45
2284 2305 1.366111 TTTACGCTGATTCGCCTGGC 61.366 55.000 9.11 9.11 0.00 4.85
2285 2306 3.733344 TACGCTGATTCGCCTGGCC 62.733 63.158 14.12 0.00 0.00 5.36
2286 2307 4.845580 CGCTGATTCGCCTGGCCT 62.846 66.667 14.12 0.00 0.00 5.19
2287 2308 2.899339 GCTGATTCGCCTGGCCTC 60.899 66.667 14.12 8.28 0.00 4.70
2288 2309 2.203126 CTGATTCGCCTGGCCTCC 60.203 66.667 14.12 0.53 0.00 4.30
2289 2310 2.688666 TGATTCGCCTGGCCTCCT 60.689 61.111 14.12 0.00 0.00 3.69
2290 2311 2.110006 GATTCGCCTGGCCTCCTC 59.890 66.667 14.12 1.25 0.00 3.71
2291 2312 3.798954 GATTCGCCTGGCCTCCTCG 62.799 68.421 14.12 2.37 0.00 4.63
2324 2345 7.426929 AAAAATTATGTGCTAGGCTAGATCG 57.573 36.000 25.37 0.00 0.00 3.69
2325 2346 5.730296 AATTATGTGCTAGGCTAGATCGT 57.270 39.130 25.37 17.93 0.00 3.73
2326 2347 4.768130 TTATGTGCTAGGCTAGATCGTC 57.232 45.455 25.37 7.40 0.00 4.20
2327 2348 2.052782 TGTGCTAGGCTAGATCGTCA 57.947 50.000 25.37 10.00 0.00 4.35
2328 2349 1.950216 TGTGCTAGGCTAGATCGTCAG 59.050 52.381 25.37 0.00 0.00 3.51
2329 2350 2.222886 GTGCTAGGCTAGATCGTCAGA 58.777 52.381 25.37 0.00 0.00 3.27
2330 2351 2.817258 GTGCTAGGCTAGATCGTCAGAT 59.183 50.000 25.37 0.00 40.38 2.90
2331 2352 3.254657 GTGCTAGGCTAGATCGTCAGATT 59.745 47.826 25.37 0.00 37.19 2.40
2332 2353 3.891977 TGCTAGGCTAGATCGTCAGATTT 59.108 43.478 25.37 0.00 37.19 2.17
2333 2354 4.233789 GCTAGGCTAGATCGTCAGATTTG 58.766 47.826 25.37 0.00 37.19 2.32
2334 2355 3.742433 AGGCTAGATCGTCAGATTTGG 57.258 47.619 0.00 0.00 37.19 3.28
2335 2356 2.366916 AGGCTAGATCGTCAGATTTGGG 59.633 50.000 0.00 0.00 37.19 4.12
2336 2357 2.365617 GGCTAGATCGTCAGATTTGGGA 59.634 50.000 0.00 0.00 37.19 4.37
2337 2358 3.181465 GGCTAGATCGTCAGATTTGGGAA 60.181 47.826 0.00 0.00 37.19 3.97
2338 2359 3.804873 GCTAGATCGTCAGATTTGGGAAC 59.195 47.826 0.00 0.00 37.19 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 0.470766 AGTTAACAGTTGTCCCGCCA 59.529 50.000 8.61 0.00 0.00 5.69
111 112 5.886609 TGGAAACAGGATCAATTAGGTCAA 58.113 37.500 0.00 0.00 35.01 3.18
176 177 6.662414 TGAAAGAATCCATTGTACATCGAC 57.338 37.500 0.00 0.00 0.00 4.20
264 266 0.963962 AGTAAGCTGACCGAACCGAA 59.036 50.000 0.00 0.00 0.00 4.30
308 310 9.733556 TTCCATTAGAGTGTCTTAATTTGCTAA 57.266 29.630 0.00 0.00 0.00 3.09
309 311 9.905713 ATTCCATTAGAGTGTCTTAATTTGCTA 57.094 29.630 0.00 0.00 0.00 3.49
349 351 9.367160 CCATATCTTACTTCAAATGGGGTTAAT 57.633 33.333 0.00 0.00 32.07 1.40
363 365 9.384764 GAACAAGCTAACTTCCATATCTTACTT 57.615 33.333 0.00 0.00 32.29 2.24
494 496 8.357402 GCTTTGTATCTTCTAAACCCTCAAAAA 58.643 33.333 0.00 0.00 0.00 1.94
495 497 7.504238 TGCTTTGTATCTTCTAAACCCTCAAAA 59.496 33.333 0.00 0.00 0.00 2.44
615 618 3.185246 AGATATTCCAACACTGCCTCG 57.815 47.619 0.00 0.00 0.00 4.63
944 955 4.485875 TCCTCCCGCAATAAATCTACCTA 58.514 43.478 0.00 0.00 0.00 3.08
990 1003 2.477189 GGTTTCCGCCATTAACACATCG 60.477 50.000 0.00 0.00 0.00 3.84
1009 1022 2.893489 GACCAAATTTGAGAGCCAAGGT 59.107 45.455 19.86 5.27 35.94 3.50
1057 1070 8.805688 GTTATCCGAGTTAATAATAAGGCGATC 58.194 37.037 0.00 0.00 0.00 3.69
1085 1098 4.334759 CCTGCATAGTTTCAATCACCTCTG 59.665 45.833 0.00 0.00 0.00 3.35
1086 1099 4.225942 TCCTGCATAGTTTCAATCACCTCT 59.774 41.667 0.00 0.00 0.00 3.69
1234 1252 8.543774 AGTCAAAGAAAATCCAGCTAATCTAGA 58.456 33.333 0.00 0.00 0.00 2.43
1246 1264 6.986250 ACCAATCAGAAGTCAAAGAAAATCC 58.014 36.000 0.00 0.00 0.00 3.01
1360 1378 5.911280 CCTACAATCGCATGACATTCATTTC 59.089 40.000 0.00 0.00 34.28 2.17
1364 1382 2.613595 GCCTACAATCGCATGACATTCA 59.386 45.455 0.00 0.00 0.00 2.57
1378 1396 3.835978 TCCACTAGCTAAAGTGCCTACAA 59.164 43.478 10.64 0.00 44.56 2.41
1380 1398 4.434520 CTTCCACTAGCTAAAGTGCCTAC 58.565 47.826 10.64 0.00 44.56 3.18
1405 1423 2.359975 GACAACCAAGCGAGGGGG 60.360 66.667 2.52 0.00 0.00 5.40
1428 1446 5.663106 TCCTAGGCTCATGAAGATTACAACT 59.337 40.000 2.96 0.00 0.00 3.16
1444 1462 0.698818 CCCAACCAAAGTCCTAGGCT 59.301 55.000 2.96 1.43 0.00 4.58
1452 1470 8.903062 ACAACTATGTATGGCCCAACCAAAGT 62.903 42.308 0.00 0.00 41.65 2.66
1458 1476 2.687935 CCACAACTATGTATGGCCCAAC 59.312 50.000 0.00 0.00 37.82 3.77
1459 1477 2.357673 CCCACAACTATGTATGGCCCAA 60.358 50.000 0.00 0.00 37.82 4.12
1462 1480 1.318576 GCCCACAACTATGTATGGCC 58.681 55.000 0.00 0.00 44.75 5.36
1481 1499 2.732619 GGAACACCTCCGGGCTAGG 61.733 68.421 0.00 3.32 40.20 3.02
1482 1500 2.732619 GGGAACACCTCCGGGCTAG 61.733 68.421 0.00 0.00 46.51 3.42
1483 1501 2.686106 GGGAACACCTCCGGGCTA 60.686 66.667 0.00 0.00 46.51 3.93
1486 1504 1.384082 ATAGGGGAACACCTCCGGG 60.384 63.158 0.00 0.00 46.51 5.73
1487 1505 0.689745 TGATAGGGGAACACCTCCGG 60.690 60.000 0.00 0.00 46.51 5.14
1489 1507 3.974642 ACTATTGATAGGGGAACACCTCC 59.025 47.826 0.00 0.00 42.09 4.30
1490 1508 4.040584 GGACTATTGATAGGGGAACACCTC 59.959 50.000 0.00 0.00 42.09 3.85
1491 1509 3.974642 GGACTATTGATAGGGGAACACCT 59.025 47.826 0.11 0.11 44.75 4.00
1492 1510 3.072622 GGGACTATTGATAGGGGAACACC 59.927 52.174 3.30 0.00 34.69 4.16
1493 1511 3.072622 GGGGACTATTGATAGGGGAACAC 59.927 52.174 3.30 0.00 34.69 3.32
1494 1512 3.323775 GGGGACTATTGATAGGGGAACA 58.676 50.000 3.30 0.00 34.69 3.18
1495 1513 2.302157 CGGGGACTATTGATAGGGGAAC 59.698 54.545 3.30 0.00 34.69 3.62
1496 1514 2.180529 TCGGGGACTATTGATAGGGGAA 59.819 50.000 3.30 0.00 34.69 3.97
1497 1515 1.790779 TCGGGGACTATTGATAGGGGA 59.209 52.381 3.30 0.00 34.69 4.81
1498 1516 2.180276 CTCGGGGACTATTGATAGGGG 58.820 57.143 3.30 0.00 34.69 4.79
1499 1517 2.826725 GACTCGGGGACTATTGATAGGG 59.173 54.545 3.30 0.00 34.69 3.53
1500 1518 2.826725 GGACTCGGGGACTATTGATAGG 59.173 54.545 3.30 0.00 34.69 2.57
1501 1519 3.497332 TGGACTCGGGGACTATTGATAG 58.503 50.000 0.00 0.00 36.46 2.08
1502 1520 3.605726 TGGACTCGGGGACTATTGATA 57.394 47.619 0.00 0.00 0.00 2.15
1503 1521 2.471815 TGGACTCGGGGACTATTGAT 57.528 50.000 0.00 0.00 0.00 2.57
1504 1522 2.317040 GATGGACTCGGGGACTATTGA 58.683 52.381 0.00 0.00 0.00 2.57
1505 1523 2.036475 CTGATGGACTCGGGGACTATTG 59.964 54.545 0.00 0.00 0.00 1.90
1506 1524 2.320781 CTGATGGACTCGGGGACTATT 58.679 52.381 0.00 0.00 0.00 1.73
1507 1525 1.481428 CCTGATGGACTCGGGGACTAT 60.481 57.143 0.00 0.00 45.55 2.12
1508 1526 0.106167 CCTGATGGACTCGGGGACTA 60.106 60.000 0.00 0.00 45.55 2.59
1509 1527 1.381872 CCTGATGGACTCGGGGACT 60.382 63.158 0.00 0.00 45.55 3.85
1510 1528 3.221222 CCTGATGGACTCGGGGAC 58.779 66.667 0.00 0.00 45.55 4.46
1514 1532 0.107654 GGAAACCCTGATGGACTCGG 60.108 60.000 0.00 0.00 38.00 4.63
1515 1533 0.905357 AGGAAACCCTGATGGACTCG 59.095 55.000 0.00 0.00 38.00 4.18
1516 1534 3.441500 AAAGGAAACCCTGATGGACTC 57.558 47.619 0.00 0.00 38.00 3.36
1517 1535 3.500343 CAAAAGGAAACCCTGATGGACT 58.500 45.455 0.00 0.00 38.00 3.85
1518 1536 2.562738 CCAAAAGGAAACCCTGATGGAC 59.437 50.000 9.10 0.00 40.31 4.02
1519 1537 2.448961 TCCAAAAGGAAACCCTGATGGA 59.551 45.455 11.99 11.99 42.45 3.41
1520 1538 2.888212 TCCAAAAGGAAACCCTGATGG 58.112 47.619 0.00 0.00 39.73 3.51
1521 1539 4.631131 GTTTCCAAAAGGAAACCCTGATG 58.369 43.478 23.10 0.00 46.84 3.07
1522 1540 4.955811 GTTTCCAAAAGGAAACCCTGAT 57.044 40.909 23.10 0.00 46.84 2.90
1564 1582 1.135199 GTTCGGTGCTCAGTCGGAATA 60.135 52.381 0.00 0.00 0.00 1.75
1578 1597 3.936203 TGGCGCTCCAAGTTCGGT 61.936 61.111 7.64 0.00 39.99 4.69
1592 1611 5.064071 GTCTCTTAGTTAGCAGTCAAATGGC 59.936 44.000 0.00 0.00 0.00 4.40
1606 1625 2.633481 AGTTCGCCAAGGTCTCTTAGTT 59.367 45.455 0.00 0.00 0.00 2.24
1623 1642 2.235898 AGGGACATGCTCTTCTGAGTTC 59.764 50.000 0.00 0.00 42.13 3.01
1653 1672 3.821033 GTCATGGTAACTTGCTCAAACCT 59.179 43.478 0.00 0.00 41.33 3.50
1670 1689 3.726607 GCTAATCCTGGACTCTGTCATG 58.273 50.000 0.00 0.00 33.68 3.07
1671 1690 2.363680 CGCTAATCCTGGACTCTGTCAT 59.636 50.000 0.00 0.00 33.68 3.06
1709 1728 2.995547 ACCCATAGGTCGGGCAAC 59.004 61.111 0.00 0.00 46.45 4.17
1764 1783 0.329931 TTTCGGGCCTAGGCAAATGA 59.670 50.000 34.09 21.62 44.11 2.57
1765 1784 0.455815 GTTTCGGGCCTAGGCAAATG 59.544 55.000 34.09 19.75 44.11 2.32
1766 1785 0.039035 TGTTTCGGGCCTAGGCAAAT 59.961 50.000 34.09 0.00 44.11 2.32
1769 1788 1.223487 GATGTTTCGGGCCTAGGCA 59.777 57.895 34.09 12.46 44.11 4.75
1770 1789 0.815615 CTGATGTTTCGGGCCTAGGC 60.816 60.000 26.55 26.55 41.06 3.93
1772 1791 0.830648 TCCTGATGTTTCGGGCCTAG 59.169 55.000 0.84 0.00 46.59 3.02
1773 1792 1.209504 CTTCCTGATGTTTCGGGCCTA 59.790 52.381 0.84 0.00 46.59 3.93
1774 1793 0.035056 CTTCCTGATGTTTCGGGCCT 60.035 55.000 0.84 0.00 46.59 5.19
1781 1800 3.173953 TGCCATTCCTTCCTGATGTTT 57.826 42.857 0.00 0.00 0.00 2.83
1788 1807 2.579860 AGTCTTCATGCCATTCCTTCCT 59.420 45.455 0.00 0.00 0.00 3.36
1800 1819 7.388776 TCTTGGAGTTTACATCAAGTCTTCATG 59.611 37.037 0.00 0.00 38.13 3.07
1813 1832 8.418597 ACTAACTCTATGTCTTGGAGTTTACA 57.581 34.615 18.52 4.89 44.63 2.41
1818 1837 5.833340 AGGACTAACTCTATGTCTTGGAGT 58.167 41.667 0.00 0.00 41.37 3.85
1834 1853 1.290955 CAACCGTGCCGAGGACTAA 59.709 57.895 0.00 0.00 0.00 2.24
1849 1868 3.373130 GTCGGTTGTATCTAAAGGGCAAC 59.627 47.826 0.00 0.00 38.78 4.17
1894 1913 3.618019 GCACCTTGGTTTATAGACACCGA 60.618 47.826 0.00 0.00 35.60 4.69
1901 1920 2.025321 ACCCTGGCACCTTGGTTTATAG 60.025 50.000 0.00 0.00 0.00 1.31
1908 1929 0.107017 CTATGACCCTGGCACCTTGG 60.107 60.000 0.00 0.00 0.00 3.61
1910 1931 1.207791 CTCTATGACCCTGGCACCTT 58.792 55.000 0.00 0.00 0.00 3.50
1924 1945 7.460402 AGATTGGATGTGAATATGTCCCTCTAT 59.540 37.037 0.00 0.00 0.00 1.98
1926 1947 5.610132 AGATTGGATGTGAATATGTCCCTCT 59.390 40.000 0.00 0.00 0.00 3.69
1927 1948 5.874093 AGATTGGATGTGAATATGTCCCTC 58.126 41.667 0.00 0.00 0.00 4.30
1928 1949 5.512060 CGAGATTGGATGTGAATATGTCCCT 60.512 44.000 0.00 0.00 0.00 4.20
1929 1950 4.692625 CGAGATTGGATGTGAATATGTCCC 59.307 45.833 0.00 0.00 0.00 4.46
1930 1951 5.178252 CACGAGATTGGATGTGAATATGTCC 59.822 44.000 0.00 0.00 34.29 4.02
2025 2046 1.741770 CCAACTTCGGGCCTTCTCG 60.742 63.158 0.84 0.00 0.00 4.04
2036 2057 1.944709 ACACGGTGTTTAGCCAACTTC 59.055 47.619 8.21 0.00 36.21 3.01
2046 2067 0.034863 ACACAAGGGACACGGTGTTT 60.035 50.000 15.94 2.92 38.68 2.83
2052 2073 0.966920 ACTAGGACACAAGGGACACG 59.033 55.000 0.00 0.00 0.00 4.49
2070 2091 6.265649 TCTGATAGTCTTGGCTAGATGGTAAC 59.734 42.308 1.20 0.00 34.79 2.50
2103 2124 2.819284 GGCGGATCTTGGGTAGGGG 61.819 68.421 0.00 0.00 0.00 4.79
2108 2129 0.181350 GAATCTGGCGGATCTTGGGT 59.819 55.000 9.72 0.00 32.76 4.51
2109 2130 0.181114 TGAATCTGGCGGATCTTGGG 59.819 55.000 9.72 0.00 32.76 4.12
2110 2131 1.139654 TCTGAATCTGGCGGATCTTGG 59.860 52.381 9.72 1.19 32.76 3.61
2111 2132 2.609427 TCTGAATCTGGCGGATCTTG 57.391 50.000 9.72 2.93 32.76 3.02
2112 2133 2.038295 GGATCTGAATCTGGCGGATCTT 59.962 50.000 9.72 0.00 44.08 2.40
2113 2134 1.622811 GGATCTGAATCTGGCGGATCT 59.377 52.381 9.72 0.00 44.08 2.75
2114 2135 1.671261 CGGATCTGAATCTGGCGGATC 60.671 57.143 9.72 4.21 43.97 3.36
2115 2136 0.319728 CGGATCTGAATCTGGCGGAT 59.680 55.000 2.10 2.10 35.03 4.18
2116 2137 0.755327 TCGGATCTGAATCTGGCGGA 60.755 55.000 0.39 0.00 38.60 5.54
2117 2138 0.598680 GTCGGATCTGAATCTGGCGG 60.599 60.000 5.62 0.00 38.60 6.13
2118 2139 0.103026 TGTCGGATCTGAATCTGGCG 59.897 55.000 5.62 0.00 44.45 5.69
2119 2140 2.540265 ATGTCGGATCTGAATCTGGC 57.460 50.000 5.62 0.00 42.29 4.85
2120 2141 3.136763 CCAATGTCGGATCTGAATCTGG 58.863 50.000 5.62 8.99 38.60 3.86
2121 2142 3.558829 CACCAATGTCGGATCTGAATCTG 59.441 47.826 5.62 3.62 39.31 2.90
2122 2143 3.432749 CCACCAATGTCGGATCTGAATCT 60.433 47.826 5.62 0.00 32.12 2.40
2123 2144 2.874701 CCACCAATGTCGGATCTGAATC 59.125 50.000 5.62 0.00 0.00 2.52
2124 2145 2.505407 TCCACCAATGTCGGATCTGAAT 59.495 45.455 5.62 0.00 0.00 2.57
2125 2146 1.905894 TCCACCAATGTCGGATCTGAA 59.094 47.619 5.62 0.00 0.00 3.02
2126 2147 1.567357 TCCACCAATGTCGGATCTGA 58.433 50.000 0.00 0.00 0.00 3.27
2127 2148 2.627515 ATCCACCAATGTCGGATCTG 57.372 50.000 0.00 0.00 34.31 2.90
2128 2149 4.982241 ATAATCCACCAATGTCGGATCT 57.018 40.909 1.77 0.00 38.62 2.75
2129 2150 5.547465 TGTATAATCCACCAATGTCGGATC 58.453 41.667 1.77 0.00 38.62 3.36
2130 2151 5.560722 TGTATAATCCACCAATGTCGGAT 57.439 39.130 0.00 0.00 41.39 4.18
2131 2152 5.104693 ACTTGTATAATCCACCAATGTCGGA 60.105 40.000 0.00 0.00 0.00 4.55
2132 2153 5.007626 CACTTGTATAATCCACCAATGTCGG 59.992 44.000 0.00 0.00 0.00 4.79
2133 2154 5.504010 GCACTTGTATAATCCACCAATGTCG 60.504 44.000 0.00 0.00 0.00 4.35
2134 2155 5.221048 GGCACTTGTATAATCCACCAATGTC 60.221 44.000 0.00 0.00 0.00 3.06
2135 2156 4.644685 GGCACTTGTATAATCCACCAATGT 59.355 41.667 0.00 0.00 0.00 2.71
2136 2157 4.889409 AGGCACTTGTATAATCCACCAATG 59.111 41.667 0.00 0.00 27.25 2.82
2137 2158 5.103940 AGAGGCACTTGTATAATCCACCAAT 60.104 40.000 0.00 0.00 41.55 3.16
2138 2159 4.227300 AGAGGCACTTGTATAATCCACCAA 59.773 41.667 0.00 0.00 41.55 3.67
2139 2160 3.780294 AGAGGCACTTGTATAATCCACCA 59.220 43.478 0.00 0.00 41.55 4.17
2140 2161 4.130118 CAGAGGCACTTGTATAATCCACC 58.870 47.826 0.00 0.00 41.55 4.61
2141 2162 5.023533 TCAGAGGCACTTGTATAATCCAC 57.976 43.478 0.00 0.00 41.55 4.02
2142 2163 4.962362 TCTCAGAGGCACTTGTATAATCCA 59.038 41.667 0.00 0.00 41.55 3.41
2143 2164 5.537300 TCTCAGAGGCACTTGTATAATCC 57.463 43.478 0.00 0.00 41.55 3.01
2144 2165 7.930865 AGATTTCTCAGAGGCACTTGTATAATC 59.069 37.037 0.00 0.00 41.55 1.75
2145 2166 7.800092 AGATTTCTCAGAGGCACTTGTATAAT 58.200 34.615 0.00 0.00 41.55 1.28
2146 2167 7.187824 AGATTTCTCAGAGGCACTTGTATAA 57.812 36.000 0.00 0.00 41.55 0.98
2147 2168 6.798427 AGATTTCTCAGAGGCACTTGTATA 57.202 37.500 0.00 0.00 41.55 1.47
2148 2169 5.690464 AGATTTCTCAGAGGCACTTGTAT 57.310 39.130 0.00 0.00 41.55 2.29
2149 2170 6.605471 TTAGATTTCTCAGAGGCACTTGTA 57.395 37.500 0.00 0.00 41.55 2.41
2150 2171 5.489792 TTAGATTTCTCAGAGGCACTTGT 57.510 39.130 0.00 0.00 41.55 3.16
2151 2172 5.936956 AGTTTAGATTTCTCAGAGGCACTTG 59.063 40.000 0.00 0.00 41.55 3.16
2152 2173 5.936956 CAGTTTAGATTTCTCAGAGGCACTT 59.063 40.000 0.00 0.00 41.55 3.16
2154 2175 4.094146 GCAGTTTAGATTTCTCAGAGGCAC 59.906 45.833 0.00 0.00 0.00 5.01
2155 2176 4.019860 AGCAGTTTAGATTTCTCAGAGGCA 60.020 41.667 0.00 0.00 0.00 4.75
2156 2177 4.512484 AGCAGTTTAGATTTCTCAGAGGC 58.488 43.478 0.00 0.00 0.00 4.70
2157 2178 4.803088 CGAGCAGTTTAGATTTCTCAGAGG 59.197 45.833 0.00 0.00 0.00 3.69
2158 2179 5.645624 TCGAGCAGTTTAGATTTCTCAGAG 58.354 41.667 0.00 0.00 0.00 3.35
2159 2180 5.644977 TCGAGCAGTTTAGATTTCTCAGA 57.355 39.130 0.00 0.00 0.00 3.27
2160 2181 5.233902 CCATCGAGCAGTTTAGATTTCTCAG 59.766 44.000 0.00 0.00 0.00 3.35
2161 2182 5.111989 CCATCGAGCAGTTTAGATTTCTCA 58.888 41.667 0.00 0.00 0.00 3.27
2162 2183 4.509600 CCCATCGAGCAGTTTAGATTTCTC 59.490 45.833 0.00 0.00 0.00 2.87
2163 2184 4.080863 ACCCATCGAGCAGTTTAGATTTCT 60.081 41.667 0.00 0.00 0.00 2.52
2164 2185 4.192317 ACCCATCGAGCAGTTTAGATTTC 58.808 43.478 0.00 0.00 0.00 2.17
2165 2186 4.192317 GACCCATCGAGCAGTTTAGATTT 58.808 43.478 0.00 0.00 0.00 2.17
2166 2187 3.798202 GACCCATCGAGCAGTTTAGATT 58.202 45.455 0.00 0.00 0.00 2.40
2167 2188 3.460857 GACCCATCGAGCAGTTTAGAT 57.539 47.619 0.00 0.00 0.00 1.98
2168 2189 2.961526 GACCCATCGAGCAGTTTAGA 57.038 50.000 0.00 0.00 0.00 2.10
2180 2201 0.533755 CAATCTGGAGGCGACCCATC 60.534 60.000 0.00 0.00 32.49 3.51
2181 2202 0.982852 TCAATCTGGAGGCGACCCAT 60.983 55.000 0.00 0.00 32.49 4.00
2182 2203 1.612146 TCAATCTGGAGGCGACCCA 60.612 57.895 0.00 0.00 0.00 4.51
2183 2204 1.153349 GTCAATCTGGAGGCGACCC 60.153 63.158 0.00 0.00 0.00 4.46
2184 2205 1.519455 CGTCAATCTGGAGGCGACC 60.519 63.158 0.00 0.00 0.00 4.79
2185 2206 0.802607 GTCGTCAATCTGGAGGCGAC 60.803 60.000 3.80 3.80 41.04 5.19
2186 2207 1.248101 TGTCGTCAATCTGGAGGCGA 61.248 55.000 0.00 0.00 0.00 5.54
2187 2208 0.803768 CTGTCGTCAATCTGGAGGCG 60.804 60.000 0.00 0.00 0.00 5.52
2188 2209 1.086634 GCTGTCGTCAATCTGGAGGC 61.087 60.000 0.00 0.00 0.00 4.70
2189 2210 0.247460 TGCTGTCGTCAATCTGGAGG 59.753 55.000 0.00 0.00 0.00 4.30
2190 2211 2.200067 GATGCTGTCGTCAATCTGGAG 58.800 52.381 0.00 0.00 0.00 3.86
2191 2212 1.469767 CGATGCTGTCGTCAATCTGGA 60.470 52.381 4.26 0.00 45.19 3.86
2192 2213 0.926155 CGATGCTGTCGTCAATCTGG 59.074 55.000 4.26 0.00 45.19 3.86
2206 2227 1.502163 GGTCATGCTACAGCCGATGC 61.502 60.000 0.00 0.00 41.18 3.91
2207 2228 0.105593 AGGTCATGCTACAGCCGATG 59.894 55.000 0.00 0.00 41.18 3.84
2208 2229 0.390860 GAGGTCATGCTACAGCCGAT 59.609 55.000 0.00 0.00 41.18 4.18
2209 2230 0.684479 AGAGGTCATGCTACAGCCGA 60.684 55.000 0.00 0.00 41.18 5.54
2210 2231 0.176680 AAGAGGTCATGCTACAGCCG 59.823 55.000 0.00 0.00 41.18 5.52
2211 2232 2.093235 AGAAAGAGGTCATGCTACAGCC 60.093 50.000 0.00 0.00 41.18 4.85
2212 2233 3.258971 AGAAAGAGGTCATGCTACAGC 57.741 47.619 0.00 0.00 42.50 4.40
2213 2234 4.646945 TCCTAGAAAGAGGTCATGCTACAG 59.353 45.833 0.00 0.00 37.88 2.74
2214 2235 4.402793 GTCCTAGAAAGAGGTCATGCTACA 59.597 45.833 0.00 0.00 37.88 2.74
2215 2236 4.402793 TGTCCTAGAAAGAGGTCATGCTAC 59.597 45.833 0.00 0.00 37.88 3.58
2216 2237 4.402793 GTGTCCTAGAAAGAGGTCATGCTA 59.597 45.833 0.00 0.00 37.07 3.49
2217 2238 3.196685 GTGTCCTAGAAAGAGGTCATGCT 59.803 47.826 0.00 0.00 37.07 3.79
2218 2239 3.526534 GTGTCCTAGAAAGAGGTCATGC 58.473 50.000 0.00 0.00 37.07 4.06
2219 2240 3.772025 AGGTGTCCTAGAAAGAGGTCATG 59.228 47.826 0.00 0.00 37.07 3.07
2220 2241 4.027437 GAGGTGTCCTAGAAAGAGGTCAT 58.973 47.826 0.00 0.00 37.07 3.06
2221 2242 3.076182 AGAGGTGTCCTAGAAAGAGGTCA 59.924 47.826 0.00 0.00 37.88 4.02
2222 2243 3.703921 AGAGGTGTCCTAGAAAGAGGTC 58.296 50.000 0.00 0.00 37.88 3.85
2223 2244 3.837399 AGAGGTGTCCTAGAAAGAGGT 57.163 47.619 0.00 0.00 37.88 3.85
2224 2245 4.284746 ACAAAGAGGTGTCCTAGAAAGAGG 59.715 45.833 0.00 0.00 38.03 3.69
2225 2246 5.474825 GACAAAGAGGTGTCCTAGAAAGAG 58.525 45.833 0.00 0.00 41.79 2.85
2226 2247 5.470047 GACAAAGAGGTGTCCTAGAAAGA 57.530 43.478 0.00 0.00 41.79 2.52
2235 2256 4.574828 TGCTGTTAAAGACAAAGAGGTGTC 59.425 41.667 0.00 0.00 46.90 3.67
2236 2257 4.523083 TGCTGTTAAAGACAAAGAGGTGT 58.477 39.130 0.00 0.00 37.93 4.16
2237 2258 5.695851 ATGCTGTTAAAGACAAAGAGGTG 57.304 39.130 0.00 0.00 37.93 4.00
2238 2259 6.073222 CGTAATGCTGTTAAAGACAAAGAGGT 60.073 38.462 0.00 0.00 37.93 3.85
2239 2260 6.307155 CGTAATGCTGTTAAAGACAAAGAGG 58.693 40.000 0.00 0.00 37.93 3.69
2240 2261 5.790495 GCGTAATGCTGTTAAAGACAAAGAG 59.210 40.000 0.00 0.00 41.73 2.85
2241 2262 5.685841 GCGTAATGCTGTTAAAGACAAAGA 58.314 37.500 0.00 0.00 41.73 2.52
2242 2263 5.975138 GCGTAATGCTGTTAAAGACAAAG 57.025 39.130 0.00 0.00 41.73 2.77
2264 2285 0.652592 CCAGGCGAATCAGCGTAAAG 59.347 55.000 0.00 0.00 38.18 1.85
2265 2286 1.366111 GCCAGGCGAATCAGCGTAAA 61.366 55.000 0.00 0.00 38.18 2.01
2266 2287 1.813753 GCCAGGCGAATCAGCGTAA 60.814 57.895 0.00 0.00 38.18 3.18
2267 2288 2.202878 GCCAGGCGAATCAGCGTA 60.203 61.111 0.00 0.00 38.18 4.42
2269 2290 4.845580 AGGCCAGGCGAATCAGCG 62.846 66.667 5.01 0.00 38.18 5.18
2270 2291 2.899339 GAGGCCAGGCGAATCAGC 60.899 66.667 5.01 0.00 0.00 4.26
2271 2292 2.203126 GGAGGCCAGGCGAATCAG 60.203 66.667 5.01 0.00 0.00 2.90
2272 2293 2.688666 AGGAGGCCAGGCGAATCA 60.689 61.111 5.01 0.00 0.00 2.57
2273 2294 2.110006 GAGGAGGCCAGGCGAATC 59.890 66.667 5.01 3.24 0.00 2.52
2274 2295 3.854669 CGAGGAGGCCAGGCGAAT 61.855 66.667 5.01 0.00 0.00 3.34
2300 2321 6.992715 ACGATCTAGCCTAGCACATAATTTTT 59.007 34.615 0.00 0.00 0.00 1.94
2301 2322 6.525629 ACGATCTAGCCTAGCACATAATTTT 58.474 36.000 0.00 0.00 0.00 1.82
2302 2323 6.102897 ACGATCTAGCCTAGCACATAATTT 57.897 37.500 0.00 0.00 0.00 1.82
2303 2324 5.243954 TGACGATCTAGCCTAGCACATAATT 59.756 40.000 0.00 0.00 0.00 1.40
2304 2325 4.767409 TGACGATCTAGCCTAGCACATAAT 59.233 41.667 0.00 0.00 0.00 1.28
2305 2326 4.142038 TGACGATCTAGCCTAGCACATAA 58.858 43.478 0.00 0.00 0.00 1.90
2306 2327 3.751518 TGACGATCTAGCCTAGCACATA 58.248 45.455 0.00 0.00 0.00 2.29
2307 2328 2.556189 CTGACGATCTAGCCTAGCACAT 59.444 50.000 0.00 0.00 0.00 3.21
2308 2329 1.950216 CTGACGATCTAGCCTAGCACA 59.050 52.381 0.00 0.00 0.00 4.57
2309 2330 2.222886 TCTGACGATCTAGCCTAGCAC 58.777 52.381 0.00 0.00 0.00 4.40
2310 2331 2.640316 TCTGACGATCTAGCCTAGCA 57.360 50.000 0.00 0.00 0.00 3.49
2311 2332 4.233789 CAAATCTGACGATCTAGCCTAGC 58.766 47.826 0.00 0.00 0.00 3.42
2312 2333 4.321601 CCCAAATCTGACGATCTAGCCTAG 60.322 50.000 0.00 0.00 0.00 3.02
2313 2334 3.574396 CCCAAATCTGACGATCTAGCCTA 59.426 47.826 0.00 0.00 0.00 3.93
2314 2335 2.366916 CCCAAATCTGACGATCTAGCCT 59.633 50.000 0.00 0.00 0.00 4.58
2315 2336 2.365617 TCCCAAATCTGACGATCTAGCC 59.634 50.000 0.00 0.00 0.00 3.93
2316 2337 3.735237 TCCCAAATCTGACGATCTAGC 57.265 47.619 0.00 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.