Multiple sequence alignment - TraesCS1A01G007800

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 TraesCS1A01G007800 chr1A 100.000 2219 0 0 1 2219 4053742 4055960 0.000000e+00 4098
1 TraesCS1A01G007800 chr1D 85.174 951 80 28 493 1425 209134 208227 0.000000e+00 918
2 TraesCS1A01G007800 chr1D 92.095 506 21 7 1 496 209689 209193 0.000000e+00 695
3 TraesCS1A01G007800 chr1D 93.261 460 29 2 975 1432 122225 121766 0.000000e+00 676
4 TraesCS1A01G007800 chr1D 76.113 494 79 26 1550 2027 131622 131152 2.870000e-54 222
5 TraesCS1A01G007800 chr1D 82.222 90 13 3 914 1001 122313 122225 8.500000e-10 75
6 TraesCS1A01G007800 chr1B 91.963 535 39 3 1465 1996 5186877 5187410 0.000000e+00 747
7 TraesCS1A01G007800 chr1B 90.814 479 34 7 957 1432 5177316 5177787 1.120000e-177 632
8 TraesCS1A01G007800 chr1B 92.216 334 13 7 1 324 5176105 5176435 5.580000e-126 460
9 TraesCS1A01G007800 chr1B 92.857 196 13 1 704 898 5177103 5177298 1.300000e-72 283
10 TraesCS1A01G007800 chr1B 89.143 175 9 2 322 494 5176692 5176858 2.230000e-50 209


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 TraesCS1A01G007800 chr1A 4053742 4055960 2218 False 4098.0 4098 100.0000 1 2219 1 chr1A.!!$F1 2218
1 TraesCS1A01G007800 chr1D 208227 209689 1462 True 806.5 918 88.6345 1 1425 2 chr1D.!!$R3 1424
2 TraesCS1A01G007800 chr1D 121766 122313 547 True 375.5 676 87.7415 914 1432 2 chr1D.!!$R2 518
3 TraesCS1A01G007800 chr1B 5186877 5187410 533 False 747.0 747 91.9630 1465 1996 1 chr1B.!!$F1 531
4 TraesCS1A01G007800 chr1B 5176105 5177787 1682 False 396.0 632 91.2575 1 1432 4 chr1B.!!$F2 1431

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
828 1184 0.77681 TCCATTTTCCCTGCTGTCCA 59.223 50.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2478 0.0982 CGCATTGAGCAGTGGACATG 59.902 55.0 0.0 0.0 46.13 3.21 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
50 51 2.785269 ACACCACCATATCACCATCCAT 59.215 45.455 0.00 0.00 0.00 3.41
85 94 2.136878 ATGGGCGGCTACTGAGAGG 61.137 63.158 9.56 0.00 0.00 3.69
102 111 6.127675 ACTGAGAGGTCTAGTATCCGAAAAAC 60.128 42.308 0.00 0.00 0.00 2.43
206 217 2.173782 TGGCACTAGTTCAAACTTGGGA 59.826 45.455 10.19 0.00 37.35 4.37
261 272 4.081322 AGTGTTATTGGTCGGTGTTTCT 57.919 40.909 0.00 0.00 0.00 2.52
341 611 8.244113 AGCTTTGTATGTAGCAAAATAACCTTC 58.756 33.333 0.00 0.00 39.85 3.46
342 612 7.218204 GCTTTGTATGTAGCAAAATAACCTTCG 59.782 37.037 0.00 0.00 35.71 3.79
361 633 8.343168 ACCTTCGAAATAATCAAATGGTTGTA 57.657 30.769 0.00 0.00 36.07 2.41
406 678 7.664961 TCCCTATTAAGGTAAGGAGTAAGGAA 58.335 38.462 0.00 0.00 41.89 3.36
407 679 7.566509 TCCCTATTAAGGTAAGGAGTAAGGAAC 59.433 40.741 0.00 0.00 41.89 3.62
408 680 7.567994 CCCTATTAAGGTAAGGAGTAAGGAACT 59.432 40.741 0.00 0.00 41.89 3.01
409 681 9.652114 CCTATTAAGGTAAGGAGTAAGGAACTA 57.348 37.037 0.00 0.00 36.97 2.24
412 684 6.870895 AAGGTAAGGAGTAAGGAACTAAGG 57.129 41.667 0.00 0.00 38.49 2.69
413 685 6.163110 AGGTAAGGAGTAAGGAACTAAGGA 57.837 41.667 0.00 0.00 38.49 3.36
426 698 5.368816 AGGAACTAAGGACTAACCACAAACT 59.631 40.000 0.00 0.00 38.00 2.66
440 712 6.327279 ACCACAAACTAACTCTTTAATGGC 57.673 37.500 0.00 0.00 0.00 4.40
453 725 2.779755 TAATGGCGAGCCTTCTGAAA 57.220 45.000 15.75 0.00 36.94 2.69
508 863 9.507329 AGTTCTAAATAGTATATGGCATTGGTG 57.493 33.333 4.78 0.00 0.00 4.17
523 878 2.673775 TGGTGTCAATGTGGTCCATT 57.326 45.000 0.00 0.00 44.73 3.16
537 892 6.919721 TGTGGTCCATTTAAGATTTTACTGC 58.080 36.000 0.00 0.00 0.00 4.40
544 899 8.646900 TCCATTTAAGATTTTACTGCTGGTTTT 58.353 29.630 0.00 0.00 0.00 2.43
549 904 6.076981 AGATTTTACTGCTGGTTTTGACTG 57.923 37.500 0.00 0.00 0.00 3.51
567 922 1.667724 CTGTAGAGAGCGGGCAATTTG 59.332 52.381 0.00 0.00 0.00 2.32
615 970 4.877378 ATTTTGCTCTCCAGAAAATGCA 57.123 36.364 0.00 0.00 30.05 3.96
618 973 5.981088 TTTGCTCTCCAGAAAATGCATTA 57.019 34.783 13.39 0.00 0.00 1.90
663 1018 5.582689 AAACTCAAACAGACAAAGGAAGG 57.417 39.130 0.00 0.00 0.00 3.46
674 1029 2.175715 ACAAAGGAAGGAAGCCACTCTT 59.824 45.455 0.00 0.00 37.83 2.85
675 1030 3.225940 CAAAGGAAGGAAGCCACTCTTT 58.774 45.455 0.00 0.00 34.56 2.52
676 1031 3.602205 AAGGAAGGAAGCCACTCTTTT 57.398 42.857 0.00 0.00 34.56 2.27
677 1032 3.602205 AGGAAGGAAGCCACTCTTTTT 57.398 42.857 0.00 0.00 34.56 1.94
678 1033 3.491342 AGGAAGGAAGCCACTCTTTTTC 58.509 45.455 0.00 0.00 34.56 2.29
679 1034 2.558795 GGAAGGAAGCCACTCTTTTTCC 59.441 50.000 0.00 0.00 39.45 3.13
680 1035 3.222603 GAAGGAAGCCACTCTTTTTCCA 58.777 45.455 5.07 0.00 41.19 3.53
681 1036 2.587522 AGGAAGCCACTCTTTTTCCAC 58.412 47.619 5.07 0.00 41.19 4.02
682 1037 2.175715 AGGAAGCCACTCTTTTTCCACT 59.824 45.455 5.07 0.00 41.19 4.00
683 1038 2.554462 GGAAGCCACTCTTTTTCCACTC 59.446 50.000 0.00 0.00 39.09 3.51
684 1039 3.481453 GAAGCCACTCTTTTTCCACTCT 58.519 45.455 0.00 0.00 34.56 3.24
685 1040 2.856222 AGCCACTCTTTTTCCACTCTG 58.144 47.619 0.00 0.00 0.00 3.35
686 1041 2.439507 AGCCACTCTTTTTCCACTCTGA 59.560 45.455 0.00 0.00 0.00 3.27
687 1042 3.073650 AGCCACTCTTTTTCCACTCTGAT 59.926 43.478 0.00 0.00 0.00 2.90
688 1043 3.823304 GCCACTCTTTTTCCACTCTGATT 59.177 43.478 0.00 0.00 0.00 2.57
689 1044 4.320788 GCCACTCTTTTTCCACTCTGATTG 60.321 45.833 0.00 0.00 0.00 2.67
690 1045 5.065914 CCACTCTTTTTCCACTCTGATTGA 58.934 41.667 0.00 0.00 0.00 2.57
692 1047 5.994054 CACTCTTTTTCCACTCTGATTGAGA 59.006 40.000 0.00 0.00 45.39 3.27
693 1048 6.654161 CACTCTTTTTCCACTCTGATTGAGAT 59.346 38.462 0.00 0.00 45.39 2.75
694 1049 6.654161 ACTCTTTTTCCACTCTGATTGAGATG 59.346 38.462 0.00 0.00 45.39 2.90
695 1050 5.413833 TCTTTTTCCACTCTGATTGAGATGC 59.586 40.000 0.00 0.00 45.39 3.91
696 1051 2.996249 TCCACTCTGATTGAGATGCC 57.004 50.000 0.00 0.00 45.39 4.40
697 1052 2.190538 TCCACTCTGATTGAGATGCCA 58.809 47.619 0.00 0.00 45.39 4.92
698 1053 2.573009 TCCACTCTGATTGAGATGCCAA 59.427 45.455 0.00 0.00 45.39 4.52
699 1054 3.201487 TCCACTCTGATTGAGATGCCAAT 59.799 43.478 0.00 0.00 45.39 3.16
828 1184 0.776810 TCCATTTTCCCTGCTGTCCA 59.223 50.000 0.00 0.00 0.00 4.02
840 1196 1.207089 TGCTGTCCAGGCAGTACATAC 59.793 52.381 11.25 0.00 38.65 2.39
846 1202 4.100963 TGTCCAGGCAGTACATACATAAGG 59.899 45.833 0.00 0.00 0.00 2.69
907 1263 8.916628 ATAAAGAAAAGGCCATCTTCTATCTC 57.083 34.615 16.03 0.00 34.90 2.75
908 1264 4.954875 AGAAAAGGCCATCTTCTATCTCG 58.045 43.478 5.01 0.00 33.94 4.04
941 1297 1.646189 GCTGTAGCTGGCTTGAGTAC 58.354 55.000 0.00 0.00 38.21 2.73
953 1309 4.406649 TGGCTTGAGTACTCATCATCATCA 59.593 41.667 25.68 13.84 39.64 3.07
954 1310 5.071384 TGGCTTGAGTACTCATCATCATCAT 59.929 40.000 25.68 0.00 39.64 2.45
955 1311 5.996513 GGCTTGAGTACTCATCATCATCATT 59.003 40.000 25.68 0.00 39.64 2.57
956 1312 7.157347 GGCTTGAGTACTCATCATCATCATTA 58.843 38.462 25.68 5.90 39.64 1.90
957 1313 7.823310 GGCTTGAGTACTCATCATCATCATTAT 59.177 37.037 25.68 0.00 39.64 1.28
958 1314 8.871862 GCTTGAGTACTCATCATCATCATTATC 58.128 37.037 25.68 0.00 39.64 1.75
959 1315 9.924650 CTTGAGTACTCATCATCATCATTATCA 57.075 33.333 25.68 4.64 39.64 2.15
978 1334 9.020731 CATTATCATCATCATCATCCCAAAGAA 57.979 33.333 0.00 0.00 0.00 2.52
979 1335 6.896021 ATCATCATCATCATCCCAAAGAAC 57.104 37.500 0.00 0.00 0.00 3.01
981 1337 7.140522 TCATCATCATCATCCCAAAGAACTA 57.859 36.000 0.00 0.00 0.00 2.24
1012 1411 2.544721 AGAAGAAGATGCAGGACTGGA 58.455 47.619 1.01 0.00 34.81 3.86
1048 1447 4.964897 TCTCCTTCATGCTCTTCATCCTTA 59.035 41.667 0.00 0.00 31.79 2.69
1068 1467 1.360393 TGTCCCCAGGGCTTGTCTTT 61.360 55.000 0.00 0.00 34.68 2.52
1116 1515 1.372872 GTGCGGCAAATTCCACACC 60.373 57.895 3.23 0.00 34.08 4.16
1119 1518 1.805428 GCGGCAAATTCCACACCAGT 61.805 55.000 0.00 0.00 0.00 4.00
1226 1625 4.148838 GGCTCCTCATCATGAGTAGTAGT 58.851 47.826 13.82 0.00 42.80 2.73
1275 1677 6.238484 GCTGTTTCTTTTGCTCTTTCTGTCTA 60.238 38.462 0.00 0.00 0.00 2.59
1305 1707 7.438160 GGTTCTTGCTGCTTGTTAATTAGTTTT 59.562 33.333 0.00 0.00 0.00 2.43
1306 1708 8.817100 GTTCTTGCTGCTTGTTAATTAGTTTTT 58.183 29.630 0.00 0.00 0.00 1.94
1310 1723 6.922957 TGCTGCTTGTTAATTAGTTTTTCTGG 59.077 34.615 0.00 0.00 0.00 3.86
1316 1729 7.589958 TGTTAATTAGTTTTTCTGGGCTCAA 57.410 32.000 0.00 0.00 0.00 3.02
1327 1740 1.676529 CTGGGCTCAATCATTGCTGAG 59.323 52.381 9.88 9.88 41.71 3.35
1356 1794 2.653726 TGTTACATGGTGGGATCATGC 58.346 47.619 0.00 0.00 44.09 4.06
1369 1807 6.808212 GGTGGGATCATGCGAAATTTATATTG 59.192 38.462 0.00 0.00 0.00 1.90
1437 1876 8.968242 ACTTTTTCGATAATTTTGCTTGAGAAC 58.032 29.630 0.00 0.00 0.00 3.01
1438 1877 8.864069 TTTTTCGATAATTTTGCTTGAGAACA 57.136 26.923 0.00 0.00 0.00 3.18
1439 1878 8.864069 TTTTCGATAATTTTGCTTGAGAACAA 57.136 26.923 0.00 0.00 34.65 2.83
1440 1879 8.864069 TTTCGATAATTTTGCTTGAGAACAAA 57.136 26.923 0.00 0.00 35.49 2.83
1441 1880 9.474920 TTTCGATAATTTTGCTTGAGAACAAAT 57.525 25.926 0.00 0.00 35.81 2.32
1447 1886 8.992835 AATTTTGCTTGAGAACAAATATCCTC 57.007 30.769 0.00 0.00 35.81 3.71
1448 1887 7.523293 TTTTGCTTGAGAACAAATATCCTCA 57.477 32.000 0.00 0.00 35.81 3.86
1449 1888 6.500684 TTGCTTGAGAACAAATATCCTCAC 57.499 37.500 0.00 0.00 35.63 3.51
1450 1889 5.809001 TGCTTGAGAACAAATATCCTCACT 58.191 37.500 0.00 0.00 35.63 3.41
1451 1890 5.877012 TGCTTGAGAACAAATATCCTCACTC 59.123 40.000 0.00 0.00 35.63 3.51
1452 1891 6.112058 GCTTGAGAACAAATATCCTCACTCT 58.888 40.000 0.00 0.00 35.63 3.24
1453 1892 6.257630 GCTTGAGAACAAATATCCTCACTCTC 59.742 42.308 0.00 0.00 35.63 3.20
1454 1893 6.857437 TGAGAACAAATATCCTCACTCTCA 57.143 37.500 0.00 0.00 36.59 3.27
1455 1894 6.634805 TGAGAACAAATATCCTCACTCTCAC 58.365 40.000 0.00 0.00 34.61 3.51
1456 1895 5.983540 AGAACAAATATCCTCACTCTCACC 58.016 41.667 0.00 0.00 0.00 4.02
1457 1896 4.392921 ACAAATATCCTCACTCTCACCG 57.607 45.455 0.00 0.00 0.00 4.94
1458 1897 3.769844 ACAAATATCCTCACTCTCACCGT 59.230 43.478 0.00 0.00 0.00 4.83
1459 1898 4.142138 ACAAATATCCTCACTCTCACCGTC 60.142 45.833 0.00 0.00 0.00 4.79
1460 1899 3.586470 ATATCCTCACTCTCACCGTCT 57.414 47.619 0.00 0.00 0.00 4.18
1461 1900 1.757682 ATCCTCACTCTCACCGTCTC 58.242 55.000 0.00 0.00 0.00 3.36
1462 1901 0.693622 TCCTCACTCTCACCGTCTCT 59.306 55.000 0.00 0.00 0.00 3.10
1463 1902 0.808125 CCTCACTCTCACCGTCTCTG 59.192 60.000 0.00 0.00 0.00 3.35
1540 1979 4.553756 TGGATTAGAATCTCGACGAGTG 57.446 45.455 23.41 0.96 35.73 3.51
1546 1985 1.199327 GAATCTCGACGAGTGGTGTCA 59.801 52.381 23.41 3.71 36.11 3.58
1559 1998 2.679837 GTGGTGTCATGCTCTACCAATG 59.320 50.000 10.41 0.00 44.13 2.82
1563 2002 2.092267 TGTCATGCTCTACCAATGCCAT 60.092 45.455 0.00 0.00 0.00 4.40
1576 2015 4.641989 ACCAATGCCATGTTCTCTTATCAC 59.358 41.667 0.00 0.00 0.00 3.06
1582 2021 5.059833 GCCATGTTCTCTTATCACCTTAGG 58.940 45.833 0.00 0.00 0.00 2.69
1591 2030 7.159372 TCTCTTATCACCTTAGGAAACACAAC 58.841 38.462 4.77 0.00 0.00 3.32
1598 2037 6.033966 CACCTTAGGAAACACAACAAAGTTC 58.966 40.000 4.77 0.00 0.00 3.01
1608 2047 4.216687 ACACAACAAAGTTCGTTCCAGAAA 59.783 37.500 0.00 0.00 0.00 2.52
1636 2078 8.910351 AAACTCAAGCTTTACTAATCTTGTCT 57.090 30.769 0.00 0.00 38.21 3.41
1655 2097 4.081972 TGTCTATCTCAAGCCACAGAAGAC 60.082 45.833 0.00 0.00 32.79 3.01
1657 2099 1.423584 TCTCAAGCCACAGAAGACCA 58.576 50.000 0.00 0.00 0.00 4.02
1683 2125 3.822735 ACTTAGCTCTACACAACCGTACA 59.177 43.478 0.00 0.00 0.00 2.90
1695 2137 3.742369 ACAACCGTACAAAGTTCCATACG 59.258 43.478 0.00 6.57 40.01 3.06
1696 2138 2.340337 ACCGTACAAAGTTCCATACGC 58.660 47.619 7.62 0.00 39.21 4.42
1713 2155 1.733526 GCCGGCCGCAATAAAGAAT 59.266 52.632 22.85 0.00 37.47 2.40
1760 2202 6.463995 TGTAAAGTGAAAAAGGCAAGTCAT 57.536 33.333 0.00 0.00 0.00 3.06
1788 2230 5.705905 CCCCTCAAAAAGTAAGGTGAGTAAG 59.294 44.000 0.00 0.00 36.56 2.34
1821 2263 2.040813 ACCATGCTTTCCTGACACTCAT 59.959 45.455 0.00 0.00 0.00 2.90
1831 2273 7.066766 GCTTTCCTGACACTCATATGATCTTTT 59.933 37.037 5.72 0.00 0.00 2.27
1834 2276 5.587443 CCTGACACTCATATGATCTTTTGCA 59.413 40.000 5.72 0.00 0.00 4.08
1845 2287 3.503363 TGATCTTTTGCACAACTAGCCAG 59.497 43.478 0.00 0.00 0.00 4.85
1874 2316 9.573166 AACTTTGATGATCGATCCCATATTAAA 57.427 29.630 22.31 15.37 0.00 1.52
1892 2334 2.428544 AACTTGTGGGTAGTGCAACA 57.571 45.000 0.00 0.00 41.43 3.33
1896 2338 4.662278 ACTTGTGGGTAGTGCAACATAAT 58.338 39.130 0.00 0.00 41.43 1.28
1916 2358 8.939929 ACATAATAGAGCATACAAAATGATCCG 58.060 33.333 0.00 0.00 35.24 4.18
1935 2377 3.004315 TCCGTTTCAGAAGCATCCAAAAC 59.996 43.478 6.68 6.68 31.79 2.43
1937 2379 4.549458 CGTTTCAGAAGCATCCAAAACAT 58.451 39.130 13.73 0.00 33.39 2.71
1939 2381 5.107760 CGTTTCAGAAGCATCCAAAACATTG 60.108 40.000 13.73 0.00 33.39 2.82
1940 2382 5.787953 TTCAGAAGCATCCAAAACATTGA 57.212 34.783 0.00 0.00 0.00 2.57
1945 2387 5.482878 AGAAGCATCCAAAACATTGAGGAAT 59.517 36.000 0.00 0.00 33.17 3.01
1954 2396 6.205076 CCAAAACATTGAGGAATGCAAAATGA 59.795 34.615 0.00 0.00 42.54 2.57
1955 2397 7.255173 CCAAAACATTGAGGAATGCAAAATGAA 60.255 33.333 0.00 0.00 42.54 2.57
1996 2438 6.267817 TGGAATTTCATTCAATCTTCGCATC 58.732 36.000 0.00 0.00 41.03 3.91
1997 2439 6.127675 TGGAATTTCATTCAATCTTCGCATCA 60.128 34.615 0.00 0.00 41.03 3.07
1998 2440 6.753279 GGAATTTCATTCAATCTTCGCATCAA 59.247 34.615 0.00 0.00 41.03 2.57
1999 2441 7.043590 GGAATTTCATTCAATCTTCGCATCAAG 60.044 37.037 0.00 0.00 41.03 3.02
2000 2442 4.888038 TCATTCAATCTTCGCATCAAGG 57.112 40.909 0.00 0.00 0.00 3.61
2001 2443 4.264253 TCATTCAATCTTCGCATCAAGGT 58.736 39.130 0.00 0.00 0.00 3.50
2002 2444 4.095334 TCATTCAATCTTCGCATCAAGGTG 59.905 41.667 0.00 0.00 0.00 4.00
2003 2445 2.358957 TCAATCTTCGCATCAAGGTGG 58.641 47.619 0.00 0.00 0.00 4.61
2004 2446 2.086869 CAATCTTCGCATCAAGGTGGT 58.913 47.619 0.00 0.00 0.00 4.16
2005 2447 3.055458 TCAATCTTCGCATCAAGGTGGTA 60.055 43.478 0.00 0.00 0.00 3.25
2006 2448 2.380084 TCTTCGCATCAAGGTGGTAC 57.620 50.000 0.00 0.00 0.00 3.34
2007 2449 1.621317 TCTTCGCATCAAGGTGGTACA 59.379 47.619 0.00 0.00 0.00 2.90
2008 2450 2.037902 TCTTCGCATCAAGGTGGTACAA 59.962 45.455 0.00 0.00 44.16 2.41
2019 2461 2.129620 TGGTACAACCACAGCGAGT 58.870 52.632 0.00 0.00 44.79 4.18
2020 2462 0.249699 TGGTACAACCACAGCGAGTG 60.250 55.000 5.48 5.48 44.79 3.51
2027 2469 2.639286 CACAGCGAGTGCAAACCC 59.361 61.111 0.00 0.00 46.23 4.11
2028 2470 2.186160 CACAGCGAGTGCAAACCCA 61.186 57.895 0.00 0.00 46.23 4.51
2029 2471 1.893808 ACAGCGAGTGCAAACCCAG 60.894 57.895 0.00 0.00 46.23 4.45
2030 2472 2.980233 AGCGAGTGCAAACCCAGC 60.980 61.111 0.00 0.00 46.23 4.85
2031 2473 3.286751 GCGAGTGCAAACCCAGCA 61.287 61.111 0.00 0.00 42.15 4.41
2032 2474 2.629656 GCGAGTGCAAACCCAGCAT 61.630 57.895 0.00 0.00 44.79 3.79
2033 2475 1.959085 CGAGTGCAAACCCAGCATT 59.041 52.632 0.00 0.00 44.79 3.56
2034 2476 0.314935 CGAGTGCAAACCCAGCATTT 59.685 50.000 0.00 0.00 44.79 2.32
2035 2477 1.787012 GAGTGCAAACCCAGCATTTG 58.213 50.000 0.00 0.00 44.79 2.32
2040 2482 2.172851 CAAACCCAGCATTTGCATGT 57.827 45.000 5.20 0.00 45.16 3.21
2041 2483 2.070783 CAAACCCAGCATTTGCATGTC 58.929 47.619 5.20 0.00 45.16 3.06
2042 2484 0.609662 AACCCAGCATTTGCATGTCC 59.390 50.000 5.20 0.00 45.16 4.02
2043 2485 0.542467 ACCCAGCATTTGCATGTCCA 60.542 50.000 5.20 0.00 45.16 4.02
2044 2486 0.108520 CCCAGCATTTGCATGTCCAC 60.109 55.000 5.20 0.00 45.16 4.02
2045 2487 0.892755 CCAGCATTTGCATGTCCACT 59.107 50.000 5.20 0.00 45.16 4.00
2046 2488 1.403647 CCAGCATTTGCATGTCCACTG 60.404 52.381 5.20 0.00 45.16 3.66
2047 2489 0.245539 AGCATTTGCATGTCCACTGC 59.754 50.000 5.20 0.00 45.16 4.40
2048 2490 0.245539 GCATTTGCATGTCCACTGCT 59.754 50.000 0.00 0.00 40.34 4.24
2049 2491 1.734707 GCATTTGCATGTCCACTGCTC 60.735 52.381 0.00 0.00 40.34 4.26
2050 2492 1.542472 CATTTGCATGTCCACTGCTCA 59.458 47.619 0.00 0.00 40.34 4.26
2051 2493 1.689984 TTTGCATGTCCACTGCTCAA 58.310 45.000 0.00 0.00 40.34 3.02
2052 2494 1.913778 TTGCATGTCCACTGCTCAAT 58.086 45.000 0.00 0.00 40.34 2.57
2053 2495 1.170442 TGCATGTCCACTGCTCAATG 58.830 50.000 0.00 0.00 40.34 2.82
2054 2496 0.179145 GCATGTCCACTGCTCAATGC 60.179 55.000 0.00 0.00 43.25 3.56
2055 2497 0.098200 CATGTCCACTGCTCAATGCG 59.902 55.000 0.00 0.00 46.63 4.73
2056 2498 1.651240 ATGTCCACTGCTCAATGCGC 61.651 55.000 0.00 0.00 46.63 6.09
2057 2499 2.747460 TCCACTGCTCAATGCGCC 60.747 61.111 4.18 0.00 46.63 6.53
2058 2500 4.170062 CCACTGCTCAATGCGCCG 62.170 66.667 4.18 0.00 46.63 6.46
2059 2501 4.170062 CACTGCTCAATGCGCCGG 62.170 66.667 4.18 0.00 46.63 6.13
2060 2502 4.393155 ACTGCTCAATGCGCCGGA 62.393 61.111 5.05 0.00 46.63 5.14
2061 2503 3.126879 CTGCTCAATGCGCCGGAA 61.127 61.111 5.05 0.00 46.63 4.30
2062 2504 2.671276 TGCTCAATGCGCCGGAAA 60.671 55.556 5.05 0.00 46.63 3.13
2063 2505 2.198906 CTGCTCAATGCGCCGGAAAA 62.199 55.000 5.05 0.00 46.63 2.29
2064 2506 1.080839 GCTCAATGCGCCGGAAAAA 60.081 52.632 5.05 0.00 0.00 1.94
2084 2526 5.957910 AAAAACACGAAATCAATTGCGAA 57.042 30.435 10.02 0.00 41.31 4.70
2085 2527 6.523676 AAAAACACGAAATCAATTGCGAAT 57.476 29.167 10.02 0.00 41.31 3.34
2086 2528 5.499268 AAACACGAAATCAATTGCGAATG 57.501 34.783 10.02 1.74 41.31 2.67
2087 2529 2.916716 ACACGAAATCAATTGCGAATGC 59.083 40.909 10.02 0.00 41.31 3.56
2100 2542 3.559238 GCGAATGCAAAGAAAGGAAGA 57.441 42.857 0.00 0.00 42.15 2.87
2101 2543 3.496155 GCGAATGCAAAGAAAGGAAGAG 58.504 45.455 0.00 0.00 42.15 2.85
2102 2544 3.189287 GCGAATGCAAAGAAAGGAAGAGA 59.811 43.478 0.00 0.00 42.15 3.10
2103 2545 4.142513 GCGAATGCAAAGAAAGGAAGAGAT 60.143 41.667 0.00 0.00 42.15 2.75
2104 2546 5.065218 GCGAATGCAAAGAAAGGAAGAGATA 59.935 40.000 0.00 0.00 42.15 1.98
2105 2547 6.403636 GCGAATGCAAAGAAAGGAAGAGATAA 60.404 38.462 0.00 0.00 42.15 1.75
2106 2548 7.680588 GCGAATGCAAAGAAAGGAAGAGATAAT 60.681 37.037 0.00 0.00 42.15 1.28
2107 2549 7.642978 CGAATGCAAAGAAAGGAAGAGATAATG 59.357 37.037 0.00 0.00 0.00 1.90
2108 2550 6.199937 TGCAAAGAAAGGAAGAGATAATGC 57.800 37.500 0.00 0.00 0.00 3.56
2109 2551 5.126061 TGCAAAGAAAGGAAGAGATAATGCC 59.874 40.000 0.00 0.00 0.00 4.40
2110 2552 5.126061 GCAAAGAAAGGAAGAGATAATGCCA 59.874 40.000 0.00 0.00 0.00 4.92
2111 2553 6.183360 GCAAAGAAAGGAAGAGATAATGCCAT 60.183 38.462 0.00 0.00 0.00 4.40
2112 2554 7.424001 CAAAGAAAGGAAGAGATAATGCCATC 58.576 38.462 0.00 0.00 0.00 3.51
2113 2555 5.303971 AGAAAGGAAGAGATAATGCCATCG 58.696 41.667 0.00 0.00 0.00 3.84
2114 2556 3.051081 AGGAAGAGATAATGCCATCGC 57.949 47.619 0.00 0.00 0.00 4.58
2115 2557 1.728971 GGAAGAGATAATGCCATCGCG 59.271 52.381 0.00 0.00 38.08 5.87
2116 2558 1.728971 GAAGAGATAATGCCATCGCGG 59.271 52.381 6.13 0.00 38.08 6.46
2128 2570 3.201726 CCATCGCGGCCATTAATTAAG 57.798 47.619 6.13 0.00 0.00 1.85
2129 2571 2.811431 CCATCGCGGCCATTAATTAAGA 59.189 45.455 6.13 0.00 0.00 2.10
2130 2572 3.120199 CCATCGCGGCCATTAATTAAGAG 60.120 47.826 6.13 0.00 0.00 2.85
2131 2573 3.188159 TCGCGGCCATTAATTAAGAGT 57.812 42.857 6.13 0.00 0.00 3.24
2132 2574 2.869801 TCGCGGCCATTAATTAAGAGTG 59.130 45.455 6.13 0.00 0.00 3.51
2133 2575 2.869801 CGCGGCCATTAATTAAGAGTGA 59.130 45.455 2.24 0.00 0.00 3.41
2134 2576 3.303132 CGCGGCCATTAATTAAGAGTGAC 60.303 47.826 2.24 0.00 0.00 3.67
2135 2577 3.625764 GCGGCCATTAATTAAGAGTGACA 59.374 43.478 2.24 0.00 0.00 3.58
2136 2578 4.275936 GCGGCCATTAATTAAGAGTGACAT 59.724 41.667 2.24 0.00 0.00 3.06
2137 2579 5.560953 GCGGCCATTAATTAAGAGTGACATC 60.561 44.000 2.24 0.00 0.00 3.06
2138 2580 5.527214 CGGCCATTAATTAAGAGTGACATCA 59.473 40.000 2.24 0.00 0.00 3.07
2139 2581 6.038161 CGGCCATTAATTAAGAGTGACATCAA 59.962 38.462 2.24 0.00 0.00 2.57
2140 2582 7.420800 GGCCATTAATTAAGAGTGACATCAAG 58.579 38.462 0.00 0.00 0.00 3.02
2141 2583 7.067494 GGCCATTAATTAAGAGTGACATCAAGT 59.933 37.037 0.00 0.00 0.00 3.16
2142 2584 8.462016 GCCATTAATTAAGAGTGACATCAAGTT 58.538 33.333 3.94 0.00 0.00 2.66
2172 2614 6.662414 TTTGAAACCAGATTCTATAGTGCG 57.338 37.500 0.00 0.00 0.00 5.34
2173 2615 5.592104 TGAAACCAGATTCTATAGTGCGA 57.408 39.130 0.00 0.00 0.00 5.10
2174 2616 6.161855 TGAAACCAGATTCTATAGTGCGAT 57.838 37.500 0.00 0.00 0.00 4.58
2175 2617 7.284919 TGAAACCAGATTCTATAGTGCGATA 57.715 36.000 0.00 0.00 0.00 2.92
2176 2618 7.896811 TGAAACCAGATTCTATAGTGCGATAT 58.103 34.615 0.00 0.00 0.00 1.63
2177 2619 8.367911 TGAAACCAGATTCTATAGTGCGATATT 58.632 33.333 0.00 0.00 0.00 1.28
2178 2620 8.764524 AAACCAGATTCTATAGTGCGATATTC 57.235 34.615 0.00 0.00 0.00 1.75
2179 2621 7.468141 ACCAGATTCTATAGTGCGATATTCA 57.532 36.000 0.00 0.00 0.00 2.57
2180 2622 8.072321 ACCAGATTCTATAGTGCGATATTCAT 57.928 34.615 0.00 0.00 0.00 2.57
2181 2623 8.535335 ACCAGATTCTATAGTGCGATATTCATT 58.465 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 0.389296 CATGCCGGTAGTGACGTCAA 60.389 55.000 21.95 2.04 0.00 3.18
102 111 2.422597 TGACTAAACAATGCTGGTCCG 58.577 47.619 0.00 0.00 0.00 4.79
112 121 4.258543 GGATCGGACCATTGACTAAACAA 58.741 43.478 0.00 0.00 0.00 2.83
242 253 5.349270 CGAATAGAAACACCGACCAATAACA 59.651 40.000 0.00 0.00 0.00 2.41
248 259 1.066716 CCCGAATAGAAACACCGACCA 60.067 52.381 0.00 0.00 0.00 4.02
249 260 1.648504 CCCGAATAGAAACACCGACC 58.351 55.000 0.00 0.00 0.00 4.79
261 272 1.216977 CTCCACGTGTGCCCGAATA 59.783 57.895 15.65 0.00 0.00 1.75
349 621 6.826231 TCAGTCTGACTTTTACAACCATTTGA 59.174 34.615 7.77 0.00 36.48 2.69
361 633 4.161377 GGGATCTAGCTCAGTCTGACTTTT 59.839 45.833 7.77 0.00 0.00 2.27
406 678 7.289549 AGAGTTAGTTTGTGGTTAGTCCTTAGT 59.710 37.037 0.00 0.00 37.07 2.24
407 679 7.668492 AGAGTTAGTTTGTGGTTAGTCCTTAG 58.332 38.462 0.00 0.00 37.07 2.18
408 680 7.607615 AGAGTTAGTTTGTGGTTAGTCCTTA 57.392 36.000 0.00 0.00 37.07 2.69
409 681 6.496144 AGAGTTAGTTTGTGGTTAGTCCTT 57.504 37.500 0.00 0.00 37.07 3.36
410 682 6.496144 AAGAGTTAGTTTGTGGTTAGTCCT 57.504 37.500 0.00 0.00 37.07 3.85
411 683 8.667076 TTAAAGAGTTAGTTTGTGGTTAGTCC 57.333 34.615 0.00 0.00 0.00 3.85
413 685 9.063615 CCATTAAAGAGTTAGTTTGTGGTTAGT 57.936 33.333 0.00 0.00 0.00 2.24
426 698 3.906720 AGGCTCGCCATTAAAGAGTTA 57.093 42.857 11.02 0.00 38.92 2.24
440 712 3.077359 AGGTCAAATTTCAGAAGGCTCG 58.923 45.455 0.00 0.00 0.00 5.03
453 725 6.944290 TGTGAATCATCTCAAGAAGGTCAAAT 59.056 34.615 0.00 0.00 0.00 2.32
523 878 8.134895 CAGTCAAAACCAGCAGTAAAATCTTAA 58.865 33.333 0.00 0.00 0.00 1.85
537 892 2.989840 CGCTCTCTACAGTCAAAACCAG 59.010 50.000 0.00 0.00 0.00 4.00
544 899 0.898326 TTGCCCGCTCTCTACAGTCA 60.898 55.000 0.00 0.00 0.00 3.41
549 904 1.666189 GACAAATTGCCCGCTCTCTAC 59.334 52.381 0.00 0.00 0.00 2.59
663 1018 3.251972 CAGAGTGGAAAAAGAGTGGCTTC 59.748 47.826 0.00 0.00 35.24 3.86
674 1029 4.012374 GGCATCTCAATCAGAGTGGAAAA 58.988 43.478 0.00 0.00 44.98 2.29
675 1030 3.009363 TGGCATCTCAATCAGAGTGGAAA 59.991 43.478 0.00 0.00 44.98 3.13
676 1031 2.573009 TGGCATCTCAATCAGAGTGGAA 59.427 45.455 0.00 0.00 44.98 3.53
677 1032 2.190538 TGGCATCTCAATCAGAGTGGA 58.809 47.619 0.00 0.00 44.98 4.02
678 1033 2.704464 TGGCATCTCAATCAGAGTGG 57.296 50.000 0.00 0.00 44.98 4.00
696 1051 3.129988 GGAGGAAGCAACCAATCAGATTG 59.870 47.826 15.40 15.40 39.94 2.67
697 1052 3.359950 GGAGGAAGCAACCAATCAGATT 58.640 45.455 0.00 0.00 0.00 2.40
698 1053 2.357569 GGGAGGAAGCAACCAATCAGAT 60.358 50.000 2.26 0.00 0.00 2.90
699 1054 1.004745 GGGAGGAAGCAACCAATCAGA 59.995 52.381 2.26 0.00 0.00 3.27
700 1055 1.005215 AGGGAGGAAGCAACCAATCAG 59.995 52.381 2.26 0.00 0.00 2.90
701 1056 1.004745 GAGGGAGGAAGCAACCAATCA 59.995 52.381 2.26 0.00 0.00 2.57
716 1071 2.649742 ATTCTGTGGAAGAGGAGGGA 57.350 50.000 0.00 0.00 35.91 4.20
828 1184 7.814693 ATTATCCCTTATGTATGTACTGCCT 57.185 36.000 0.00 0.00 0.00 4.75
840 1196 7.880160 TCCTTGTTGTGAATTATCCCTTATG 57.120 36.000 0.00 0.00 0.00 1.90
846 1202 6.773976 TTCCATCCTTGTTGTGAATTATCC 57.226 37.500 0.00 0.00 0.00 2.59
907 1263 3.912909 GCTACAGCTATGCTTCTAGAGCG 60.913 52.174 8.88 0.00 45.67 5.03
908 1264 3.574614 GCTACAGCTATGCTTCTAGAGC 58.425 50.000 7.10 7.10 44.20 4.09
953 1309 9.021807 GTTCTTTGGGATGATGATGATGATAAT 57.978 33.333 0.00 0.00 0.00 1.28
954 1310 8.222637 AGTTCTTTGGGATGATGATGATGATAA 58.777 33.333 0.00 0.00 0.00 1.75
955 1311 7.752638 AGTTCTTTGGGATGATGATGATGATA 58.247 34.615 0.00 0.00 0.00 2.15
956 1312 6.611785 AGTTCTTTGGGATGATGATGATGAT 58.388 36.000 0.00 0.00 0.00 2.45
957 1313 6.009908 AGTTCTTTGGGATGATGATGATGA 57.990 37.500 0.00 0.00 0.00 2.92
958 1314 7.222161 TCTAGTTCTTTGGGATGATGATGATG 58.778 38.462 0.00 0.00 0.00 3.07
959 1315 7.384524 TCTAGTTCTTTGGGATGATGATGAT 57.615 36.000 0.00 0.00 0.00 2.45
960 1316 6.813293 TCTAGTTCTTTGGGATGATGATGA 57.187 37.500 0.00 0.00 0.00 2.92
961 1317 7.278135 TCTTCTAGTTCTTTGGGATGATGATG 58.722 38.462 0.00 0.00 0.00 3.07
962 1318 7.346698 TCTCTTCTAGTTCTTTGGGATGATGAT 59.653 37.037 0.00 0.00 0.00 2.45
963 1319 6.669591 TCTCTTCTAGTTCTTTGGGATGATGA 59.330 38.462 0.00 0.00 0.00 2.92
964 1320 6.882656 TCTCTTCTAGTTCTTTGGGATGATG 58.117 40.000 0.00 0.00 0.00 3.07
978 1334 7.178274 TGCATCTTCTTCTTCTTCTCTTCTAGT 59.822 37.037 0.00 0.00 0.00 2.57
979 1335 7.546358 TGCATCTTCTTCTTCTTCTCTTCTAG 58.454 38.462 0.00 0.00 0.00 2.43
981 1337 6.357579 TGCATCTTCTTCTTCTTCTCTTCT 57.642 37.500 0.00 0.00 0.00 2.85
1012 1411 0.616111 AAGGAGATGAGCACCGGACT 60.616 55.000 9.46 4.56 31.80 3.85
1048 1447 1.142688 AAGACAAGCCCTGGGGACAT 61.143 55.000 16.03 0.00 41.51 3.06
1068 1467 0.464373 GCGATTTGCCAGGGATCTGA 60.464 55.000 0.00 0.00 43.49 3.27
1116 1515 1.177401 TGAGGATGGAGACGACACTG 58.823 55.000 0.00 0.00 0.00 3.66
1119 1518 1.341976 TGGATGAGGATGGAGACGACA 60.342 52.381 0.00 0.00 0.00 4.35
1226 1625 6.015856 GCTAGAACAGGATGAAGCAGAGTATA 60.016 42.308 0.00 0.00 39.69 1.47
1275 1677 3.825143 AACAAGCAGCAAGAACCAAAT 57.175 38.095 0.00 0.00 0.00 2.32
1305 1707 2.097036 CAGCAATGATTGAGCCCAGAA 58.903 47.619 9.76 0.00 0.00 3.02
1306 1708 1.282738 TCAGCAATGATTGAGCCCAGA 59.717 47.619 9.76 0.00 0.00 3.86
1316 1729 3.074094 ACATATCCCAGCTCAGCAATGAT 59.926 43.478 0.00 0.00 0.00 2.45
1327 1740 3.149196 CCACCATGTAACATATCCCAGC 58.851 50.000 0.00 0.00 0.00 4.85
1432 1871 6.045955 GGTGAGAGTGAGGATATTTGTTCTC 58.954 44.000 0.00 0.00 0.00 2.87
1433 1872 5.394663 CGGTGAGAGTGAGGATATTTGTTCT 60.395 44.000 0.00 0.00 0.00 3.01
1434 1873 4.806247 CGGTGAGAGTGAGGATATTTGTTC 59.194 45.833 0.00 0.00 0.00 3.18
1435 1874 4.223032 ACGGTGAGAGTGAGGATATTTGTT 59.777 41.667 0.00 0.00 0.00 2.83
1436 1875 3.769844 ACGGTGAGAGTGAGGATATTTGT 59.230 43.478 0.00 0.00 0.00 2.83
1437 1876 4.098654 AGACGGTGAGAGTGAGGATATTTG 59.901 45.833 0.00 0.00 0.00 2.32
1438 1877 4.282496 AGACGGTGAGAGTGAGGATATTT 58.718 43.478 0.00 0.00 0.00 1.40
1439 1878 3.886505 GAGACGGTGAGAGTGAGGATATT 59.113 47.826 0.00 0.00 0.00 1.28
1440 1879 3.137544 AGAGACGGTGAGAGTGAGGATAT 59.862 47.826 0.00 0.00 0.00 1.63
1441 1880 2.506231 AGAGACGGTGAGAGTGAGGATA 59.494 50.000 0.00 0.00 0.00 2.59
1442 1881 1.283613 AGAGACGGTGAGAGTGAGGAT 59.716 52.381 0.00 0.00 0.00 3.24
1443 1882 0.693622 AGAGACGGTGAGAGTGAGGA 59.306 55.000 0.00 0.00 0.00 3.71
1444 1883 0.808125 CAGAGACGGTGAGAGTGAGG 59.192 60.000 0.00 0.00 0.00 3.86
1445 1884 0.170116 GCAGAGACGGTGAGAGTGAG 59.830 60.000 0.00 0.00 0.00 3.51
1446 1885 0.537371 TGCAGAGACGGTGAGAGTGA 60.537 55.000 0.00 0.00 0.00 3.41
1447 1886 0.529833 ATGCAGAGACGGTGAGAGTG 59.470 55.000 0.00 0.00 0.00 3.51
1448 1887 0.529833 CATGCAGAGACGGTGAGAGT 59.470 55.000 0.00 0.00 0.00 3.24
1449 1888 0.529833 ACATGCAGAGACGGTGAGAG 59.470 55.000 0.00 0.00 0.00 3.20
1450 1889 0.528017 GACATGCAGAGACGGTGAGA 59.472 55.000 0.00 0.00 0.00 3.27
1451 1890 0.529833 AGACATGCAGAGACGGTGAG 59.470 55.000 0.00 0.00 0.00 3.51
1452 1891 0.244721 CAGACATGCAGAGACGGTGA 59.755 55.000 0.00 0.00 0.00 4.02
1453 1892 0.037882 ACAGACATGCAGAGACGGTG 60.038 55.000 0.00 0.00 0.00 4.94
1454 1893 0.244994 GACAGACATGCAGAGACGGT 59.755 55.000 0.00 0.00 0.00 4.83
1455 1894 0.244721 TGACAGACATGCAGAGACGG 59.755 55.000 0.00 0.00 0.00 4.79
1456 1895 2.191802 GATGACAGACATGCAGAGACG 58.808 52.381 0.00 0.00 39.56 4.18
1457 1896 3.188492 CTGATGACAGACATGCAGAGAC 58.812 50.000 0.00 0.00 46.03 3.36
1458 1897 2.418334 GCTGATGACAGACATGCAGAGA 60.418 50.000 12.79 0.00 46.03 3.10
1459 1898 1.934525 GCTGATGACAGACATGCAGAG 59.065 52.381 12.79 0.00 46.03 3.35
1460 1899 1.276989 TGCTGATGACAGACATGCAGA 59.723 47.619 12.79 1.65 46.03 4.26
1461 1900 1.734163 TGCTGATGACAGACATGCAG 58.266 50.000 0.00 0.00 46.03 4.41
1462 1901 2.188062 TTGCTGATGACAGACATGCA 57.812 45.000 0.00 0.00 46.03 3.96
1463 1902 2.486982 AGTTTGCTGATGACAGACATGC 59.513 45.455 0.00 0.00 46.03 4.06
1532 1971 1.073216 GAGCATGACACCACTCGTCG 61.073 60.000 0.00 0.00 36.11 5.12
1540 1979 1.672881 GCATTGGTAGAGCATGACACC 59.327 52.381 0.00 0.00 0.00 4.16
1546 1985 2.742428 ACATGGCATTGGTAGAGCAT 57.258 45.000 0.00 0.00 0.00 3.79
1559 1998 5.059833 CCTAAGGTGATAAGAGAACATGGC 58.940 45.833 0.00 0.00 0.00 4.40
1563 2002 7.159372 GTGTTTCCTAAGGTGATAAGAGAACA 58.841 38.462 0.00 0.00 0.00 3.18
1576 2015 5.163693 ACGAACTTTGTTGTGTTTCCTAAGG 60.164 40.000 0.00 0.00 0.00 2.69
1582 2021 4.477780 TGGAACGAACTTTGTTGTGTTTC 58.522 39.130 0.00 0.00 0.00 2.78
1619 2061 8.760569 GCTTGAGATAGACAAGATTAGTAAAGC 58.239 37.037 11.08 0.00 44.92 3.51
1630 2072 4.462508 TCTGTGGCTTGAGATAGACAAG 57.537 45.455 0.00 0.00 44.92 3.16
1636 2078 3.055819 GTGGTCTTCTGTGGCTTGAGATA 60.056 47.826 0.00 0.00 0.00 1.98
1655 2097 5.109903 GGTTGTGTAGAGCTAAGTATGTGG 58.890 45.833 0.00 0.00 0.00 4.17
1657 2099 4.461781 ACGGTTGTGTAGAGCTAAGTATGT 59.538 41.667 0.00 0.00 0.00 2.29
1683 2125 1.747745 GGCCGGCGTATGGAACTTT 60.748 57.895 22.54 0.00 0.00 2.66
1695 2137 0.948678 TATTCTTTATTGCGGCCGGC 59.051 50.000 29.38 21.18 43.96 6.13
1696 2138 3.701532 TTTATTCTTTATTGCGGCCGG 57.298 42.857 29.38 8.29 0.00 6.13
1734 2176 5.049828 ACTTGCCTTTTTCACTTTACATGC 58.950 37.500 0.00 0.00 0.00 4.06
1760 2202 5.520751 TCACCTTACTTTTTGAGGGGAAAA 58.479 37.500 0.00 0.00 39.94 2.29
1788 2230 8.097038 TCAGGAAAGCATGGTACTTGATATATC 58.903 37.037 5.73 5.73 0.00 1.63
1821 2263 5.252547 TGGCTAGTTGTGCAAAAGATCATA 58.747 37.500 0.00 0.00 0.00 2.15
1831 2273 1.150308 TTGCCTGGCTAGTTGTGCA 59.850 52.632 21.03 0.00 0.00 4.57
1834 2276 1.956477 CAAAGTTGCCTGGCTAGTTGT 59.044 47.619 21.03 10.48 28.70 3.32
1845 2287 2.291741 GGGATCGATCATCAAAGTTGCC 59.708 50.000 25.93 10.51 32.33 4.52
1857 2299 7.133891 CCACAAGTTTAATATGGGATCGATC 57.866 40.000 17.36 17.36 0.00 3.69
1874 2316 2.656947 ATGTTGCACTACCCACAAGT 57.343 45.000 0.00 0.00 0.00 3.16
1892 2334 9.507329 AACGGATCATTTTGTATGCTCTATTAT 57.493 29.630 0.00 0.00 0.00 1.28
1896 2338 6.821160 TGAAACGGATCATTTTGTATGCTCTA 59.179 34.615 0.00 0.00 0.00 2.43
1916 2358 5.984926 TCAATGTTTTGGATGCTTCTGAAAC 59.015 36.000 16.76 16.76 33.44 2.78
1935 2377 7.661127 TCTTTTCATTTTGCATTCCTCAATG 57.339 32.000 0.00 0.00 42.26 2.82
1937 2379 8.680039 AAATCTTTTCATTTTGCATTCCTCAA 57.320 26.923 0.00 0.00 0.00 3.02
2002 2444 1.566018 GCACTCGCTGTGGTTGTACC 61.566 60.000 9.71 0.00 46.27 3.34
2003 2445 0.878523 TGCACTCGCTGTGGTTGTAC 60.879 55.000 9.71 0.00 46.27 2.90
2004 2446 0.179070 TTGCACTCGCTGTGGTTGTA 60.179 50.000 9.71 0.00 46.27 2.41
2005 2447 1.029408 TTTGCACTCGCTGTGGTTGT 61.029 50.000 9.71 0.00 46.27 3.32
2006 2448 0.592247 GTTTGCACTCGCTGTGGTTG 60.592 55.000 9.71 0.00 46.27 3.77
2007 2449 1.724582 GGTTTGCACTCGCTGTGGTT 61.725 55.000 9.71 0.00 46.27 3.67
2008 2450 2.186826 GGTTTGCACTCGCTGTGGT 61.187 57.895 9.71 0.00 46.27 4.16
2009 2451 2.639286 GGTTTGCACTCGCTGTGG 59.361 61.111 9.71 0.00 46.27 4.17
2011 2453 1.893808 CTGGGTTTGCACTCGCTGT 60.894 57.895 0.00 0.00 39.64 4.40
2012 2454 2.949106 CTGGGTTTGCACTCGCTG 59.051 61.111 0.00 0.00 39.64 5.18
2013 2455 2.980233 GCTGGGTTTGCACTCGCT 60.980 61.111 0.00 0.00 39.64 4.93
2014 2456 2.146073 AATGCTGGGTTTGCACTCGC 62.146 55.000 0.00 0.00 43.59 5.03
2015 2457 0.314935 AAATGCTGGGTTTGCACTCG 59.685 50.000 0.00 0.00 43.59 4.18
2016 2458 1.787012 CAAATGCTGGGTTTGCACTC 58.213 50.000 0.00 0.00 43.59 3.51
2017 2459 3.993382 CAAATGCTGGGTTTGCACT 57.007 47.368 0.00 0.00 43.59 4.40
2021 2463 2.070783 GACATGCAAATGCTGGGTTTG 58.929 47.619 6.97 0.00 42.66 2.93
2022 2464 1.002315 GGACATGCAAATGCTGGGTTT 59.998 47.619 6.97 0.00 42.66 3.27
2023 2465 0.609662 GGACATGCAAATGCTGGGTT 59.390 50.000 6.97 0.00 42.66 4.11
2024 2466 0.542467 TGGACATGCAAATGCTGGGT 60.542 50.000 6.97 2.25 42.66 4.51
2025 2467 0.108520 GTGGACATGCAAATGCTGGG 60.109 55.000 6.97 0.00 42.66 4.45
2026 2468 0.892755 AGTGGACATGCAAATGCTGG 59.107 50.000 6.97 1.47 42.66 4.85
2027 2469 1.990799 CAGTGGACATGCAAATGCTG 58.009 50.000 6.97 5.31 42.66 4.41
2028 2470 0.245539 GCAGTGGACATGCAAATGCT 59.754 50.000 6.97 0.00 43.31 3.79
2029 2471 0.245539 AGCAGTGGACATGCAAATGC 59.754 50.000 8.34 8.34 46.31 3.56
2030 2472 1.542472 TGAGCAGTGGACATGCAAATG 59.458 47.619 0.00 0.00 46.31 2.32
2031 2473 1.913778 TGAGCAGTGGACATGCAAAT 58.086 45.000 0.00 0.00 46.31 2.32
2032 2474 1.689984 TTGAGCAGTGGACATGCAAA 58.310 45.000 0.00 0.00 46.31 3.68
2033 2475 1.542472 CATTGAGCAGTGGACATGCAA 59.458 47.619 0.00 0.00 46.31 4.08
2034 2476 1.170442 CATTGAGCAGTGGACATGCA 58.830 50.000 0.00 0.00 46.31 3.96
2035 2477 0.179145 GCATTGAGCAGTGGACATGC 60.179 55.000 0.00 0.00 44.79 4.06
2036 2478 0.098200 CGCATTGAGCAGTGGACATG 59.902 55.000 0.00 0.00 46.13 3.21
2037 2479 1.651240 GCGCATTGAGCAGTGGACAT 61.651 55.000 0.30 0.00 46.13 3.06
2038 2480 2.327343 GCGCATTGAGCAGTGGACA 61.327 57.895 0.30 0.00 46.13 4.02
2039 2481 2.482374 GCGCATTGAGCAGTGGAC 59.518 61.111 0.30 0.00 46.13 4.02
2040 2482 2.747460 GGCGCATTGAGCAGTGGA 60.747 61.111 10.83 0.00 46.13 4.02
2041 2483 4.170062 CGGCGCATTGAGCAGTGG 62.170 66.667 10.83 0.00 46.13 4.00
2042 2484 4.170062 CCGGCGCATTGAGCAGTG 62.170 66.667 10.83 3.49 46.13 3.66
2043 2485 3.899981 TTCCGGCGCATTGAGCAGT 62.900 57.895 10.83 0.00 46.13 4.40
2044 2486 2.198906 TTTTCCGGCGCATTGAGCAG 62.199 55.000 10.83 9.98 46.13 4.24
2045 2487 1.800283 TTTTTCCGGCGCATTGAGCA 61.800 50.000 10.83 0.00 46.13 4.26
2046 2488 1.080839 TTTTTCCGGCGCATTGAGC 60.081 52.632 10.83 3.53 40.87 4.26
2062 2504 5.957910 TTCGCAATTGATTTCGTGTTTTT 57.042 30.435 10.34 0.00 0.00 1.94
2063 2505 5.612276 GCATTCGCAATTGATTTCGTGTTTT 60.612 36.000 10.34 0.00 38.36 2.43
2064 2506 4.143347 GCATTCGCAATTGATTTCGTGTTT 60.143 37.500 10.34 0.00 38.36 2.83
2065 2507 3.364621 GCATTCGCAATTGATTTCGTGTT 59.635 39.130 10.34 0.00 38.36 3.32
2066 2508 2.916716 GCATTCGCAATTGATTTCGTGT 59.083 40.909 10.34 0.00 38.36 4.49
2067 2509 3.541792 GCATTCGCAATTGATTTCGTG 57.458 42.857 10.34 0.00 38.36 4.35
2080 2522 3.189287 TCTCTTCCTTTCTTTGCATTCGC 59.811 43.478 0.00 0.00 39.24 4.70
2081 2523 5.557891 ATCTCTTCCTTTCTTTGCATTCG 57.442 39.130 0.00 0.00 0.00 3.34
2082 2524 7.434602 GCATTATCTCTTCCTTTCTTTGCATTC 59.565 37.037 0.00 0.00 0.00 2.67
2083 2525 7.263496 GCATTATCTCTTCCTTTCTTTGCATT 58.737 34.615 0.00 0.00 0.00 3.56
2084 2526 6.183360 GGCATTATCTCTTCCTTTCTTTGCAT 60.183 38.462 0.00 0.00 0.00 3.96
2085 2527 5.126061 GGCATTATCTCTTCCTTTCTTTGCA 59.874 40.000 0.00 0.00 0.00 4.08
2086 2528 5.126061 TGGCATTATCTCTTCCTTTCTTTGC 59.874 40.000 0.00 0.00 0.00 3.68
2087 2529 6.764308 TGGCATTATCTCTTCCTTTCTTTG 57.236 37.500 0.00 0.00 0.00 2.77
2088 2530 6.261826 CGATGGCATTATCTCTTCCTTTCTTT 59.738 38.462 0.00 0.00 0.00 2.52
2089 2531 5.762218 CGATGGCATTATCTCTTCCTTTCTT 59.238 40.000 0.00 0.00 0.00 2.52
2090 2532 5.303971 CGATGGCATTATCTCTTCCTTTCT 58.696 41.667 0.00 0.00 0.00 2.52
2091 2533 4.083590 GCGATGGCATTATCTCTTCCTTTC 60.084 45.833 0.00 0.00 39.62 2.62
2092 2534 3.817647 GCGATGGCATTATCTCTTCCTTT 59.182 43.478 0.00 0.00 39.62 3.11
2093 2535 3.406764 GCGATGGCATTATCTCTTCCTT 58.593 45.455 0.00 0.00 39.62 3.36
2094 2536 2.611473 CGCGATGGCATTATCTCTTCCT 60.611 50.000 0.00 0.00 39.92 3.36
2095 2537 1.728971 CGCGATGGCATTATCTCTTCC 59.271 52.381 0.00 0.00 39.92 3.46
2096 2538 1.728971 CCGCGATGGCATTATCTCTTC 59.271 52.381 8.23 0.00 39.92 2.87
2097 2539 1.800805 CCGCGATGGCATTATCTCTT 58.199 50.000 8.23 0.00 39.92 2.85
2098 2540 3.521995 CCGCGATGGCATTATCTCT 57.478 52.632 8.23 0.00 39.92 3.10
2108 2550 2.811431 TCTTAATTAATGGCCGCGATGG 59.189 45.455 8.23 0.00 42.50 3.51
2109 2551 3.498397 ACTCTTAATTAATGGCCGCGATG 59.502 43.478 8.23 0.00 0.00 3.84
2110 2552 3.498397 CACTCTTAATTAATGGCCGCGAT 59.502 43.478 8.23 0.00 0.00 4.58
2111 2553 2.869801 CACTCTTAATTAATGGCCGCGA 59.130 45.455 8.23 0.00 0.00 5.87
2112 2554 2.869801 TCACTCTTAATTAATGGCCGCG 59.130 45.455 0.00 0.00 0.00 6.46
2113 2555 3.625764 TGTCACTCTTAATTAATGGCCGC 59.374 43.478 0.00 0.00 0.00 6.53
2114 2556 5.527214 TGATGTCACTCTTAATTAATGGCCG 59.473 40.000 0.00 0.00 0.00 6.13
2115 2557 6.942532 TGATGTCACTCTTAATTAATGGCC 57.057 37.500 0.00 0.00 0.00 5.36
2116 2558 7.989826 ACTTGATGTCACTCTTAATTAATGGC 58.010 34.615 0.00 0.00 0.00 4.40
2147 2589 7.389330 TCGCACTATAGAATCTGGTTTCAAAAA 59.611 33.333 6.78 0.00 0.00 1.94
2148 2590 6.876789 TCGCACTATAGAATCTGGTTTCAAAA 59.123 34.615 6.78 0.00 0.00 2.44
2149 2591 6.403049 TCGCACTATAGAATCTGGTTTCAAA 58.597 36.000 6.78 0.00 0.00 2.69
2150 2592 5.972935 TCGCACTATAGAATCTGGTTTCAA 58.027 37.500 6.78 0.00 0.00 2.69
2151 2593 5.592104 TCGCACTATAGAATCTGGTTTCA 57.408 39.130 6.78 0.00 0.00 2.69
2152 2594 8.764524 AATATCGCACTATAGAATCTGGTTTC 57.235 34.615 6.78 0.00 0.00 2.78
2153 2595 8.367911 TGAATATCGCACTATAGAATCTGGTTT 58.632 33.333 6.78 0.00 0.00 3.27
2154 2596 7.896811 TGAATATCGCACTATAGAATCTGGTT 58.103 34.615 6.78 0.00 0.00 3.67
2155 2597 7.468141 TGAATATCGCACTATAGAATCTGGT 57.532 36.000 6.78 0.00 0.00 4.00
2156 2598 8.939201 AATGAATATCGCACTATAGAATCTGG 57.061 34.615 6.78 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.