Multiple sequence alignment - TraesCS4A01G318600

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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 TraesCS4A01G318600 chr4A 100.000 2756 0 0 1 2756 607377184 607379939 0.000000e+00 5090
1 TraesCS4A01G318600 chr4A 99.226 1034 6 2 1 1033 309239388 309240420 0.000000e+00 1864
2 TraesCS4A01G318600 chr6B 99.420 1034 5 1 1 1033 482527809 482528842 0.000000e+00 1875
3 TraesCS4A01G318600 chr3A 99.323 1034 6 1 1 1033 75544441 75543408 0.000000e+00 1869
4 TraesCS4A01G318600 chr3A 99.226 1034 7 1 1 1033 708638266 708637233 0.000000e+00 1864
5 TraesCS4A01G318600 chr2A 99.323 1034 6 1 1 1033 172530428 172531461 0.000000e+00 1869
6 TraesCS4A01G318600 chr2A 92.308 728 53 3 2031 2756 203887961 203887235 0.000000e+00 1031
7 TraesCS4A01G318600 chr1B 99.323 1034 6 1 1 1033 120394702 120393669 0.000000e+00 1869
8 TraesCS4A01G318600 chr7A 99.226 1034 7 1 1 1033 672067421 672068454 0.000000e+00 1864
9 TraesCS4A01G318600 chr7A 99.130 1034 8 1 1 1033 128054113 128055146 0.000000e+00 1858
10 TraesCS4A01G318600 chr5B 99.130 1034 8 1 1 1033 403528090 403527057 0.000000e+00 1858
11 TraesCS4A01G318600 chr5B 89.571 163 12 4 1044 1202 707188354 707188193 4.650000e-48 202
12 TraesCS4A01G318600 chr5B 87.500 120 15 0 1249 1368 707187488 707187369 3.700000e-29 139
13 TraesCS4A01G318600 chr6D 93.973 730 42 2 2029 2756 12026458 12025729 0.000000e+00 1103
14 TraesCS4A01G318600 chr6D 74.348 460 87 18 1243 1688 433605881 433606323 1.700000e-37 167
15 TraesCS4A01G318600 chr5D 93.956 728 43 1 2029 2756 27045002 27045728 0.000000e+00 1099
16 TraesCS4A01G318600 chr5D 92.603 730 51 3 2029 2756 136448106 136447378 0.000000e+00 1046
17 TraesCS4A01G318600 chr5D 91.155 701 38 13 1032 1726 565896512 565897194 0.000000e+00 929
18 TraesCS4A01G318600 chr1D 93.827 729 44 1 2029 2756 26406558 26405830 0.000000e+00 1096
19 TraesCS4A01G318600 chrUn 93.472 720 46 1 2029 2747 100309174 100309893 0.000000e+00 1068
20 TraesCS4A01G318600 chr5A 93.151 730 46 4 2029 2756 684668982 684669709 0.000000e+00 1068
21 TraesCS4A01G318600 chr5A 92.552 725 51 3 2029 2751 398878261 398878984 0.000000e+00 1037
22 TraesCS4A01G318600 chr7D 92.857 728 51 1 2029 2756 436489548 436490274 0.000000e+00 1055
23 TraesCS4A01G318600 chr6A 74.631 339 69 10 1243 1574 579806947 579807275 1.720000e-27 134


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 TraesCS4A01G318600 chr4A 607377184 607379939 2755 False 5090 5090 100.000 1 2756 1 chr4A.!!$F2 2755
1 TraesCS4A01G318600 chr4A 309239388 309240420 1032 False 1864 1864 99.226 1 1033 1 chr4A.!!$F1 1032
2 TraesCS4A01G318600 chr6B 482527809 482528842 1033 False 1875 1875 99.420 1 1033 1 chr6B.!!$F1 1032
3 TraesCS4A01G318600 chr3A 75543408 75544441 1033 True 1869 1869 99.323 1 1033 1 chr3A.!!$R1 1032
4 TraesCS4A01G318600 chr3A 708637233 708638266 1033 True 1864 1864 99.226 1 1033 1 chr3A.!!$R2 1032
5 TraesCS4A01G318600 chr2A 172530428 172531461 1033 False 1869 1869 99.323 1 1033 1 chr2A.!!$F1 1032
6 TraesCS4A01G318600 chr2A 203887235 203887961 726 True 1031 1031 92.308 2031 2756 1 chr2A.!!$R1 725
7 TraesCS4A01G318600 chr1B 120393669 120394702 1033 True 1869 1869 99.323 1 1033 1 chr1B.!!$R1 1032
8 TraesCS4A01G318600 chr7A 672067421 672068454 1033 False 1864 1864 99.226 1 1033 1 chr7A.!!$F2 1032
9 TraesCS4A01G318600 chr7A 128054113 128055146 1033 False 1858 1858 99.130 1 1033 1 chr7A.!!$F1 1032
10 TraesCS4A01G318600 chr5B 403527057 403528090 1033 True 1858 1858 99.130 1 1033 1 chr5B.!!$R1 1032
11 TraesCS4A01G318600 chr6D 12025729 12026458 729 True 1103 1103 93.973 2029 2756 1 chr6D.!!$R1 727
12 TraesCS4A01G318600 chr5D 27045002 27045728 726 False 1099 1099 93.956 2029 2756 1 chr5D.!!$F1 727
13 TraesCS4A01G318600 chr5D 136447378 136448106 728 True 1046 1046 92.603 2029 2756 1 chr5D.!!$R1 727
14 TraesCS4A01G318600 chr5D 565896512 565897194 682 False 929 929 91.155 1032 1726 1 chr5D.!!$F2 694
15 TraesCS4A01G318600 chr1D 26405830 26406558 728 True 1096 1096 93.827 2029 2756 1 chr1D.!!$R1 727
16 TraesCS4A01G318600 chrUn 100309174 100309893 719 False 1068 1068 93.472 2029 2747 1 chrUn.!!$F1 718
17 TraesCS4A01G318600 chr5A 684668982 684669709 727 False 1068 1068 93.151 2029 2756 1 chr5A.!!$F2 727
18 TraesCS4A01G318600 chr5A 398878261 398878984 723 False 1037 1037 92.552 2029 2751 1 chr5A.!!$F1 722
19 TraesCS4A01G318600 chr7D 436489548 436490274 726 False 1055 1055 92.857 2029 2756 1 chr7D.!!$F1 727

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
428 430 1.137675 CCTGAGGATGTGCGATGAAGA 59.862 52.381 0.0 0.0 0.0 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 1881 0.165944 CATCGAACAACCACTTCCGC 59.834 55.0 0.0 0.0 0.0 5.54 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
428 430 1.137675 CCTGAGGATGTGCGATGAAGA 59.862 52.381 0.00 0.00 0.00 2.87
476 478 1.364626 CCCGTAGCTCGTCACGTAGT 61.365 60.000 0.00 0.00 38.90 2.73
946 948 6.766467 GGTGGGATATGAGACGAAAATAAACT 59.234 38.462 0.00 0.00 0.00 2.66
1039 1041 6.071984 TCCATTAGGAGTAGAGATGACCTTC 58.928 44.000 0.00 0.00 39.61 3.46
1042 1044 6.968263 TTAGGAGTAGAGATGACCTTCATG 57.032 41.667 0.00 0.00 37.20 3.07
1043 1045 4.877773 AGGAGTAGAGATGACCTTCATGT 58.122 43.478 0.00 0.00 37.20 3.21
1059 1061 5.755375 CCTTCATGTATCAGCATAAGTTCGT 59.245 40.000 0.00 0.00 0.00 3.85
1167 1170 8.304596 TGTCGTAGTTAAGATTTTGTCATCTCT 58.695 33.333 0.00 0.00 31.87 3.10
1204 1208 1.079750 GTCAAGAGGAGGCCGTGAC 60.080 63.158 0.00 2.07 31.51 3.67
1216 1220 0.958382 GCCGTGACCATTGCCTTGTA 60.958 55.000 0.00 0.00 0.00 2.41
1222 1226 3.058224 GTGACCATTGCCTTGTACACTTC 60.058 47.826 0.00 0.00 0.00 3.01
1223 1227 3.181445 TGACCATTGCCTTGTACACTTCT 60.181 43.478 0.00 0.00 0.00 2.85
1226 1230 3.569701 CCATTGCCTTGTACACTTCTGTT 59.430 43.478 0.00 0.00 0.00 3.16
1232 1236 4.461198 CCTTGTACACTTCTGTTCCCTTT 58.539 43.478 0.00 0.00 0.00 3.11
1233 1237 4.275936 CCTTGTACACTTCTGTTCCCTTTG 59.724 45.833 0.00 0.00 0.00 2.77
1234 1238 4.764050 TGTACACTTCTGTTCCCTTTGA 57.236 40.909 0.00 0.00 0.00 2.69
1235 1239 4.703897 TGTACACTTCTGTTCCCTTTGAG 58.296 43.478 0.00 0.00 0.00 3.02
1236 1240 3.933861 ACACTTCTGTTCCCTTTGAGT 57.066 42.857 0.00 0.00 0.00 3.41
1237 1241 3.809905 ACACTTCTGTTCCCTTTGAGTC 58.190 45.455 0.00 0.00 0.00 3.36
1238 1242 3.142174 CACTTCTGTTCCCTTTGAGTCC 58.858 50.000 0.00 0.00 0.00 3.85
1239 1243 2.106684 ACTTCTGTTCCCTTTGAGTCCC 59.893 50.000 0.00 0.00 0.00 4.46
1240 1244 0.685097 TCTGTTCCCTTTGAGTCCCG 59.315 55.000 0.00 0.00 0.00 5.14
1241 1245 0.396811 CTGTTCCCTTTGAGTCCCGT 59.603 55.000 0.00 0.00 0.00 5.28
1242 1246 1.621814 CTGTTCCCTTTGAGTCCCGTA 59.378 52.381 0.00 0.00 0.00 4.02
1243 1247 2.236395 CTGTTCCCTTTGAGTCCCGTAT 59.764 50.000 0.00 0.00 0.00 3.06
1244 1248 3.443052 TGTTCCCTTTGAGTCCCGTATA 58.557 45.455 0.00 0.00 0.00 1.47
1259 1263 4.767409 TCCCGTATAGAACATCTGATCCAG 59.233 45.833 0.00 0.00 0.00 3.86
1362 1370 4.512571 GCTGGACGGTGTAAGAAACTAAAA 59.487 41.667 0.00 0.00 0.00 1.52
1372 1380 7.918562 GGTGTAAGAAACTAAAATTCTTGTGCA 59.081 33.333 10.82 5.61 44.55 4.57
1375 1383 9.296400 GTAAGAAACTAAAATTCTTGTGCACAA 57.704 29.630 29.36 29.36 44.55 3.33
1379 1387 9.636965 GAAACTAAAATTCTTGTGCACAATTTC 57.363 29.630 31.17 26.23 35.02 2.17
1382 1390 6.981762 AAAATTCTTGTGCACAATTTCACA 57.018 29.167 31.17 8.87 40.98 3.58
1439 1447 9.184062 ACGCATGATTTTGCAAATAATATACAG 57.816 29.630 13.65 3.25 42.91 2.74
1447 1455 7.801716 TTGCAAATAATATACAGGTCACCTC 57.198 36.000 0.00 0.00 0.00 3.85
1459 1467 1.608283 GGTCACCTCGTGGAAGAAAGG 60.608 57.143 11.17 0.00 37.04 3.11
1580 1588 4.876679 GGGATTGTAAGACTAAAGAGGTGC 59.123 45.833 0.00 0.00 0.00 5.01
1599 1607 2.249413 CTCTGGACCGAGCCATGCTT 62.249 60.000 0.00 0.00 39.88 3.91
1601 1609 2.249413 CTGGACCGAGCCATGCTTCT 62.249 60.000 0.00 0.00 39.88 2.85
1613 1621 0.538977 ATGCTTCTGCTGCCTTGTGT 60.539 50.000 0.00 0.00 40.48 3.72
1688 1696 1.603455 TGCAACCCCAAGTGCTAGC 60.603 57.895 8.10 8.10 0.00 3.42
1689 1697 1.303643 GCAACCCCAAGTGCTAGCT 60.304 57.895 17.23 0.00 0.00 3.32
1690 1698 0.035439 GCAACCCCAAGTGCTAGCTA 60.035 55.000 17.23 0.00 0.00 3.32
1691 1699 2.014068 GCAACCCCAAGTGCTAGCTAG 61.014 57.143 16.84 16.84 0.00 3.42
1692 1700 1.555075 CAACCCCAAGTGCTAGCTAGA 59.445 52.381 25.15 6.86 0.00 2.43
1693 1701 2.171448 CAACCCCAAGTGCTAGCTAGAT 59.829 50.000 25.15 6.34 0.00 1.98
1711 1719 5.642491 GCTAGATCTAGAATTGCATGCATGA 59.358 40.000 30.06 10.92 35.21 3.07
1715 1723 6.824196 AGATCTAGAATTGCATGCATGATAGG 59.176 38.462 30.64 11.08 0.00 2.57
1726 1734 6.016024 TGCATGCATGATAGGAAAATTAGGAC 60.016 38.462 30.64 6.47 0.00 3.85
1727 1735 6.016024 GCATGCATGATAGGAAAATTAGGACA 60.016 38.462 30.64 0.00 0.00 4.02
1728 1736 6.942532 TGCATGATAGGAAAATTAGGACAC 57.057 37.500 0.00 0.00 0.00 3.67
1729 1737 5.527214 TGCATGATAGGAAAATTAGGACACG 59.473 40.000 0.00 0.00 0.00 4.49
1730 1738 5.049405 GCATGATAGGAAAATTAGGACACGG 60.049 44.000 0.00 0.00 0.00 4.94
1731 1739 5.687166 TGATAGGAAAATTAGGACACGGT 57.313 39.130 0.00 0.00 0.00 4.83
1732 1740 6.795144 TGATAGGAAAATTAGGACACGGTA 57.205 37.500 0.00 0.00 0.00 4.02
1733 1741 7.369551 TGATAGGAAAATTAGGACACGGTAT 57.630 36.000 0.00 0.00 0.00 2.73
1734 1742 7.214381 TGATAGGAAAATTAGGACACGGTATG 58.786 38.462 0.00 0.00 0.00 2.39
1735 1743 5.687166 AGGAAAATTAGGACACGGTATGA 57.313 39.130 0.00 0.00 0.00 2.15
1736 1744 5.671493 AGGAAAATTAGGACACGGTATGAG 58.329 41.667 0.00 0.00 0.00 2.90
1737 1745 5.189145 AGGAAAATTAGGACACGGTATGAGT 59.811 40.000 0.00 0.00 0.00 3.41
1738 1746 5.293569 GGAAAATTAGGACACGGTATGAGTG 59.706 44.000 0.00 0.00 44.57 3.51
1739 1747 2.953466 TTAGGACACGGTATGAGTGC 57.047 50.000 0.00 0.00 42.94 4.40
1740 1748 1.108776 TAGGACACGGTATGAGTGCC 58.891 55.000 0.00 0.00 42.94 5.01
1741 1749 0.614979 AGGACACGGTATGAGTGCCT 60.615 55.000 6.53 6.53 42.94 4.75
1742 1750 0.249398 GGACACGGTATGAGTGCCTT 59.751 55.000 0.00 0.00 42.94 4.35
1743 1751 1.479323 GGACACGGTATGAGTGCCTTA 59.521 52.381 0.00 0.00 42.94 2.69
1744 1752 2.102588 GGACACGGTATGAGTGCCTTAT 59.897 50.000 0.00 0.00 42.94 1.73
1745 1753 3.319972 GGACACGGTATGAGTGCCTTATA 59.680 47.826 0.00 0.00 42.94 0.98
1746 1754 4.021368 GGACACGGTATGAGTGCCTTATAT 60.021 45.833 0.00 0.00 42.94 0.86
1747 1755 5.510861 GGACACGGTATGAGTGCCTTATATT 60.511 44.000 0.00 0.00 42.94 1.28
1748 1756 6.294899 GGACACGGTATGAGTGCCTTATATTA 60.295 42.308 0.00 0.00 42.94 0.98
1749 1757 6.688578 ACACGGTATGAGTGCCTTATATTAG 58.311 40.000 0.00 0.00 42.94 1.73
1750 1758 6.492429 ACACGGTATGAGTGCCTTATATTAGA 59.508 38.462 0.00 0.00 42.94 2.10
1751 1759 7.014905 ACACGGTATGAGTGCCTTATATTAGAA 59.985 37.037 0.00 0.00 42.94 2.10
1752 1760 8.035394 CACGGTATGAGTGCCTTATATTAGAAT 58.965 37.037 0.00 0.00 32.52 2.40
1753 1761 9.251440 ACGGTATGAGTGCCTTATATTAGAATA 57.749 33.333 0.00 0.00 0.00 1.75
1794 1802 7.775053 TTTTAGTGGAATTAGTTGAATGCCT 57.225 32.000 0.00 0.00 43.32 4.75
1795 1803 7.391148 TTTAGTGGAATTAGTTGAATGCCTC 57.609 36.000 0.00 0.00 43.32 4.70
1796 1804 5.184892 AGTGGAATTAGTTGAATGCCTCT 57.815 39.130 0.00 0.00 43.32 3.69
1797 1805 4.946157 AGTGGAATTAGTTGAATGCCTCTG 59.054 41.667 0.00 0.00 43.04 3.35
1798 1806 4.702131 GTGGAATTAGTTGAATGCCTCTGT 59.298 41.667 0.00 0.00 43.32 3.41
1799 1807 5.183904 GTGGAATTAGTTGAATGCCTCTGTT 59.816 40.000 0.00 0.00 43.32 3.16
1800 1808 5.774690 TGGAATTAGTTGAATGCCTCTGTTT 59.225 36.000 0.00 0.00 43.32 2.83
1801 1809 6.267471 TGGAATTAGTTGAATGCCTCTGTTTT 59.733 34.615 0.00 0.00 43.32 2.43
1802 1810 6.587608 GGAATTAGTTGAATGCCTCTGTTTTG 59.412 38.462 0.00 0.00 39.97 2.44
1803 1811 6.655078 ATTAGTTGAATGCCTCTGTTTTGT 57.345 33.333 0.00 0.00 0.00 2.83
1804 1812 4.574599 AGTTGAATGCCTCTGTTTTGTC 57.425 40.909 0.00 0.00 0.00 3.18
1805 1813 3.953612 AGTTGAATGCCTCTGTTTTGTCA 59.046 39.130 0.00 0.00 0.00 3.58
1806 1814 3.988379 TGAATGCCTCTGTTTTGTCAC 57.012 42.857 0.00 0.00 0.00 3.67
1807 1815 2.290367 TGAATGCCTCTGTTTTGTCACG 59.710 45.455 0.00 0.00 0.00 4.35
1808 1816 1.238439 ATGCCTCTGTTTTGTCACGG 58.762 50.000 0.00 0.00 0.00 4.94
1809 1817 0.179234 TGCCTCTGTTTTGTCACGGA 59.821 50.000 0.00 0.00 0.00 4.69
1810 1818 1.305201 GCCTCTGTTTTGTCACGGAA 58.695 50.000 0.00 0.00 31.42 4.30
1811 1819 1.002792 GCCTCTGTTTTGTCACGGAAC 60.003 52.381 0.00 0.00 31.42 3.62
1812 1820 2.285083 CCTCTGTTTTGTCACGGAACA 58.715 47.619 0.00 0.00 31.42 3.18
1813 1821 2.680841 CCTCTGTTTTGTCACGGAACAA 59.319 45.455 1.23 1.23 37.37 2.83
1814 1822 3.486875 CCTCTGTTTTGTCACGGAACAAC 60.487 47.826 4.57 0.00 38.80 3.32
1815 1823 3.075148 TCTGTTTTGTCACGGAACAACA 58.925 40.909 4.57 1.71 38.80 3.33
1816 1824 3.502595 TCTGTTTTGTCACGGAACAACAA 59.497 39.130 4.57 0.00 38.80 2.83
1817 1825 4.023107 TCTGTTTTGTCACGGAACAACAAA 60.023 37.500 4.57 2.54 38.80 2.83
1818 1826 4.810790 TGTTTTGTCACGGAACAACAAAT 58.189 34.783 4.57 0.00 41.16 2.32
1819 1827 5.230942 TGTTTTGTCACGGAACAACAAATT 58.769 33.333 4.57 0.00 41.16 1.82
1820 1828 5.696724 TGTTTTGTCACGGAACAACAAATTT 59.303 32.000 4.57 0.00 41.16 1.82
1821 1829 6.866770 TGTTTTGTCACGGAACAACAAATTTA 59.133 30.769 4.57 0.00 41.16 1.40
1822 1830 7.062371 TGTTTTGTCACGGAACAACAAATTTAG 59.938 33.333 4.57 0.00 41.16 1.85
1823 1831 6.438259 TTGTCACGGAACAACAAATTTAGA 57.562 33.333 1.23 0.00 34.31 2.10
1824 1832 5.812652 TGTCACGGAACAACAAATTTAGAC 58.187 37.500 0.00 0.00 0.00 2.59
1825 1833 5.354513 TGTCACGGAACAACAAATTTAGACA 59.645 36.000 0.00 0.00 0.00 3.41
1826 1834 6.038825 TGTCACGGAACAACAAATTTAGACAT 59.961 34.615 0.00 0.00 0.00 3.06
1827 1835 7.226918 TGTCACGGAACAACAAATTTAGACATA 59.773 33.333 0.00 0.00 0.00 2.29
1828 1836 7.744715 GTCACGGAACAACAAATTTAGACATAG 59.255 37.037 0.00 0.00 0.00 2.23
1829 1837 7.442969 TCACGGAACAACAAATTTAGACATAGT 59.557 33.333 0.00 0.00 0.00 2.12
1830 1838 7.744715 CACGGAACAACAAATTTAGACATAGTC 59.255 37.037 0.00 0.00 0.00 2.59
1831 1839 7.660208 ACGGAACAACAAATTTAGACATAGTCT 59.340 33.333 4.93 4.93 45.54 3.24
1832 1840 7.957484 CGGAACAACAAATTTAGACATAGTCTG 59.043 37.037 9.78 0.00 43.30 3.51
1833 1841 8.784043 GGAACAACAAATTTAGACATAGTCTGT 58.216 33.333 9.78 0.00 43.30 3.41
1836 1844 9.998106 ACAACAAATTTAGACATAGTCTGTAGT 57.002 29.630 9.78 0.00 43.30 2.73
1839 1847 9.998106 ACAAATTTAGACATAGTCTGTAGTTGT 57.002 29.630 16.20 16.20 43.30 3.32
1841 1849 8.480643 AATTTAGACATAGTCTGTAGTTGTGC 57.519 34.615 9.78 0.00 43.30 4.57
1842 1850 4.457834 AGACATAGTCTGTAGTTGTGCC 57.542 45.455 0.00 0.00 41.76 5.01
1843 1851 4.090090 AGACATAGTCTGTAGTTGTGCCT 58.910 43.478 0.00 0.00 41.76 4.75
1844 1852 5.262009 AGACATAGTCTGTAGTTGTGCCTA 58.738 41.667 0.00 0.00 41.76 3.93
1845 1853 5.715279 AGACATAGTCTGTAGTTGTGCCTAA 59.285 40.000 0.00 0.00 41.76 2.69
1846 1854 6.381420 AGACATAGTCTGTAGTTGTGCCTAAT 59.619 38.462 0.00 0.00 41.76 1.73
1847 1855 6.341316 ACATAGTCTGTAGTTGTGCCTAATG 58.659 40.000 0.00 0.00 35.91 1.90
1848 1856 6.154534 ACATAGTCTGTAGTTGTGCCTAATGA 59.845 38.462 0.00 0.00 35.91 2.57
1849 1857 5.483685 AGTCTGTAGTTGTGCCTAATGAA 57.516 39.130 0.00 0.00 0.00 2.57
1850 1858 5.482908 AGTCTGTAGTTGTGCCTAATGAAG 58.517 41.667 0.00 0.00 0.00 3.02
1851 1859 5.246203 AGTCTGTAGTTGTGCCTAATGAAGA 59.754 40.000 0.00 0.00 0.00 2.87
1852 1860 5.348997 GTCTGTAGTTGTGCCTAATGAAGAC 59.651 44.000 0.00 0.00 0.00 3.01
1853 1861 5.011635 TCTGTAGTTGTGCCTAATGAAGACA 59.988 40.000 0.00 0.00 0.00 3.41
1854 1862 5.804639 TGTAGTTGTGCCTAATGAAGACAT 58.195 37.500 0.00 0.00 38.50 3.06
1855 1863 5.643348 TGTAGTTGTGCCTAATGAAGACATG 59.357 40.000 0.00 0.00 36.79 3.21
1856 1864 4.910195 AGTTGTGCCTAATGAAGACATGA 58.090 39.130 0.00 0.00 36.79 3.07
1857 1865 5.316167 AGTTGTGCCTAATGAAGACATGAA 58.684 37.500 0.00 0.00 36.79 2.57
1858 1866 5.413833 AGTTGTGCCTAATGAAGACATGAAG 59.586 40.000 0.00 0.00 36.79 3.02
1859 1867 5.164620 TGTGCCTAATGAAGACATGAAGA 57.835 39.130 0.00 0.00 36.79 2.87
1860 1868 4.937620 TGTGCCTAATGAAGACATGAAGAC 59.062 41.667 0.00 0.00 36.79 3.01
1861 1869 4.937620 GTGCCTAATGAAGACATGAAGACA 59.062 41.667 0.00 0.00 36.79 3.41
1862 1870 5.412594 GTGCCTAATGAAGACATGAAGACAA 59.587 40.000 0.00 0.00 36.79 3.18
1863 1871 5.645067 TGCCTAATGAAGACATGAAGACAAG 59.355 40.000 0.00 0.00 36.79 3.16
1864 1872 5.065731 GCCTAATGAAGACATGAAGACAAGG 59.934 44.000 0.00 1.13 36.79 3.61
1865 1873 6.176183 CCTAATGAAGACATGAAGACAAGGT 58.824 40.000 0.00 0.00 36.79 3.50
1866 1874 6.314896 CCTAATGAAGACATGAAGACAAGGTC 59.685 42.308 0.00 0.00 36.79 3.85
1867 1875 4.687901 TGAAGACATGAAGACAAGGTCA 57.312 40.909 0.00 0.00 37.08 4.02
1868 1876 4.635223 TGAAGACATGAAGACAAGGTCAG 58.365 43.478 0.00 0.00 37.08 3.51
1869 1877 3.692257 AGACATGAAGACAAGGTCAGG 57.308 47.619 0.00 0.00 37.08 3.86
1870 1878 2.079925 GACATGAAGACAAGGTCAGGC 58.920 52.381 0.00 0.00 35.74 4.85
1871 1879 1.701847 ACATGAAGACAAGGTCAGGCT 59.298 47.619 0.00 0.00 34.60 4.58
1872 1880 2.082231 CATGAAGACAAGGTCAGGCTG 58.918 52.381 8.58 8.58 34.60 4.85
1873 1881 0.397941 TGAAGACAAGGTCAGGCTGG 59.602 55.000 15.73 0.00 34.60 4.85
1874 1882 0.957888 GAAGACAAGGTCAGGCTGGC 60.958 60.000 15.73 13.70 34.60 4.85
1875 1883 2.738213 AAGACAAGGTCAGGCTGGCG 62.738 60.000 15.73 2.46 34.60 5.69
1876 1884 4.335647 ACAAGGTCAGGCTGGCGG 62.336 66.667 15.73 8.56 0.00 6.13
1877 1885 4.020617 CAAGGTCAGGCTGGCGGA 62.021 66.667 15.73 0.00 0.00 5.54
1878 1886 3.249189 AAGGTCAGGCTGGCGGAA 61.249 61.111 15.73 0.00 0.00 4.30
1879 1887 3.259633 AAGGTCAGGCTGGCGGAAG 62.260 63.158 15.73 0.00 0.00 3.46
1880 1888 4.021925 GGTCAGGCTGGCGGAAGT 62.022 66.667 15.73 0.00 0.00 3.01
1881 1889 2.743928 GTCAGGCTGGCGGAAGTG 60.744 66.667 15.73 0.00 0.00 3.16
1882 1890 4.020617 TCAGGCTGGCGGAAGTGG 62.021 66.667 15.73 0.00 0.00 4.00
1883 1891 4.335647 CAGGCTGGCGGAAGTGGT 62.336 66.667 6.61 0.00 0.00 4.16
1884 1892 3.570212 AGGCTGGCGGAAGTGGTT 61.570 61.111 0.00 0.00 0.00 3.67
1885 1893 3.365265 GGCTGGCGGAAGTGGTTG 61.365 66.667 0.00 0.00 0.00 3.77
1886 1894 2.594592 GCTGGCGGAAGTGGTTGT 60.595 61.111 0.00 0.00 0.00 3.32
1887 1895 2.193536 GCTGGCGGAAGTGGTTGTT 61.194 57.895 0.00 0.00 0.00 2.83
1888 1896 1.949257 CTGGCGGAAGTGGTTGTTC 59.051 57.895 0.00 0.00 0.00 3.18
1889 1897 1.841663 CTGGCGGAAGTGGTTGTTCG 61.842 60.000 0.00 0.00 0.00 3.95
1890 1898 1.595929 GGCGGAAGTGGTTGTTCGA 60.596 57.895 0.00 0.00 0.00 3.71
1891 1899 0.953960 GGCGGAAGTGGTTGTTCGAT 60.954 55.000 0.00 0.00 0.00 3.59
1892 1900 0.165944 GCGGAAGTGGTTGTTCGATG 59.834 55.000 0.00 0.00 0.00 3.84
1893 1901 0.796312 CGGAAGTGGTTGTTCGATGG 59.204 55.000 0.00 0.00 0.00 3.51
1894 1902 1.876416 CGGAAGTGGTTGTTCGATGGT 60.876 52.381 0.00 0.00 0.00 3.55
1895 1903 1.804748 GGAAGTGGTTGTTCGATGGTC 59.195 52.381 0.00 0.00 0.00 4.02
1896 1904 2.550208 GGAAGTGGTTGTTCGATGGTCT 60.550 50.000 0.00 0.00 0.00 3.85
1897 1905 3.306502 GGAAGTGGTTGTTCGATGGTCTA 60.307 47.826 0.00 0.00 0.00 2.59
1898 1906 3.594603 AGTGGTTGTTCGATGGTCTAG 57.405 47.619 0.00 0.00 0.00 2.43
1899 1907 2.233922 AGTGGTTGTTCGATGGTCTAGG 59.766 50.000 0.00 0.00 0.00 3.02
1900 1908 2.232941 GTGGTTGTTCGATGGTCTAGGA 59.767 50.000 0.00 0.00 0.00 2.94
1901 1909 2.901192 TGGTTGTTCGATGGTCTAGGAA 59.099 45.455 0.00 0.00 0.00 3.36
1902 1910 3.517901 TGGTTGTTCGATGGTCTAGGAAT 59.482 43.478 0.00 0.00 0.00 3.01
1903 1911 4.019681 TGGTTGTTCGATGGTCTAGGAATT 60.020 41.667 0.00 0.00 0.00 2.17
1904 1912 5.188163 TGGTTGTTCGATGGTCTAGGAATTA 59.812 40.000 0.00 0.00 0.00 1.40
1905 1913 6.126883 TGGTTGTTCGATGGTCTAGGAATTAT 60.127 38.462 0.00 0.00 0.00 1.28
1906 1914 6.202954 GGTTGTTCGATGGTCTAGGAATTATG 59.797 42.308 0.00 0.00 0.00 1.90
1907 1915 6.724893 TGTTCGATGGTCTAGGAATTATGA 57.275 37.500 0.00 0.00 0.00 2.15
1908 1916 6.513180 TGTTCGATGGTCTAGGAATTATGAC 58.487 40.000 0.00 0.00 0.00 3.06
1909 1917 5.372547 TCGATGGTCTAGGAATTATGACG 57.627 43.478 0.00 0.00 0.00 4.35
1910 1918 4.825634 TCGATGGTCTAGGAATTATGACGT 59.174 41.667 0.00 0.00 0.00 4.34
1911 1919 5.999600 TCGATGGTCTAGGAATTATGACGTA 59.000 40.000 0.00 0.00 0.00 3.57
1912 1920 6.487668 TCGATGGTCTAGGAATTATGACGTAA 59.512 38.462 0.00 0.00 0.00 3.18
1913 1921 7.176165 TCGATGGTCTAGGAATTATGACGTAAT 59.824 37.037 0.00 0.00 34.46 1.89
1914 1922 7.813148 CGATGGTCTAGGAATTATGACGTAATT 59.187 37.037 11.63 11.63 43.86 1.40
1915 1923 9.490379 GATGGTCTAGGAATTATGACGTAATTT 57.510 33.333 12.78 2.77 41.82 1.82
1916 1924 9.847224 ATGGTCTAGGAATTATGACGTAATTTT 57.153 29.630 12.78 8.13 41.82 1.82
1917 1925 9.675464 TGGTCTAGGAATTATGACGTAATTTTT 57.325 29.630 12.78 7.86 41.82 1.94
1956 1964 8.931775 GGTATTTCCCATTTTGTCAAACATAAC 58.068 33.333 0.00 0.00 0.00 1.89
1957 1965 7.650834 ATTTCCCATTTTGTCAAACATAACG 57.349 32.000 0.00 0.00 0.00 3.18
1958 1966 6.392625 TTCCCATTTTGTCAAACATAACGA 57.607 33.333 0.00 0.00 0.00 3.85
1959 1967 5.764131 TCCCATTTTGTCAAACATAACGAC 58.236 37.500 0.00 0.00 0.00 4.34
1960 1968 4.920927 CCCATTTTGTCAAACATAACGACC 59.079 41.667 0.00 0.00 0.00 4.79
1961 1969 5.508153 CCCATTTTGTCAAACATAACGACCA 60.508 40.000 0.00 0.00 0.00 4.02
1962 1970 5.980116 CCATTTTGTCAAACATAACGACCAA 59.020 36.000 0.00 0.00 0.00 3.67
1963 1971 6.644592 CCATTTTGTCAAACATAACGACCAAT 59.355 34.615 0.00 0.00 0.00 3.16
1964 1972 7.170658 CCATTTTGTCAAACATAACGACCAATT 59.829 33.333 0.00 0.00 0.00 2.32
1965 1973 9.186323 CATTTTGTCAAACATAACGACCAATTA 57.814 29.630 0.00 0.00 0.00 1.40
1966 1974 9.921637 ATTTTGTCAAACATAACGACCAATTAT 57.078 25.926 0.00 0.00 0.00 1.28
1967 1975 9.751542 TTTTGTCAAACATAACGACCAATTATT 57.248 25.926 0.00 0.00 0.00 1.40
2004 2012 8.902540 TTTTCTGTTGACTGTATCTACAATGT 57.097 30.769 0.00 0.00 41.62 2.71
2005 2013 8.902540 TTTCTGTTGACTGTATCTACAATGTT 57.097 30.769 0.00 0.00 41.62 2.71
2006 2014 8.902540 TTCTGTTGACTGTATCTACAATGTTT 57.097 30.769 0.00 0.00 41.62 2.83
2007 2015 8.310406 TCTGTTGACTGTATCTACAATGTTTG 57.690 34.615 0.00 0.00 41.62 2.93
2008 2016 6.898041 TGTTGACTGTATCTACAATGTTTGC 58.102 36.000 0.00 0.00 39.67 3.68
2009 2017 5.778161 TGACTGTATCTACAATGTTTGCG 57.222 39.130 0.00 0.00 35.50 4.85
2010 2018 4.629634 TGACTGTATCTACAATGTTTGCGG 59.370 41.667 0.00 0.00 35.50 5.69
2011 2019 4.575885 ACTGTATCTACAATGTTTGCGGT 58.424 39.130 0.00 0.00 35.50 5.68
2012 2020 5.001232 ACTGTATCTACAATGTTTGCGGTT 58.999 37.500 0.00 0.00 35.50 4.44
2013 2021 5.472137 ACTGTATCTACAATGTTTGCGGTTT 59.528 36.000 0.00 0.00 35.50 3.27
2014 2022 6.651643 ACTGTATCTACAATGTTTGCGGTTTA 59.348 34.615 0.00 0.00 35.50 2.01
2015 2023 7.173562 ACTGTATCTACAATGTTTGCGGTTTAA 59.826 33.333 0.00 0.00 35.50 1.52
2016 2024 8.046294 TGTATCTACAATGTTTGCGGTTTAAT 57.954 30.769 0.00 0.00 32.40 1.40
2017 2025 8.516234 TGTATCTACAATGTTTGCGGTTTAATT 58.484 29.630 0.00 0.00 32.40 1.40
2018 2026 9.991388 GTATCTACAATGTTTGCGGTTTAATTA 57.009 29.630 0.00 0.00 0.00 1.40
2020 2028 7.531716 TCTACAATGTTTGCGGTTTAATTAGG 58.468 34.615 0.00 0.00 0.00 2.69
2021 2029 4.926832 ACAATGTTTGCGGTTTAATTAGGC 59.073 37.500 0.00 0.00 0.00 3.93
2022 2030 5.167845 CAATGTTTGCGGTTTAATTAGGCT 58.832 37.500 0.00 0.00 0.00 4.58
2023 2031 4.428615 TGTTTGCGGTTTAATTAGGCTC 57.571 40.909 0.00 0.00 0.00 4.70
2024 2032 4.076394 TGTTTGCGGTTTAATTAGGCTCT 58.924 39.130 0.00 0.00 0.00 4.09
2025 2033 4.083003 TGTTTGCGGTTTAATTAGGCTCTG 60.083 41.667 0.00 0.00 0.00 3.35
2026 2034 2.014128 TGCGGTTTAATTAGGCTCTGC 58.986 47.619 0.00 0.00 0.00 4.26
2027 2035 2.289565 GCGGTTTAATTAGGCTCTGCT 58.710 47.619 0.00 0.00 0.00 4.24
2050 2058 6.091986 GCTTCAAGAACAGATGTCTTCTTAGG 59.908 42.308 0.00 0.00 32.99 2.69
2070 2078 5.733620 AGGAAGTGGTTGTCGAAGTTATA 57.266 39.130 0.00 0.00 0.00 0.98
2141 2149 3.053991 TCACTCCAAAACTTTGTCCCAGA 60.054 43.478 1.76 0.00 36.45 3.86
2197 2205 6.592220 GGAAAGGTCTTATGAGAGTCAAAGTC 59.408 42.308 0.00 0.00 31.07 3.01
2304 2316 5.447624 TTGCGATTCAATATCCGTCTCTA 57.552 39.130 0.00 0.00 0.00 2.43
2321 2333 7.068962 TCCGTCTCTATATGGTATTGTTCAACA 59.931 37.037 0.00 0.00 0.00 3.33
2398 2411 1.078426 AGAACGCTAGCCGGCAATT 60.078 52.632 31.54 14.72 42.52 2.32
2404 2417 1.312371 GCTAGCCGGCAATTGTTGGA 61.312 55.000 31.54 0.45 0.00 3.53
2475 2488 3.864243 ACAACCCGATAAATTACGCTGA 58.136 40.909 0.00 0.00 0.00 4.26
2699 2712 4.256920 AGTTTCTGTGATCGGGATGAAAG 58.743 43.478 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
428 430 2.352503 GTGATGTTTTGGCATCGCTT 57.647 45.000 11.06 0.00 46.81 4.68
946 948 3.992643 TCGTCTGGTTTATTTTCGTCCA 58.007 40.909 0.00 0.00 0.00 4.02
1039 1041 6.421801 TCATGACGAACTTATGCTGATACATG 59.578 38.462 0.00 0.00 33.86 3.21
1042 1044 6.642540 TGATCATGACGAACTTATGCTGATAC 59.357 38.462 0.00 0.00 0.00 2.24
1043 1045 6.748132 TGATCATGACGAACTTATGCTGATA 58.252 36.000 0.00 0.00 0.00 2.15
1141 1144 8.304596 AGAGATGACAAAATCTTAACTACGACA 58.695 33.333 0.00 0.00 37.03 4.35
1142 1145 8.690680 AGAGATGACAAAATCTTAACTACGAC 57.309 34.615 0.00 0.00 37.03 4.34
1145 1148 9.141400 ACGAAGAGATGACAAAATCTTAACTAC 57.859 33.333 0.00 0.00 37.03 2.73
1179 1182 2.393646 GGCCTCCTCTTGACTCAGTAT 58.606 52.381 0.00 0.00 0.00 2.12
1180 1183 1.853963 GGCCTCCTCTTGACTCAGTA 58.146 55.000 0.00 0.00 0.00 2.74
1187 1191 2.283529 GGTCACGGCCTCCTCTTGA 61.284 63.158 0.00 0.00 0.00 3.02
1189 1193 1.201429 AATGGTCACGGCCTCCTCTT 61.201 55.000 0.00 0.00 0.00 2.85
1204 1208 3.149196 ACAGAAGTGTACAAGGCAATGG 58.851 45.455 0.00 0.00 34.05 3.16
1216 1220 3.433740 GGACTCAAAGGGAACAGAAGTGT 60.434 47.826 0.00 0.00 39.19 3.55
1222 1226 0.396811 ACGGGACTCAAAGGGAACAG 59.603 55.000 0.00 0.00 0.00 3.16
1223 1227 1.719529 TACGGGACTCAAAGGGAACA 58.280 50.000 0.00 0.00 0.00 3.18
1226 1230 3.675348 TCTATACGGGACTCAAAGGGA 57.325 47.619 0.00 0.00 0.00 4.20
1232 1236 4.788679 TCAGATGTTCTATACGGGACTCA 58.211 43.478 0.00 0.00 0.00 3.41
1233 1237 5.106078 GGATCAGATGTTCTATACGGGACTC 60.106 48.000 0.00 0.00 0.00 3.36
1234 1238 4.767928 GGATCAGATGTTCTATACGGGACT 59.232 45.833 0.00 0.00 0.00 3.85
1235 1239 4.523173 TGGATCAGATGTTCTATACGGGAC 59.477 45.833 0.00 0.00 0.00 4.46
1236 1240 4.736473 TGGATCAGATGTTCTATACGGGA 58.264 43.478 0.00 0.00 0.00 5.14
1237 1241 4.619394 GCTGGATCAGATGTTCTATACGGG 60.619 50.000 0.00 0.00 32.44 5.28
1238 1242 4.021981 TGCTGGATCAGATGTTCTATACGG 60.022 45.833 0.00 0.00 32.44 4.02
1239 1243 5.126396 TGCTGGATCAGATGTTCTATACG 57.874 43.478 0.00 0.00 32.44 3.06
1240 1244 6.753180 TCTTGCTGGATCAGATGTTCTATAC 58.247 40.000 0.00 0.00 32.44 1.47
1241 1245 6.014755 CCTCTTGCTGGATCAGATGTTCTATA 60.015 42.308 0.00 0.00 32.44 1.31
1242 1246 5.221682 CCTCTTGCTGGATCAGATGTTCTAT 60.222 44.000 0.00 0.00 32.44 1.98
1243 1247 4.100653 CCTCTTGCTGGATCAGATGTTCTA 59.899 45.833 0.00 0.00 32.44 2.10
1244 1248 3.118334 CCTCTTGCTGGATCAGATGTTCT 60.118 47.826 0.00 0.00 32.44 3.01
1259 1263 6.140303 TCATATTTGATCTTTGCCTCTTGC 57.860 37.500 0.00 0.00 41.77 4.01
1271 1275 3.505293 GCTGCTCCCCTTCATATTTGATC 59.495 47.826 0.00 0.00 0.00 2.92
1339 1347 2.165319 AGTTTCTTACACCGTCCAGC 57.835 50.000 0.00 0.00 0.00 4.85
1362 1370 8.836268 ATAAATGTGAAATTGTGCACAAGAAT 57.164 26.923 33.44 22.72 46.74 2.40
1439 1447 1.608283 CCTTTCTTCCACGAGGTGACC 60.608 57.143 0.00 0.00 35.23 4.02
1447 1455 2.544726 GTGGCTCCTTTCTTCCACG 58.455 57.895 0.00 0.00 39.46 4.94
1580 1588 2.202987 GCATGGCTCGGTCCAGAG 60.203 66.667 0.00 6.42 39.89 3.35
1599 1607 2.195567 GGCAACACAAGGCAGCAGA 61.196 57.895 0.00 0.00 0.00 4.26
1601 1609 3.594775 CGGCAACACAAGGCAGCA 61.595 61.111 0.00 0.00 0.00 4.41
1633 1641 3.832171 CACTCGCTTCGCTCACGC 61.832 66.667 0.00 0.00 39.84 5.34
1688 1696 7.851387 ATCATGCATGCAATTCTAGATCTAG 57.149 36.000 26.68 21.81 34.56 2.43
1689 1697 7.985752 CCTATCATGCATGCAATTCTAGATCTA 59.014 37.037 26.68 1.69 0.00 1.98
1690 1698 6.824196 CCTATCATGCATGCAATTCTAGATCT 59.176 38.462 26.68 0.00 0.00 2.75
1691 1699 6.822170 TCCTATCATGCATGCAATTCTAGATC 59.178 38.462 26.68 0.00 0.00 2.75
1692 1700 6.718294 TCCTATCATGCATGCAATTCTAGAT 58.282 36.000 26.68 20.42 0.00 1.98
1693 1701 6.117975 TCCTATCATGCATGCAATTCTAGA 57.882 37.500 26.68 14.90 0.00 2.43
1711 1719 7.070821 ACTCATACCGTGTCCTAATTTTCCTAT 59.929 37.037 0.00 0.00 0.00 2.57
1715 1723 5.220605 GCACTCATACCGTGTCCTAATTTTC 60.221 44.000 0.00 0.00 34.91 2.29
1726 1734 6.920817 TCTAATATAAGGCACTCATACCGTG 58.079 40.000 0.00 0.00 38.49 4.94
1727 1735 7.534723 TTCTAATATAAGGCACTCATACCGT 57.465 36.000 0.00 0.00 38.49 4.83
1768 1776 9.474313 AGGCATTCAACTAATTCCACTAAAATA 57.526 29.630 0.00 0.00 33.65 1.40
1769 1777 8.366359 AGGCATTCAACTAATTCCACTAAAAT 57.634 30.769 0.00 0.00 33.65 1.82
1770 1778 7.669722 AGAGGCATTCAACTAATTCCACTAAAA 59.330 33.333 0.00 0.00 31.84 1.52
1771 1779 7.121168 CAGAGGCATTCAACTAATTCCACTAAA 59.879 37.037 0.00 0.00 31.84 1.85
1772 1780 6.599244 CAGAGGCATTCAACTAATTCCACTAA 59.401 38.462 0.00 0.00 31.84 2.24
1773 1781 6.115446 CAGAGGCATTCAACTAATTCCACTA 58.885 40.000 0.00 0.00 31.84 2.74
1774 1782 4.946157 CAGAGGCATTCAACTAATTCCACT 59.054 41.667 0.00 0.00 33.35 4.00
1775 1783 4.702131 ACAGAGGCATTCAACTAATTCCAC 59.298 41.667 0.00 0.00 33.65 4.02
1776 1784 4.922206 ACAGAGGCATTCAACTAATTCCA 58.078 39.130 0.00 0.00 33.65 3.53
1777 1785 5.904362 AACAGAGGCATTCAACTAATTCC 57.096 39.130 0.00 0.00 31.52 3.01
1778 1786 7.147976 ACAAAACAGAGGCATTCAACTAATTC 58.852 34.615 0.00 0.00 0.00 2.17
1779 1787 7.054491 ACAAAACAGAGGCATTCAACTAATT 57.946 32.000 0.00 0.00 0.00 1.40
1780 1788 6.265196 TGACAAAACAGAGGCATTCAACTAAT 59.735 34.615 0.00 0.00 0.00 1.73
1781 1789 5.592282 TGACAAAACAGAGGCATTCAACTAA 59.408 36.000 0.00 0.00 0.00 2.24
1782 1790 5.008613 GTGACAAAACAGAGGCATTCAACTA 59.991 40.000 0.00 0.00 0.00 2.24
1783 1791 3.953612 TGACAAAACAGAGGCATTCAACT 59.046 39.130 0.00 0.00 0.00 3.16
1784 1792 4.044426 GTGACAAAACAGAGGCATTCAAC 58.956 43.478 0.00 0.00 0.00 3.18
1785 1793 3.243035 CGTGACAAAACAGAGGCATTCAA 60.243 43.478 0.00 0.00 0.00 2.69
1786 1794 2.290367 CGTGACAAAACAGAGGCATTCA 59.710 45.455 0.00 0.00 0.00 2.57
1787 1795 2.350772 CCGTGACAAAACAGAGGCATTC 60.351 50.000 0.00 0.00 0.00 2.67
1788 1796 1.608590 CCGTGACAAAACAGAGGCATT 59.391 47.619 0.00 0.00 0.00 3.56
1789 1797 1.202758 TCCGTGACAAAACAGAGGCAT 60.203 47.619 0.00 0.00 0.00 4.40
1790 1798 0.179234 TCCGTGACAAAACAGAGGCA 59.821 50.000 0.00 0.00 0.00 4.75
1791 1799 1.002792 GTTCCGTGACAAAACAGAGGC 60.003 52.381 0.00 0.00 0.00 4.70
1792 1800 2.285083 TGTTCCGTGACAAAACAGAGG 58.715 47.619 0.00 0.00 0.00 3.69
1793 1801 3.126171 TGTTGTTCCGTGACAAAACAGAG 59.874 43.478 2.84 0.00 40.86 3.35
1794 1802 3.075148 TGTTGTTCCGTGACAAAACAGA 58.925 40.909 2.84 0.00 40.86 3.41
1795 1803 3.479505 TGTTGTTCCGTGACAAAACAG 57.520 42.857 2.84 0.00 40.86 3.16
1796 1804 3.917329 TTGTTGTTCCGTGACAAAACA 57.083 38.095 2.84 0.00 40.86 2.83
1797 1805 5.771602 AATTTGTTGTTCCGTGACAAAAC 57.228 34.783 5.17 0.00 43.82 2.43
1798 1806 7.273815 GTCTAAATTTGTTGTTCCGTGACAAAA 59.726 33.333 0.00 0.00 43.82 2.44
1799 1807 6.748198 GTCTAAATTTGTTGTTCCGTGACAAA 59.252 34.615 0.00 3.72 44.45 2.83
1800 1808 6.127980 TGTCTAAATTTGTTGTTCCGTGACAA 60.128 34.615 0.00 0.00 37.20 3.18
1801 1809 5.354513 TGTCTAAATTTGTTGTTCCGTGACA 59.645 36.000 0.00 0.00 0.00 3.58
1802 1810 5.812652 TGTCTAAATTTGTTGTTCCGTGAC 58.187 37.500 0.00 0.00 0.00 3.67
1803 1811 6.627395 ATGTCTAAATTTGTTGTTCCGTGA 57.373 33.333 0.00 0.00 0.00 4.35
1804 1812 7.581476 ACTATGTCTAAATTTGTTGTTCCGTG 58.419 34.615 0.00 0.00 0.00 4.94
1805 1813 7.660208 AGACTATGTCTAAATTTGTTGTTCCGT 59.340 33.333 0.00 0.00 41.51 4.69
1806 1814 7.957484 CAGACTATGTCTAAATTTGTTGTTCCG 59.043 37.037 0.00 0.00 41.37 4.30
1807 1815 8.784043 ACAGACTATGTCTAAATTTGTTGTTCC 58.216 33.333 0.00 0.00 41.37 3.62
1810 1818 9.998106 ACTACAGACTATGTCTAAATTTGTTGT 57.002 29.630 0.00 0.00 41.37 3.32
1813 1821 9.998106 ACAACTACAGACTATGTCTAAATTTGT 57.002 29.630 0.00 5.89 41.37 2.83
1815 1823 8.936864 GCACAACTACAGACTATGTCTAAATTT 58.063 33.333 0.00 0.00 41.37 1.82
1816 1824 7.549488 GGCACAACTACAGACTATGTCTAAATT 59.451 37.037 0.00 0.00 41.37 1.82
1817 1825 7.042335 GGCACAACTACAGACTATGTCTAAAT 58.958 38.462 0.00 0.00 41.37 1.40
1818 1826 6.210784 AGGCACAACTACAGACTATGTCTAAA 59.789 38.462 0.00 0.00 41.37 1.85
1819 1827 5.715279 AGGCACAACTACAGACTATGTCTAA 59.285 40.000 0.00 0.00 41.37 2.10
1820 1828 5.262009 AGGCACAACTACAGACTATGTCTA 58.738 41.667 0.00 0.00 41.37 2.59
1821 1829 4.090090 AGGCACAACTACAGACTATGTCT 58.910 43.478 0.00 0.00 44.44 3.41
1822 1830 4.457834 AGGCACAACTACAGACTATGTC 57.542 45.455 0.00 0.00 42.70 3.06
1823 1831 5.995565 TTAGGCACAACTACAGACTATGT 57.004 39.130 0.00 0.00 46.45 2.29
1824 1832 6.573434 TCATTAGGCACAACTACAGACTATG 58.427 40.000 0.00 0.00 0.00 2.23
1825 1833 6.791867 TCATTAGGCACAACTACAGACTAT 57.208 37.500 0.00 0.00 0.00 2.12
1826 1834 6.436218 TCTTCATTAGGCACAACTACAGACTA 59.564 38.462 0.00 0.00 0.00 2.59
1827 1835 5.246203 TCTTCATTAGGCACAACTACAGACT 59.754 40.000 0.00 0.00 0.00 3.24
1828 1836 5.348997 GTCTTCATTAGGCACAACTACAGAC 59.651 44.000 0.00 0.00 0.00 3.51
1829 1837 5.011635 TGTCTTCATTAGGCACAACTACAGA 59.988 40.000 0.00 0.00 32.31 3.41
1830 1838 5.237815 TGTCTTCATTAGGCACAACTACAG 58.762 41.667 0.00 0.00 32.31 2.74
1831 1839 5.222079 TGTCTTCATTAGGCACAACTACA 57.778 39.130 0.00 0.00 32.31 2.74
1832 1840 5.874810 TCATGTCTTCATTAGGCACAACTAC 59.125 40.000 0.00 0.00 42.29 2.73
1833 1841 6.048732 TCATGTCTTCATTAGGCACAACTA 57.951 37.500 0.00 0.00 42.29 2.24
1834 1842 4.910195 TCATGTCTTCATTAGGCACAACT 58.090 39.130 0.00 0.00 42.29 3.16
1835 1843 5.412594 TCTTCATGTCTTCATTAGGCACAAC 59.587 40.000 0.00 0.00 42.29 3.32
1836 1844 5.412594 GTCTTCATGTCTTCATTAGGCACAA 59.587 40.000 0.00 0.00 42.29 3.33
1837 1845 4.937620 GTCTTCATGTCTTCATTAGGCACA 59.062 41.667 0.00 0.00 42.29 4.57
1838 1846 4.937620 TGTCTTCATGTCTTCATTAGGCAC 59.062 41.667 0.00 0.00 42.29 5.01
1839 1847 5.164620 TGTCTTCATGTCTTCATTAGGCA 57.835 39.130 0.00 0.00 43.95 4.75
1840 1848 5.065731 CCTTGTCTTCATGTCTTCATTAGGC 59.934 44.000 0.00 0.00 31.15 3.93
1841 1849 6.176183 ACCTTGTCTTCATGTCTTCATTAGG 58.824 40.000 0.00 0.00 31.15 2.69
1842 1850 6.875726 TGACCTTGTCTTCATGTCTTCATTAG 59.124 38.462 0.00 0.00 33.15 1.73
1843 1851 6.768483 TGACCTTGTCTTCATGTCTTCATTA 58.232 36.000 0.00 0.00 33.15 1.90
1844 1852 5.624159 TGACCTTGTCTTCATGTCTTCATT 58.376 37.500 0.00 0.00 33.15 2.57
1845 1853 5.233083 TGACCTTGTCTTCATGTCTTCAT 57.767 39.130 0.00 0.00 33.15 2.57
1846 1854 4.503817 CCTGACCTTGTCTTCATGTCTTCA 60.504 45.833 0.00 0.00 33.15 3.02
1847 1855 3.999663 CCTGACCTTGTCTTCATGTCTTC 59.000 47.826 0.00 0.00 33.15 2.87
1848 1856 3.808618 GCCTGACCTTGTCTTCATGTCTT 60.809 47.826 0.00 0.00 33.15 3.01
1849 1857 2.289945 GCCTGACCTTGTCTTCATGTCT 60.290 50.000 0.00 0.00 33.15 3.41
1850 1858 2.079925 GCCTGACCTTGTCTTCATGTC 58.920 52.381 0.00 0.00 33.15 3.06
1851 1859 1.701847 AGCCTGACCTTGTCTTCATGT 59.298 47.619 0.00 0.00 33.15 3.21
1852 1860 2.082231 CAGCCTGACCTTGTCTTCATG 58.918 52.381 0.00 0.00 33.15 3.07
1853 1861 1.004044 CCAGCCTGACCTTGTCTTCAT 59.996 52.381 0.00 0.00 33.15 2.57
1854 1862 0.397941 CCAGCCTGACCTTGTCTTCA 59.602 55.000 0.00 0.00 33.15 3.02
1855 1863 0.957888 GCCAGCCTGACCTTGTCTTC 60.958 60.000 0.00 0.00 33.15 2.87
1856 1864 1.073897 GCCAGCCTGACCTTGTCTT 59.926 57.895 0.00 0.00 33.15 3.01
1857 1865 2.753029 GCCAGCCTGACCTTGTCT 59.247 61.111 0.00 0.00 33.15 3.41
1858 1866 2.743928 CGCCAGCCTGACCTTGTC 60.744 66.667 0.00 0.00 0.00 3.18
1859 1867 4.335647 CCGCCAGCCTGACCTTGT 62.336 66.667 0.00 0.00 0.00 3.16
1860 1868 3.551496 TTCCGCCAGCCTGACCTTG 62.551 63.158 0.00 0.00 0.00 3.61
1861 1869 3.249189 TTCCGCCAGCCTGACCTT 61.249 61.111 0.00 0.00 0.00 3.50
1862 1870 3.710722 CTTCCGCCAGCCTGACCT 61.711 66.667 0.00 0.00 0.00 3.85
1863 1871 4.021925 ACTTCCGCCAGCCTGACC 62.022 66.667 0.00 0.00 0.00 4.02
1864 1872 2.743928 CACTTCCGCCAGCCTGAC 60.744 66.667 0.00 0.00 0.00 3.51
1865 1873 4.020617 CCACTTCCGCCAGCCTGA 62.021 66.667 0.00 0.00 0.00 3.86
1866 1874 3.850098 AACCACTTCCGCCAGCCTG 62.850 63.158 0.00 0.00 0.00 4.85
1867 1875 3.570212 AACCACTTCCGCCAGCCT 61.570 61.111 0.00 0.00 0.00 4.58
1868 1876 3.365265 CAACCACTTCCGCCAGCC 61.365 66.667 0.00 0.00 0.00 4.85
1869 1877 2.130073 GAACAACCACTTCCGCCAGC 62.130 60.000 0.00 0.00 0.00 4.85
1870 1878 1.841663 CGAACAACCACTTCCGCCAG 61.842 60.000 0.00 0.00 0.00 4.85
1871 1879 1.890041 CGAACAACCACTTCCGCCA 60.890 57.895 0.00 0.00 0.00 5.69
1872 1880 0.953960 ATCGAACAACCACTTCCGCC 60.954 55.000 0.00 0.00 0.00 6.13
1873 1881 0.165944 CATCGAACAACCACTTCCGC 59.834 55.000 0.00 0.00 0.00 5.54
1874 1882 0.796312 CCATCGAACAACCACTTCCG 59.204 55.000 0.00 0.00 0.00 4.30
1875 1883 1.804748 GACCATCGAACAACCACTTCC 59.195 52.381 0.00 0.00 0.00 3.46
1876 1884 2.767505 AGACCATCGAACAACCACTTC 58.232 47.619 0.00 0.00 0.00 3.01
1877 1885 2.930826 AGACCATCGAACAACCACTT 57.069 45.000 0.00 0.00 0.00 3.16
1878 1886 2.233922 CCTAGACCATCGAACAACCACT 59.766 50.000 0.00 0.00 0.00 4.00
1879 1887 2.232941 TCCTAGACCATCGAACAACCAC 59.767 50.000 0.00 0.00 0.00 4.16
1880 1888 2.531771 TCCTAGACCATCGAACAACCA 58.468 47.619 0.00 0.00 0.00 3.67
1881 1889 3.604875 TTCCTAGACCATCGAACAACC 57.395 47.619 0.00 0.00 0.00 3.77
1882 1890 6.984474 TCATAATTCCTAGACCATCGAACAAC 59.016 38.462 0.00 0.00 0.00 3.32
1883 1891 6.984474 GTCATAATTCCTAGACCATCGAACAA 59.016 38.462 0.00 0.00 0.00 2.83
1884 1892 6.513180 GTCATAATTCCTAGACCATCGAACA 58.487 40.000 0.00 0.00 0.00 3.18
1885 1893 5.629849 CGTCATAATTCCTAGACCATCGAAC 59.370 44.000 0.00 0.00 0.00 3.95
1886 1894 5.301045 ACGTCATAATTCCTAGACCATCGAA 59.699 40.000 0.00 0.00 0.00 3.71
1887 1895 4.825634 ACGTCATAATTCCTAGACCATCGA 59.174 41.667 0.00 0.00 0.00 3.59
1888 1896 5.122512 ACGTCATAATTCCTAGACCATCG 57.877 43.478 0.00 0.00 0.00 3.84
1889 1897 9.490379 AAATTACGTCATAATTCCTAGACCATC 57.510 33.333 0.00 0.00 41.73 3.51
1890 1898 9.847224 AAAATTACGTCATAATTCCTAGACCAT 57.153 29.630 0.00 0.00 41.73 3.55
1891 1899 9.675464 AAAAATTACGTCATAATTCCTAGACCA 57.325 29.630 0.00 0.00 41.73 4.02
1930 1938 8.931775 GTTATGTTTGACAAAATGGGAAATACC 58.068 33.333 1.27 0.00 38.08 2.73
1931 1939 8.643752 CGTTATGTTTGACAAAATGGGAAATAC 58.356 33.333 1.27 0.00 0.00 1.89
1932 1940 8.577296 TCGTTATGTTTGACAAAATGGGAAATA 58.423 29.630 1.27 0.00 0.00 1.40
1933 1941 7.383843 GTCGTTATGTTTGACAAAATGGGAAAT 59.616 33.333 1.27 0.00 32.91 2.17
1934 1942 6.697892 GTCGTTATGTTTGACAAAATGGGAAA 59.302 34.615 1.27 0.00 32.91 3.13
1935 1943 6.210078 GTCGTTATGTTTGACAAAATGGGAA 58.790 36.000 1.27 0.00 32.91 3.97
1936 1944 5.278561 GGTCGTTATGTTTGACAAAATGGGA 60.279 40.000 1.27 0.00 34.32 4.37
1937 1945 4.920927 GGTCGTTATGTTTGACAAAATGGG 59.079 41.667 1.27 0.00 34.32 4.00
1938 1946 5.524284 TGGTCGTTATGTTTGACAAAATGG 58.476 37.500 1.27 0.00 34.32 3.16
1939 1947 7.636259 ATTGGTCGTTATGTTTGACAAAATG 57.364 32.000 1.27 0.00 34.32 2.32
1940 1948 9.921637 ATAATTGGTCGTTATGTTTGACAAAAT 57.078 25.926 1.27 2.11 34.32 1.82
1941 1949 9.751542 AATAATTGGTCGTTATGTTTGACAAAA 57.248 25.926 1.27 0.00 34.32 2.44
1978 1986 9.337396 ACATTGTAGATACAGTCAACAGAAAAA 57.663 29.630 0.00 0.00 37.52 1.94
1979 1987 8.902540 ACATTGTAGATACAGTCAACAGAAAA 57.097 30.769 0.00 0.00 37.52 2.29
1980 1988 8.902540 AACATTGTAGATACAGTCAACAGAAA 57.097 30.769 0.00 0.00 37.52 2.52
1981 1989 8.773645 CAAACATTGTAGATACAGTCAACAGAA 58.226 33.333 0.00 0.00 37.52 3.02
1982 1990 7.095229 GCAAACATTGTAGATACAGTCAACAGA 60.095 37.037 0.00 0.00 37.52 3.41
1983 1991 7.017645 GCAAACATTGTAGATACAGTCAACAG 58.982 38.462 0.00 0.00 37.52 3.16
1984 1992 6.347321 CGCAAACATTGTAGATACAGTCAACA 60.347 38.462 0.00 0.00 37.52 3.33
1985 1993 6.015504 CGCAAACATTGTAGATACAGTCAAC 58.984 40.000 0.00 0.00 37.52 3.18
1986 1994 5.121611 CCGCAAACATTGTAGATACAGTCAA 59.878 40.000 0.00 0.00 37.52 3.18
1987 1995 4.629634 CCGCAAACATTGTAGATACAGTCA 59.370 41.667 0.00 0.00 37.52 3.41
1988 1996 4.630069 ACCGCAAACATTGTAGATACAGTC 59.370 41.667 0.00 0.00 37.52 3.51
1989 1997 4.575885 ACCGCAAACATTGTAGATACAGT 58.424 39.130 0.00 0.00 37.52 3.55
1990 1998 5.545658 AACCGCAAACATTGTAGATACAG 57.454 39.130 0.00 0.00 37.52 2.74
1991 1999 5.950758 AAACCGCAAACATTGTAGATACA 57.049 34.783 0.00 0.00 0.00 2.29
1992 2000 8.905103 AATTAAACCGCAAACATTGTAGATAC 57.095 30.769 0.00 0.00 0.00 2.24
1994 2002 8.188139 CCTAATTAAACCGCAAACATTGTAGAT 58.812 33.333 0.00 0.00 0.00 1.98
1995 2003 7.531716 CCTAATTAAACCGCAAACATTGTAGA 58.468 34.615 0.00 0.00 0.00 2.59
1996 2004 6.252655 GCCTAATTAAACCGCAAACATTGTAG 59.747 38.462 0.00 0.00 0.00 2.74
1997 2005 6.071840 AGCCTAATTAAACCGCAAACATTGTA 60.072 34.615 0.00 0.00 0.00 2.41
1998 2006 4.926832 GCCTAATTAAACCGCAAACATTGT 59.073 37.500 0.00 0.00 0.00 2.71
1999 2007 5.167845 AGCCTAATTAAACCGCAAACATTG 58.832 37.500 0.00 0.00 0.00 2.82
2000 2008 5.185056 AGAGCCTAATTAAACCGCAAACATT 59.815 36.000 0.00 0.00 0.00 2.71
2001 2009 4.705023 AGAGCCTAATTAAACCGCAAACAT 59.295 37.500 0.00 0.00 0.00 2.71
2002 2010 4.076394 AGAGCCTAATTAAACCGCAAACA 58.924 39.130 0.00 0.00 0.00 2.83
2003 2011 4.412207 CAGAGCCTAATTAAACCGCAAAC 58.588 43.478 0.00 0.00 0.00 2.93
2004 2012 3.119637 GCAGAGCCTAATTAAACCGCAAA 60.120 43.478 0.00 0.00 0.00 3.68
2005 2013 2.422127 GCAGAGCCTAATTAAACCGCAA 59.578 45.455 0.00 0.00 0.00 4.85
2006 2014 2.014128 GCAGAGCCTAATTAAACCGCA 58.986 47.619 0.00 0.00 0.00 5.69
2007 2015 2.289565 AGCAGAGCCTAATTAAACCGC 58.710 47.619 0.00 0.00 0.00 5.68
2008 2016 3.938963 TGAAGCAGAGCCTAATTAAACCG 59.061 43.478 0.00 0.00 0.00 4.44
2009 2017 5.648092 TCTTGAAGCAGAGCCTAATTAAACC 59.352 40.000 0.00 0.00 0.00 3.27
2010 2018 6.743575 TCTTGAAGCAGAGCCTAATTAAAC 57.256 37.500 0.00 0.00 0.00 2.01
2011 2019 6.714810 TGTTCTTGAAGCAGAGCCTAATTAAA 59.285 34.615 0.00 0.00 0.00 1.52
2012 2020 6.237901 TGTTCTTGAAGCAGAGCCTAATTAA 58.762 36.000 0.00 0.00 0.00 1.40
2013 2021 5.804639 TGTTCTTGAAGCAGAGCCTAATTA 58.195 37.500 0.00 0.00 0.00 1.40
2014 2022 4.655963 TGTTCTTGAAGCAGAGCCTAATT 58.344 39.130 0.00 0.00 0.00 1.40
2015 2023 4.019860 TCTGTTCTTGAAGCAGAGCCTAAT 60.020 41.667 0.00 0.00 34.72 1.73
2016 2024 3.324846 TCTGTTCTTGAAGCAGAGCCTAA 59.675 43.478 0.00 0.00 34.72 2.69
2017 2025 2.899900 TCTGTTCTTGAAGCAGAGCCTA 59.100 45.455 0.00 0.00 34.72 3.93
2018 2026 1.696336 TCTGTTCTTGAAGCAGAGCCT 59.304 47.619 0.00 0.00 34.72 4.58
2019 2027 2.175878 TCTGTTCTTGAAGCAGAGCC 57.824 50.000 0.00 0.00 34.72 4.70
2020 2028 3.072944 ACATCTGTTCTTGAAGCAGAGC 58.927 45.455 8.19 0.00 41.73 4.09
2021 2029 4.567971 AGACATCTGTTCTTGAAGCAGAG 58.432 43.478 8.19 0.00 41.73 3.35
2022 2030 4.613925 AGACATCTGTTCTTGAAGCAGA 57.386 40.909 5.24 5.24 42.49 4.26
2023 2031 4.996122 AGAAGACATCTGTTCTTGAAGCAG 59.004 41.667 0.00 0.00 36.88 4.24
2024 2032 4.965814 AGAAGACATCTGTTCTTGAAGCA 58.034 39.130 0.00 0.00 36.88 3.91
2025 2033 5.938438 AAGAAGACATCTGTTCTTGAAGC 57.062 39.130 0.00 0.00 40.68 3.86
2026 2034 7.382110 TCCTAAGAAGACATCTGTTCTTGAAG 58.618 38.462 3.75 0.00 41.90 3.02
2027 2035 7.303182 TCCTAAGAAGACATCTGTTCTTGAA 57.697 36.000 3.75 0.00 41.90 2.69
2050 2058 4.919754 ACGTATAACTTCGACAACCACTTC 59.080 41.667 0.00 0.00 0.00 3.01
2070 2078 1.213013 GTGGCATCAGTCTCGACGT 59.787 57.895 0.00 0.00 36.20 4.34
2141 2149 3.071206 AGTCGGCCTCGCAGTCAT 61.071 61.111 0.00 0.00 36.13 3.06
2267 2277 0.326927 CGCAAGGGGGTCTTTCCTAA 59.673 55.000 0.00 0.00 32.41 2.69
2273 2283 0.404040 TTGAATCGCAAGGGGGTCTT 59.596 50.000 0.00 0.00 35.79 3.01
2304 2316 8.970020 ACATCATGTTGTTGAACAATACCATAT 58.030 29.630 14.40 5.53 45.23 1.78
2346 2358 9.934784 TGAATATTAAGGGGAATGATTTGAAGA 57.065 29.630 0.00 0.00 0.00 2.87
2353 2365 9.813826 CCTAAACTGAATATTAAGGGGAATGAT 57.186 33.333 4.78 0.00 0.00 2.45
2398 2411 2.136298 TGAAGCCACTGTTTCCAACA 57.864 45.000 0.00 0.00 39.52 3.33
2404 2417 4.573900 CTCACTAGATGAAGCCACTGTTT 58.426 43.478 0.00 0.00 36.69 2.83
2475 2488 4.679331 ACTCTCCAGACCTAGTAAGCTTT 58.321 43.478 3.20 0.00 0.00 3.51
2521 2534 9.638176 AGGAATAGAGCTTGAATTGATAACATT 57.362 29.630 0.00 0.00 0.00 2.71
2699 2712 7.095649 GGCAATCAAGAAAAAGGTGTTTGATAC 60.096 37.037 0.00 0.00 37.47 2.24


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

AutoCloner maintained by Alex Coulton.