Multiple sequence alignment - TraesCS2D01G595800

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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 TraesCS2D01G595800 chr2D 100.000 2337 0 0 1 2337 649062776 649060440 0.000000e+00 4316.0
1 TraesCS2D01G595800 chr2B 92.413 949 50 13 953 1890 784754364 784753427 0.000000e+00 1334.0
2 TraesCS2D01G595800 chr2B 92.513 187 10 3 2017 2200 784753397 784753212 4.950000e-67 265.0
3 TraesCS2D01G595800 chr2B 86.611 239 11 9 489 719 784754694 784754469 6.450000e-61 244.0
4 TraesCS2D01G595800 chr2B 80.645 310 20 23 139 421 784755162 784754866 1.090000e-48 204.0
5 TraesCS2D01G595800 chr2A 88.102 1059 52 21 804 1815 775658684 775659715 0.000000e+00 1190.0
6 TraesCS2D01G595800 chr2A 81.818 814 51 35 33 807 775657966 775658721 5.560000e-166 593.0
7 TraesCS2D01G595800 chr2A 89.529 191 15 4 1704 1892 775659654 775659841 1.080000e-58 237.0
8 TraesCS2D01G595800 chr2A 93.421 152 10 0 1973 2124 775659846 775659997 2.340000e-55 226.0
9 TraesCS2D01G595800 chr2A 85.714 70 4 4 2234 2298 775665328 775665396 4.170000e-08 69.4
10 TraesCS2D01G595800 chrUn 78.905 1114 146 48 985 2067 294783009 294781954 0.000000e+00 673.0
11 TraesCS2D01G595800 chr7A 84.203 690 86 16 979 1656 20096885 20097563 0.000000e+00 649.0
12 TraesCS2D01G595800 chr7A 82.623 305 43 4 1145 1440 20152318 20152621 6.410000e-66 261.0
13 TraesCS2D01G595800 chr7A 87.826 115 12 2 1219 1332 19319088 19318975 1.460000e-27 134.0
14 TraesCS2D01G595800 chr7D 84.058 690 86 17 979 1654 19961808 19962487 0.000000e+00 643.0
15 TraesCS2D01G595800 chr7D 88.696 115 11 2 1219 1332 18912620 18912507 3.130000e-29 139.0
16 TraesCS2D01G595800 chr5D 77.892 389 29 18 151 494 297581109 297580733 3.070000e-44 189.0
17 TraesCS2D01G595800 chr5D 88.421 95 8 2 52 144 297581250 297581157 6.830000e-21 111.0
18 TraesCS2D01G595800 chr4A 88.696 115 11 2 1219 1332 713352179 713352066 3.130000e-29 139.0
19 TraesCS2D01G595800 chr5A 88.776 98 8 2 49 144 401438106 401438202 1.470000e-22 117.0
20 TraesCS2D01G595800 chr5B 88.750 80 7 1 52 129 337907854 337907775 1.910000e-16 97.1


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 TraesCS2D01G595800 chr2D 649060440 649062776 2336 True 4316.00 4316 100.0000 1 2337 1 chr2D.!!$R1 2336
1 TraesCS2D01G595800 chr2B 784753212 784755162 1950 True 511.75 1334 88.0455 139 2200 4 chr2B.!!$R1 2061
2 TraesCS2D01G595800 chr2A 775657966 775659997 2031 False 561.50 1190 88.2175 33 2124 4 chr2A.!!$F2 2091
3 TraesCS2D01G595800 chrUn 294781954 294783009 1055 True 673.00 673 78.9050 985 2067 1 chrUn.!!$R1 1082
4 TraesCS2D01G595800 chr7A 20096885 20097563 678 False 649.00 649 84.2030 979 1656 1 chr7A.!!$F1 677
5 TraesCS2D01G595800 chr7D 19961808 19962487 679 False 643.00 643 84.0580 979 1654 1 chr7D.!!$F1 675

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
461 506 0.163788 GTGCGCTGTGTGTGTGTATC 59.836 55.0 9.73 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2283 2658 0.038159 AGGCGTGTACTGCAAGACTC 60.038 55.0 11.8 0.0 41.08 3.36 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
20 21 3.469008 TTCTTCAGACTCTTTCCGCAA 57.531 42.857 0.00 0.00 0.00 4.85
21 22 3.469008 TCTTCAGACTCTTTCCGCAAA 57.531 42.857 0.00 0.00 0.00 3.68
22 23 3.804036 TCTTCAGACTCTTTCCGCAAAA 58.196 40.909 0.00 0.00 0.00 2.44
23 24 4.196193 TCTTCAGACTCTTTCCGCAAAAA 58.804 39.130 0.00 0.00 0.00 1.94
75 76 3.827898 CGTGGCCTCTCCGTCCTC 61.828 72.222 3.32 0.00 37.80 3.71
108 111 3.083997 AGACCCATCCCACCGCTC 61.084 66.667 0.00 0.00 0.00 5.03
109 112 3.083997 GACCCATCCCACCGCTCT 61.084 66.667 0.00 0.00 0.00 4.09
120 123 1.363744 CACCGCTCTTTCCAGATCAC 58.636 55.000 0.00 0.00 0.00 3.06
133 136 3.932580 GATCACACGGCTCCGCACA 62.933 63.158 8.41 0.00 44.19 4.57
175 178 1.132913 TCATCCCTCTCCCTCCAGATG 60.133 57.143 0.00 0.00 33.92 2.90
190 193 2.465813 CAGATGGACCTCTCAGTTCCT 58.534 52.381 0.00 0.00 0.00 3.36
191 194 2.430332 CAGATGGACCTCTCAGTTCCTC 59.570 54.545 0.00 0.00 0.00 3.71
192 195 1.407258 GATGGACCTCTCAGTTCCTCG 59.593 57.143 0.00 0.00 0.00 4.63
193 196 1.251527 TGGACCTCTCAGTTCCTCGC 61.252 60.000 0.00 0.00 0.00 5.03
196 199 2.303175 GACCTCTCAGTTCCTCGCTAT 58.697 52.381 0.00 0.00 0.00 2.97
197 200 2.691011 GACCTCTCAGTTCCTCGCTATT 59.309 50.000 0.00 0.00 0.00 1.73
225 236 0.257616 ACCTCTCTCTTCCCTCCTCG 59.742 60.000 0.00 0.00 0.00 4.63
226 237 0.548989 CCTCTCTCTTCCCTCCTCGA 59.451 60.000 0.00 0.00 0.00 4.04
252 263 0.882927 CCCGTAGCTCTCTCTCCTCG 60.883 65.000 0.00 0.00 0.00 4.63
255 266 1.227704 TAGCTCTCTCTCCTCGCCG 60.228 63.158 0.00 0.00 0.00 6.46
376 415 2.516225 CCTTTCCCCCGATTCGCC 60.516 66.667 0.00 0.00 0.00 5.54
377 416 2.895372 CTTTCCCCCGATTCGCCG 60.895 66.667 0.00 0.00 0.00 6.46
396 441 1.855213 GCTGCCGCAAATCTGTGTCA 61.855 55.000 0.00 0.00 35.78 3.58
430 475 1.874019 CGCCTGATCCGTGTCGAAG 60.874 63.158 0.00 0.00 0.00 3.79
461 506 0.163788 GTGCGCTGTGTGTGTGTATC 59.836 55.000 9.73 0.00 0.00 2.24
557 715 3.075884 GCATGTTGAAATGGGCACAAAT 58.924 40.909 0.00 0.00 0.00 2.32
558 716 3.125658 GCATGTTGAAATGGGCACAAATC 59.874 43.478 0.00 0.00 0.00 2.17
559 717 4.571919 CATGTTGAAATGGGCACAAATCT 58.428 39.130 0.00 0.00 0.00 2.40
560 718 3.992643 TGTTGAAATGGGCACAAATCTG 58.007 40.909 0.00 0.00 0.00 2.90
561 719 3.244146 TGTTGAAATGGGCACAAATCTGG 60.244 43.478 0.00 0.00 0.00 3.86
562 720 1.275856 TGAAATGGGCACAAATCTGGC 59.724 47.619 0.00 0.00 35.98 4.85
563 721 1.551883 GAAATGGGCACAAATCTGGCT 59.448 47.619 0.00 0.00 36.92 4.75
564 722 2.530460 AATGGGCACAAATCTGGCTA 57.470 45.000 0.00 0.00 36.92 3.93
565 723 2.530460 ATGGGCACAAATCTGGCTAA 57.470 45.000 0.00 0.00 36.92 3.09
566 724 2.530460 TGGGCACAAATCTGGCTAAT 57.470 45.000 0.00 0.00 36.92 1.73
567 725 2.818921 TGGGCACAAATCTGGCTAATT 58.181 42.857 0.00 0.00 36.92 1.40
568 726 3.172339 TGGGCACAAATCTGGCTAATTT 58.828 40.909 0.00 0.00 36.92 1.82
625 787 0.901827 TACACATCCACGCACCAGAT 59.098 50.000 0.00 0.00 0.00 2.90
626 788 0.901827 ACACATCCACGCACCAGATA 59.098 50.000 0.00 0.00 0.00 1.98
627 789 1.486310 ACACATCCACGCACCAGATAT 59.514 47.619 0.00 0.00 0.00 1.63
628 790 2.698274 ACACATCCACGCACCAGATATA 59.302 45.455 0.00 0.00 0.00 0.86
711 881 2.633488 GGTACTTCATCTGCACCCTTC 58.367 52.381 0.00 0.00 0.00 3.46
765 935 5.126869 TCACTTGCCCAATAATACCACAATG 59.873 40.000 0.00 0.00 0.00 2.82
766 936 4.405358 ACTTGCCCAATAATACCACAATGG 59.595 41.667 0.00 0.00 45.02 3.16
767 937 4.256983 TGCCCAATAATACCACAATGGA 57.743 40.909 0.84 0.00 40.96 3.41
768 938 4.813809 TGCCCAATAATACCACAATGGAT 58.186 39.130 0.84 0.00 40.96 3.41
797 967 4.690748 TCGTGTTCAACTGGATTGATTCTC 59.309 41.667 0.00 0.00 46.80 2.87
807 977 6.825610 ACTGGATTGATTCTCTTCTACCATC 58.174 40.000 0.00 0.00 0.00 3.51
810 980 7.278135 TGGATTGATTCTCTTCTACCATCTTG 58.722 38.462 0.00 0.00 0.00 3.02
813 983 6.611613 TGATTCTCTTCTACCATCTTGTGT 57.388 37.500 0.00 0.00 0.00 3.72
816 986 6.419484 TTCTCTTCTACCATCTTGTGTTCA 57.581 37.500 0.00 0.00 0.00 3.18
818 988 6.223852 TCTCTTCTACCATCTTGTGTTCAAC 58.776 40.000 0.00 0.00 0.00 3.18
819 989 6.042093 TCTCTTCTACCATCTTGTGTTCAACT 59.958 38.462 0.00 0.00 0.00 3.16
821 991 4.641396 TCTACCATCTTGTGTTCAACTGG 58.359 43.478 0.00 0.00 37.33 4.00
822 992 3.576078 ACCATCTTGTGTTCAACTGGA 57.424 42.857 0.00 0.00 36.03 3.86
823 993 4.104383 ACCATCTTGTGTTCAACTGGAT 57.896 40.909 0.00 0.00 36.03 3.41
824 994 4.473444 ACCATCTTGTGTTCAACTGGATT 58.527 39.130 0.00 0.00 36.03 3.01
825 995 4.279169 ACCATCTTGTGTTCAACTGGATTG 59.721 41.667 0.00 0.00 39.94 2.67
826 996 4.520111 CCATCTTGTGTTCAACTGGATTGA 59.480 41.667 0.00 0.00 45.92 2.57
827 997 5.184479 CCATCTTGTGTTCAACTGGATTGAT 59.816 40.000 0.00 0.00 46.80 2.57
828 998 6.294899 CCATCTTGTGTTCAACTGGATTGATT 60.295 38.462 0.00 0.00 46.80 2.57
829 999 6.317789 TCTTGTGTTCAACTGGATTGATTC 57.682 37.500 0.00 0.00 46.80 2.52
830 1000 6.064060 TCTTGTGTTCAACTGGATTGATTCT 58.936 36.000 0.00 0.00 46.80 2.40
831 1001 5.694231 TGTGTTCAACTGGATTGATTCTG 57.306 39.130 0.00 0.00 46.80 3.02
832 1002 5.132502 TGTGTTCAACTGGATTGATTCTGT 58.867 37.500 0.00 0.00 46.80 3.41
833 1003 5.593909 TGTGTTCAACTGGATTGATTCTGTT 59.406 36.000 0.00 0.00 46.80 3.16
834 1004 6.145535 GTGTTCAACTGGATTGATTCTGTTC 58.854 40.000 0.00 0.00 46.80 3.18
835 1005 6.016777 GTGTTCAACTGGATTGATTCTGTTCT 60.017 38.462 0.00 0.00 46.80 3.01
836 1006 6.016860 TGTTCAACTGGATTGATTCTGTTCTG 60.017 38.462 0.00 0.00 46.80 3.02
837 1007 4.456911 TCAACTGGATTGATTCTGTTCTGC 59.543 41.667 0.00 0.00 42.62 4.26
838 1008 4.025040 ACTGGATTGATTCTGTTCTGCA 57.975 40.909 0.00 0.00 0.00 4.41
839 1009 3.755378 ACTGGATTGATTCTGTTCTGCAC 59.245 43.478 0.00 0.00 0.00 4.57
840 1010 3.084039 TGGATTGATTCTGTTCTGCACC 58.916 45.455 0.00 0.00 0.00 5.01
841 1011 2.424956 GGATTGATTCTGTTCTGCACCC 59.575 50.000 0.00 0.00 0.00 4.61
842 1012 2.957402 TTGATTCTGTTCTGCACCCT 57.043 45.000 0.00 0.00 0.00 4.34
843 1013 2.957402 TGATTCTGTTCTGCACCCTT 57.043 45.000 0.00 0.00 0.00 3.95
844 1014 2.507484 TGATTCTGTTCTGCACCCTTG 58.493 47.619 0.00 0.00 0.00 3.61
861 1031 3.119291 CCTTGCTCATGTCGATGTCTAC 58.881 50.000 0.00 0.00 0.00 2.59
870 1040 1.774085 GTCGATGTCTACGCGAATCAC 59.226 52.381 15.93 4.04 35.66 3.06
924 1109 3.145551 GCCTGCCATGCTTCCTGG 61.146 66.667 0.00 0.00 36.81 4.45
964 1166 8.800231 TGTGCATGCATTATATTTGACAATAC 57.200 30.769 25.64 4.82 0.00 1.89
965 1167 8.631797 TGTGCATGCATTATATTTGACAATACT 58.368 29.630 25.64 0.00 0.00 2.12
976 1178 6.764308 ATTTGACAATACTTATGTGCTGCT 57.236 33.333 0.00 0.00 0.00 4.24
1065 1267 2.427905 GCGTACGTCTGCGACACA 60.428 61.111 17.90 0.00 42.00 3.72
1160 1367 3.600388 CTGTGCCTAACCTCTTGTAAGG 58.400 50.000 0.00 0.00 42.55 2.69
1328 1537 1.129437 GCCAGAACTTCATCGTCAAGC 59.871 52.381 0.00 0.00 0.00 4.01
1531 1750 1.410004 TGAACTCTGTTCCTCGGTGT 58.590 50.000 7.81 0.00 0.00 4.16
1538 1757 5.903810 ACTCTGTTCCTCGGTGTAATTATC 58.096 41.667 0.00 0.00 0.00 1.75
1542 1761 4.468510 TGTTCCTCGGTGTAATTATCCACT 59.531 41.667 6.27 0.00 0.00 4.00
1543 1762 5.657745 TGTTCCTCGGTGTAATTATCCACTA 59.342 40.000 6.27 0.00 0.00 2.74
1544 1763 6.183360 TGTTCCTCGGTGTAATTATCCACTAG 60.183 42.308 6.27 0.00 0.00 2.57
1545 1764 4.831155 TCCTCGGTGTAATTATCCACTAGG 59.169 45.833 14.92 14.92 36.69 3.02
1546 1765 4.557205 CTCGGTGTAATTATCCACTAGGC 58.443 47.826 6.27 0.00 33.74 3.93
1547 1766 3.962063 TCGGTGTAATTATCCACTAGGCA 59.038 43.478 6.27 0.00 33.74 4.75
1549 1768 4.202223 CGGTGTAATTATCCACTAGGCAGT 60.202 45.833 6.27 0.00 34.42 4.40
1550 1769 5.010314 CGGTGTAATTATCCACTAGGCAGTA 59.990 44.000 6.27 0.00 32.21 2.74
1650 1879 3.621268 TGTGATGTTAACGAGCCTATTGC 59.379 43.478 0.26 0.00 41.71 3.56
1681 1910 0.840288 AGCATGGTGGACTGGTGGTA 60.840 55.000 0.00 0.00 0.00 3.25
1747 1977 8.370940 TGGTAAACCATTGCTGAAAATAATTCA 58.629 29.630 0.00 0.00 42.01 2.57
1751 1981 9.675464 AAACCATTGCTGAAAATAATTCATCAT 57.325 25.926 0.00 0.00 0.00 2.45
1755 1985 9.529325 CATTGCTGAAAATAATTCATCATCTGT 57.471 29.630 0.00 0.00 0.00 3.41
1769 2058 8.692110 TTCATCATCTGTTGTTATTTGCAATC 57.308 30.769 0.00 0.00 0.00 2.67
1770 2059 7.259882 TCATCATCTGTTGTTATTTGCAATCC 58.740 34.615 0.00 0.00 0.00 3.01
1892 2182 1.832167 GTGCCCACTGAAGCCCAAA 60.832 57.895 0.00 0.00 0.00 3.28
1896 2186 2.243478 TGCCCACTGAAGCCCAAATATA 59.757 45.455 0.00 0.00 0.00 0.86
1897 2187 3.117169 TGCCCACTGAAGCCCAAATATAT 60.117 43.478 0.00 0.00 0.00 0.86
1898 2188 4.105537 TGCCCACTGAAGCCCAAATATATA 59.894 41.667 0.00 0.00 0.00 0.86
1899 2189 5.222316 TGCCCACTGAAGCCCAAATATATAT 60.222 40.000 0.00 0.00 0.00 0.86
1900 2190 5.126061 GCCCACTGAAGCCCAAATATATATG 59.874 44.000 0.00 0.00 0.00 1.78
1901 2191 5.653769 CCCACTGAAGCCCAAATATATATGG 59.346 44.000 0.00 0.00 36.42 2.74
1902 2192 5.126061 CCACTGAAGCCCAAATATATATGGC 59.874 44.000 12.57 12.57 42.48 4.40
1903 2193 5.126061 CACTGAAGCCCAAATATATATGGCC 59.874 44.000 15.55 0.00 43.18 5.36
1904 2194 4.609301 TGAAGCCCAAATATATATGGCCC 58.391 43.478 15.55 10.39 43.18 5.80
1905 2195 4.045207 TGAAGCCCAAATATATATGGCCCA 59.955 41.667 15.55 12.20 43.18 5.36
1906 2196 4.690767 AGCCCAAATATATATGGCCCAA 57.309 40.909 15.55 0.00 43.18 4.12
1907 2197 4.352893 AGCCCAAATATATATGGCCCAAC 58.647 43.478 15.55 0.00 43.18 3.77
1908 2198 4.093011 GCCCAAATATATATGGCCCAACA 58.907 43.478 0.00 0.00 36.07 3.33
1909 2199 4.081697 GCCCAAATATATATGGCCCAACAC 60.082 45.833 0.00 0.00 36.07 3.32
1910 2200 5.332743 CCCAAATATATATGGCCCAACACT 58.667 41.667 0.00 0.00 35.28 3.55
1911 2201 6.489603 CCCAAATATATATGGCCCAACACTA 58.510 40.000 0.00 0.00 35.28 2.74
1912 2202 6.603201 CCCAAATATATATGGCCCAACACTAG 59.397 42.308 0.00 0.00 35.28 2.57
1913 2203 7.175104 CCAAATATATATGGCCCAACACTAGT 58.825 38.462 0.00 0.00 0.00 2.57
1914 2204 8.325787 CCAAATATATATGGCCCAACACTAGTA 58.674 37.037 0.00 0.00 0.00 1.82
1915 2205 9.162764 CAAATATATATGGCCCAACACTAGTAC 57.837 37.037 0.00 0.00 0.00 2.73
1916 2206 8.444010 AATATATATGGCCCAACACTAGTACA 57.556 34.615 0.00 0.00 0.00 2.90
1917 2207 6.757173 ATATATGGCCCAACACTAGTACAA 57.243 37.500 0.00 0.00 0.00 2.41
1918 2208 2.851263 TGGCCCAACACTAGTACAAG 57.149 50.000 0.00 0.00 0.00 3.16
1919 2209 2.051692 TGGCCCAACACTAGTACAAGT 58.948 47.619 0.00 0.00 0.00 3.16
1920 2210 3.241156 TGGCCCAACACTAGTACAAGTA 58.759 45.455 0.00 0.00 0.00 2.24
1921 2211 3.841845 TGGCCCAACACTAGTACAAGTAT 59.158 43.478 0.00 0.00 0.00 2.12
1922 2212 4.081309 TGGCCCAACACTAGTACAAGTATC 60.081 45.833 0.00 0.00 0.00 2.24
1923 2213 4.161754 GGCCCAACACTAGTACAAGTATCT 59.838 45.833 0.00 0.00 0.00 1.98
1924 2214 5.109903 GCCCAACACTAGTACAAGTATCTG 58.890 45.833 0.00 0.00 0.00 2.90
1925 2215 5.337330 GCCCAACACTAGTACAAGTATCTGT 60.337 44.000 0.00 0.00 0.00 3.41
1926 2216 6.100004 CCCAACACTAGTACAAGTATCTGTG 58.900 44.000 0.00 0.00 0.00 3.66
1927 2217 5.577164 CCAACACTAGTACAAGTATCTGTGC 59.423 44.000 0.00 0.00 32.62 4.57
1928 2218 5.977489 ACACTAGTACAAGTATCTGTGCA 57.023 39.130 0.00 0.00 34.67 4.57
1929 2219 6.531503 ACACTAGTACAAGTATCTGTGCAT 57.468 37.500 0.00 0.00 34.67 3.96
1930 2220 6.333416 ACACTAGTACAAGTATCTGTGCATG 58.667 40.000 0.00 0.00 34.67 4.06
1931 2221 6.071334 ACACTAGTACAAGTATCTGTGCATGT 60.071 38.462 0.00 0.00 34.67 3.21
1932 2222 6.254373 CACTAGTACAAGTATCTGTGCATGTG 59.746 42.308 0.00 0.00 34.67 3.21
1933 2223 5.405935 AGTACAAGTATCTGTGCATGTGA 57.594 39.130 0.00 0.00 34.67 3.58
1934 2224 5.982356 AGTACAAGTATCTGTGCATGTGAT 58.018 37.500 0.00 0.00 34.67 3.06
1935 2225 6.045318 AGTACAAGTATCTGTGCATGTGATC 58.955 40.000 0.00 0.00 34.67 2.92
1936 2226 5.095145 ACAAGTATCTGTGCATGTGATCT 57.905 39.130 0.00 0.00 0.00 2.75
1937 2227 5.494724 ACAAGTATCTGTGCATGTGATCTT 58.505 37.500 0.00 0.00 0.00 2.40
1938 2228 5.583854 ACAAGTATCTGTGCATGTGATCTTC 59.416 40.000 0.00 0.00 0.00 2.87
1939 2229 5.349061 AGTATCTGTGCATGTGATCTTCA 57.651 39.130 0.00 0.00 0.00 3.02
1940 2230 5.926663 AGTATCTGTGCATGTGATCTTCAT 58.073 37.500 0.00 0.00 0.00 2.57
1941 2231 7.059202 AGTATCTGTGCATGTGATCTTCATA 57.941 36.000 0.00 0.00 0.00 2.15
1942 2232 7.503549 AGTATCTGTGCATGTGATCTTCATAA 58.496 34.615 0.00 0.00 0.00 1.90
1943 2233 8.155510 AGTATCTGTGCATGTGATCTTCATAAT 58.844 33.333 0.00 0.00 0.00 1.28
1944 2234 6.613755 TCTGTGCATGTGATCTTCATAATG 57.386 37.500 0.00 0.00 0.00 1.90
1945 2235 6.117488 TCTGTGCATGTGATCTTCATAATGT 58.883 36.000 0.00 0.00 30.57 2.71
1946 2236 6.600427 TCTGTGCATGTGATCTTCATAATGTT 59.400 34.615 0.00 0.00 30.57 2.71
1947 2237 7.121611 TCTGTGCATGTGATCTTCATAATGTTT 59.878 33.333 0.00 0.00 30.57 2.83
1948 2238 7.604549 TGTGCATGTGATCTTCATAATGTTTT 58.395 30.769 0.00 0.00 30.57 2.43
1949 2239 8.089597 TGTGCATGTGATCTTCATAATGTTTTT 58.910 29.630 0.00 0.00 30.57 1.94
1950 2240 8.589629 GTGCATGTGATCTTCATAATGTTTTTC 58.410 33.333 0.00 0.00 30.57 2.29
1951 2241 7.485595 TGCATGTGATCTTCATAATGTTTTTCG 59.514 33.333 0.00 0.00 30.57 3.46
1952 2242 7.485913 GCATGTGATCTTCATAATGTTTTTCGT 59.514 33.333 0.00 0.00 30.57 3.85
1953 2243 9.345517 CATGTGATCTTCATAATGTTTTTCGTT 57.654 29.630 0.00 0.00 0.00 3.85
1954 2244 9.912634 ATGTGATCTTCATAATGTTTTTCGTTT 57.087 25.926 0.00 0.00 0.00 3.60
1955 2245 9.743057 TGTGATCTTCATAATGTTTTTCGTTTT 57.257 25.926 0.00 0.00 0.00 2.43
1960 2250 9.574458 TCTTCATAATGTTTTTCGTTTTTGACA 57.426 25.926 0.00 0.00 0.00 3.58
1963 2253 9.574458 TCATAATGTTTTTCGTTTTTGACAAGA 57.426 25.926 0.00 0.00 0.00 3.02
1966 2256 7.883229 ATGTTTTTCGTTTTTGACAAGAACT 57.117 28.000 16.81 0.00 0.00 3.01
1967 2257 7.099666 TGTTTTTCGTTTTTGACAAGAACTG 57.900 32.000 16.81 11.51 0.00 3.16
1968 2258 6.697892 TGTTTTTCGTTTTTGACAAGAACTGT 59.302 30.769 16.81 0.00 42.61 3.55
1969 2259 6.683090 TTTTCGTTTTTGACAAGAACTGTG 57.317 33.333 16.81 4.85 38.84 3.66
1970 2260 3.753842 TCGTTTTTGACAAGAACTGTGC 58.246 40.909 16.81 0.00 38.84 4.57
1971 2261 2.525891 CGTTTTTGACAAGAACTGTGCG 59.474 45.455 16.81 2.91 38.84 5.34
1976 2266 0.510359 GACAAGAACTGTGCGAGCAG 59.490 55.000 0.00 5.32 38.84 4.24
2032 2402 1.135603 CCACAAGCCATTCACATGACG 60.136 52.381 0.00 0.00 31.07 4.35
2040 2412 2.158645 CCATTCACATGACGCAACGTTA 59.841 45.455 0.00 0.00 41.37 3.18
2047 2419 3.932710 ACATGACGCAACGTTATTGATCT 59.067 39.130 0.00 0.00 41.37 2.75
2073 2445 6.035327 GCTGAAATGGTTTACATGCAGATTTC 59.965 38.462 11.98 0.00 41.59 2.17
2124 2496 9.654417 GAACATCAGATTTCAAAATTTGTTTGG 57.346 29.630 5.56 0.00 33.59 3.28
2127 2499 9.654417 CATCAGATTTCAAAATTTGTTTGGTTC 57.346 29.630 5.56 0.00 33.59 3.62
2156 2530 1.247567 CACAAGAAAGGGGCGAACAT 58.752 50.000 0.00 0.00 0.00 2.71
2212 2587 2.373735 CAGAATTCTGCGGTTATGCG 57.626 50.000 21.96 0.00 37.15 4.73
2213 2588 0.657840 AGAATTCTGCGGTTATGCGC 59.342 50.000 7.30 0.00 37.81 6.09
2214 2589 0.376852 GAATTCTGCGGTTATGCGCA 59.623 50.000 14.96 14.96 39.40 6.09
2215 2590 1.002468 GAATTCTGCGGTTATGCGCAT 60.002 47.619 28.23 28.23 40.46 4.73
2216 2591 1.024271 ATTCTGCGGTTATGCGCATT 58.976 45.000 30.42 12.85 40.46 3.56
2217 2592 0.376852 TTCTGCGGTTATGCGCATTC 59.623 50.000 30.42 20.76 40.46 2.67
2218 2593 1.368019 CTGCGGTTATGCGCATTCG 60.368 57.895 30.42 27.24 40.46 3.34
2232 2607 4.652175 CGCATTCGCACACTATCATAAT 57.348 40.909 0.00 0.00 38.40 1.28
2233 2608 5.022335 CGCATTCGCACACTATCATAATT 57.978 39.130 0.00 0.00 38.40 1.40
2234 2609 6.151975 CGCATTCGCACACTATCATAATTA 57.848 37.500 0.00 0.00 38.40 1.40
2235 2610 6.765089 CGCATTCGCACACTATCATAATTAT 58.235 36.000 0.00 0.00 38.40 1.28
2236 2611 7.894847 CGCATTCGCACACTATCATAATTATA 58.105 34.615 0.00 0.00 38.40 0.98
2237 2612 8.542953 CGCATTCGCACACTATCATAATTATAT 58.457 33.333 0.00 0.00 38.40 0.86
2238 2613 9.855361 GCATTCGCACACTATCATAATTATATC 57.145 33.333 0.00 0.00 38.36 1.63
2241 2616 8.634475 TCGCACACTATCATAATTATATCAGC 57.366 34.615 0.00 0.00 0.00 4.26
2242 2617 7.706607 TCGCACACTATCATAATTATATCAGCC 59.293 37.037 0.00 0.00 0.00 4.85
2243 2618 7.042456 CGCACACTATCATAATTATATCAGCCC 60.042 40.741 0.00 0.00 0.00 5.19
2244 2619 7.227512 GCACACTATCATAATTATATCAGCCCC 59.772 40.741 0.00 0.00 0.00 5.80
2245 2620 8.489489 CACACTATCATAATTATATCAGCCCCT 58.511 37.037 0.00 0.00 0.00 4.79
2246 2621 8.709308 ACACTATCATAATTATATCAGCCCCTC 58.291 37.037 0.00 0.00 0.00 4.30
2247 2622 8.932610 CACTATCATAATTATATCAGCCCCTCT 58.067 37.037 0.00 0.00 0.00 3.69
2248 2623 9.153479 ACTATCATAATTATATCAGCCCCTCTC 57.847 37.037 0.00 0.00 0.00 3.20
2249 2624 9.378504 CTATCATAATTATATCAGCCCCTCTCT 57.621 37.037 0.00 0.00 0.00 3.10
2251 2626 8.774546 TCATAATTATATCAGCCCCTCTCTAG 57.225 38.462 0.00 0.00 0.00 2.43
2252 2627 8.569596 TCATAATTATATCAGCCCCTCTCTAGA 58.430 37.037 0.00 0.00 0.00 2.43
2253 2628 8.859090 CATAATTATATCAGCCCCTCTCTAGAG 58.141 40.741 13.98 13.98 41.71 2.43
2268 2643 7.673641 CTCTCTAGAGGGGCATATCATTTAT 57.326 40.000 19.67 0.00 38.48 1.40
2269 2644 8.088463 CTCTCTAGAGGGGCATATCATTTATT 57.912 38.462 19.67 0.00 38.48 1.40
2270 2645 8.454859 TCTCTAGAGGGGCATATCATTTATTT 57.545 34.615 19.67 0.00 0.00 1.40
2271 2646 8.894592 TCTCTAGAGGGGCATATCATTTATTTT 58.105 33.333 19.67 0.00 0.00 1.82
2274 2649 9.401058 CTAGAGGGGCATATCATTTATTTTAGG 57.599 37.037 0.00 0.00 0.00 2.69
2275 2650 6.665248 AGAGGGGCATATCATTTATTTTAGGC 59.335 38.462 0.00 0.00 0.00 3.93
2276 2651 6.565036 AGGGGCATATCATTTATTTTAGGCT 58.435 36.000 0.00 0.00 0.00 4.58
2277 2652 6.665248 AGGGGCATATCATTTATTTTAGGCTC 59.335 38.462 0.00 0.00 0.00 4.70
2278 2653 6.437162 GGGGCATATCATTTATTTTAGGCTCA 59.563 38.462 0.00 0.00 0.00 4.26
2279 2654 7.363268 GGGGCATATCATTTATTTTAGGCTCAG 60.363 40.741 0.00 0.00 0.00 3.35
2280 2655 7.031975 GGCATATCATTTATTTTAGGCTCAGC 58.968 38.462 0.00 0.00 0.00 4.26
2281 2656 7.094032 GGCATATCATTTATTTTAGGCTCAGCT 60.094 37.037 0.00 0.00 0.00 4.24
2282 2657 7.754027 GCATATCATTTATTTTAGGCTCAGCTG 59.246 37.037 7.63 7.63 0.00 4.24
2283 2658 6.645790 ATCATTTATTTTAGGCTCAGCTGG 57.354 37.500 15.13 5.82 0.00 4.85
2284 2659 5.754782 TCATTTATTTTAGGCTCAGCTGGA 58.245 37.500 15.13 0.00 0.00 3.86
2285 2660 5.824624 TCATTTATTTTAGGCTCAGCTGGAG 59.175 40.000 15.13 11.07 46.93 3.86
2286 2661 4.844349 TTATTTTAGGCTCAGCTGGAGT 57.156 40.909 15.13 0.00 45.88 3.85
2290 2665 4.613929 GGCTCAGCTGGAGTCTTG 57.386 61.111 15.13 0.00 45.05 3.02
2291 2666 1.744741 GGCTCAGCTGGAGTCTTGC 60.745 63.158 15.13 7.06 45.05 4.01
2292 2667 1.004080 GCTCAGCTGGAGTCTTGCA 60.004 57.895 15.13 0.00 45.88 4.08
2293 2668 1.020333 GCTCAGCTGGAGTCTTGCAG 61.020 60.000 15.13 1.06 45.88 4.41
2294 2669 0.321021 CTCAGCTGGAGTCTTGCAGT 59.679 55.000 15.13 0.00 43.95 4.40
2295 2670 1.547820 CTCAGCTGGAGTCTTGCAGTA 59.452 52.381 15.13 0.00 43.95 2.74
2296 2671 1.273606 TCAGCTGGAGTCTTGCAGTAC 59.726 52.381 15.13 0.00 43.95 2.73
2297 2672 1.001293 CAGCTGGAGTCTTGCAGTACA 59.999 52.381 5.57 0.00 43.95 2.90
2298 2673 1.001406 AGCTGGAGTCTTGCAGTACAC 59.999 52.381 9.74 0.00 43.95 2.90
2299 2674 1.702886 CTGGAGTCTTGCAGTACACG 58.297 55.000 0.00 0.00 37.92 4.49
2300 2675 0.319555 TGGAGTCTTGCAGTACACGC 60.320 55.000 0.00 0.00 0.00 5.34
2301 2676 1.014564 GGAGTCTTGCAGTACACGCC 61.015 60.000 5.00 0.00 0.00 5.68
2302 2677 0.038159 GAGTCTTGCAGTACACGCCT 60.038 55.000 5.00 0.00 0.00 5.52
2303 2678 0.393077 AGTCTTGCAGTACACGCCTT 59.607 50.000 5.00 0.00 0.00 4.35
2304 2679 0.790814 GTCTTGCAGTACACGCCTTC 59.209 55.000 5.00 0.00 0.00 3.46
2305 2680 0.679505 TCTTGCAGTACACGCCTTCT 59.320 50.000 5.00 0.00 0.00 2.85
2306 2681 1.070134 TCTTGCAGTACACGCCTTCTT 59.930 47.619 5.00 0.00 0.00 2.52
2307 2682 1.195448 CTTGCAGTACACGCCTTCTTG 59.805 52.381 5.00 0.00 0.00 3.02
2308 2683 0.391228 TGCAGTACACGCCTTCTTGA 59.609 50.000 5.00 0.00 0.00 3.02
2309 2684 1.071605 GCAGTACACGCCTTCTTGAG 58.928 55.000 0.00 0.00 0.00 3.02
2310 2685 1.071605 CAGTACACGCCTTCTTGAGC 58.928 55.000 0.00 0.00 0.00 4.26
2311 2686 0.969894 AGTACACGCCTTCTTGAGCT 59.030 50.000 0.00 0.00 0.00 4.09
2312 2687 1.067495 AGTACACGCCTTCTTGAGCTC 60.067 52.381 6.82 6.82 0.00 4.09
2313 2688 0.246635 TACACGCCTTCTTGAGCTCC 59.753 55.000 12.15 0.00 0.00 4.70
2314 2689 2.097038 CACGCCTTCTTGAGCTCCG 61.097 63.158 12.15 8.01 0.00 4.63
2315 2690 2.276116 ACGCCTTCTTGAGCTCCGA 61.276 57.895 12.15 4.90 0.00 4.55
2316 2691 1.807573 CGCCTTCTTGAGCTCCGAC 60.808 63.158 12.15 0.00 0.00 4.79
2317 2692 1.293498 GCCTTCTTGAGCTCCGACA 59.707 57.895 12.15 0.00 0.00 4.35
2318 2693 1.016653 GCCTTCTTGAGCTCCGACAC 61.017 60.000 12.15 0.00 0.00 3.67
2319 2694 0.318441 CCTTCTTGAGCTCCGACACA 59.682 55.000 12.15 0.00 0.00 3.72
2320 2695 1.671261 CCTTCTTGAGCTCCGACACAG 60.671 57.143 12.15 2.72 0.00 3.66
2321 2696 0.319900 TTCTTGAGCTCCGACACAGC 60.320 55.000 12.15 0.00 37.12 4.40
2322 2697 2.049156 TTGAGCTCCGACACAGCG 60.049 61.111 12.15 0.00 42.14 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.469008 TTGCGGAAAGAGTCTGAAGAA 57.531 42.857 0.00 0.00 34.07 2.52
2 3 4.552166 TTTTTGCGGAAAGAGTCTGAAG 57.448 40.909 1.41 0.00 34.07 3.02
27 28 7.281100 CCACAACTAGAGTCTGAAGAACTTTTT 59.719 37.037 1.86 0.00 0.00 1.94
28 29 6.763610 CCACAACTAGAGTCTGAAGAACTTTT 59.236 38.462 1.86 0.00 0.00 2.27
29 30 6.127026 ACCACAACTAGAGTCTGAAGAACTTT 60.127 38.462 1.86 0.00 0.00 2.66
30 31 5.364157 ACCACAACTAGAGTCTGAAGAACTT 59.636 40.000 1.86 0.00 0.00 2.66
31 32 4.896482 ACCACAACTAGAGTCTGAAGAACT 59.104 41.667 1.86 0.00 0.00 3.01
44 45 1.007336 GCCACGTCGACCACAACTAG 61.007 60.000 10.58 0.00 0.00 2.57
75 76 0.663568 GTCTCTGTGACGTGGAACCG 60.664 60.000 0.00 0.00 35.81 4.44
108 111 1.363744 GAGCCGTGTGATCTGGAAAG 58.636 55.000 0.00 0.00 0.00 2.62
109 112 0.036388 GGAGCCGTGTGATCTGGAAA 60.036 55.000 0.00 0.00 0.00 3.13
147 150 1.005156 GAGAGGGATGAGGATGCGC 60.005 63.158 0.00 0.00 0.00 6.09
190 193 5.145564 AGAGAGGTGGGTAATTAATAGCGA 58.854 41.667 0.00 0.00 32.63 4.93
191 194 5.244178 AGAGAGAGGTGGGTAATTAATAGCG 59.756 44.000 0.00 0.00 32.63 4.26
192 195 6.673839 AGAGAGAGGTGGGTAATTAATAGC 57.326 41.667 0.00 0.00 0.00 2.97
193 196 7.256368 GGGAAGAGAGAGGTGGGTAATTAATAG 60.256 44.444 0.00 0.00 0.00 1.73
196 199 4.720273 GGGAAGAGAGAGGTGGGTAATTAA 59.280 45.833 0.00 0.00 0.00 1.40
197 200 4.015541 AGGGAAGAGAGAGGTGGGTAATTA 60.016 45.833 0.00 0.00 0.00 1.40
225 236 1.073284 AGAGAGCTACGGGGAGAGATC 59.927 57.143 0.00 0.00 0.00 2.75
226 237 1.073284 GAGAGAGCTACGGGGAGAGAT 59.927 57.143 0.00 0.00 0.00 2.75
354 392 2.604299 GAATCGGGGGAAAGGACGGG 62.604 65.000 0.00 0.00 0.00 5.28
377 416 1.154150 GACACAGATTTGCGGCAGC 60.154 57.895 1.67 0.31 45.41 5.25
378 417 0.110056 GTGACACAGATTTGCGGCAG 60.110 55.000 1.67 0.00 0.00 4.85
386 431 2.071540 CAGCGACATGTGACACAGATT 58.928 47.619 14.66 0.15 0.00 2.40
396 441 2.325082 GCGGGAAACAGCGACATGT 61.325 57.895 0.00 0.00 42.91 3.21
442 487 0.163788 GATACACACACACAGCGCAC 59.836 55.000 11.47 0.00 0.00 5.34
461 506 2.785681 GCATGAACAAGCACGATTCGAG 60.786 50.000 13.95 6.05 0.00 4.04
561 719 3.095032 TCGCCGGCGAAAATTAGC 58.905 55.556 46.56 5.91 46.01 3.09
652 818 9.454859 CCCAACAGAAACTAATTAAGAGAGATT 57.545 33.333 0.00 0.00 0.00 2.40
740 910 4.667573 TGTGGTATTATTGGGCAAGTGAA 58.332 39.130 0.00 0.00 0.00 3.18
765 935 2.932614 CAGTTGAACACGAGATGGATCC 59.067 50.000 4.20 4.20 0.00 3.36
766 936 2.932614 CCAGTTGAACACGAGATGGATC 59.067 50.000 0.00 0.00 0.00 3.36
767 937 2.567169 TCCAGTTGAACACGAGATGGAT 59.433 45.455 0.00 0.00 30.63 3.41
768 938 1.967779 TCCAGTTGAACACGAGATGGA 59.032 47.619 0.00 0.00 33.11 3.41
797 967 5.180117 CCAGTTGAACACAAGATGGTAGAAG 59.820 44.000 0.00 0.00 31.97 2.85
816 986 4.217118 GTGCAGAACAGAATCAATCCAGTT 59.783 41.667 0.00 0.00 31.63 3.16
818 988 3.128242 GGTGCAGAACAGAATCAATCCAG 59.872 47.826 0.00 0.00 0.00 3.86
819 989 3.084039 GGTGCAGAACAGAATCAATCCA 58.916 45.455 0.00 0.00 0.00 3.41
821 991 3.350833 AGGGTGCAGAACAGAATCAATC 58.649 45.455 0.00 0.00 0.00 2.67
822 992 3.446442 AGGGTGCAGAACAGAATCAAT 57.554 42.857 0.00 0.00 0.00 2.57
823 993 2.886523 CAAGGGTGCAGAACAGAATCAA 59.113 45.455 0.00 0.00 0.00 2.57
824 994 2.507484 CAAGGGTGCAGAACAGAATCA 58.493 47.619 0.00 0.00 0.00 2.57
837 1007 1.012086 CATCGACATGAGCAAGGGTG 58.988 55.000 0.00 0.00 30.57 4.61
838 1008 0.615331 ACATCGACATGAGCAAGGGT 59.385 50.000 0.00 0.00 33.72 4.34
839 1009 1.134580 AGACATCGACATGAGCAAGGG 60.135 52.381 0.00 0.00 33.72 3.95
840 1010 2.306341 AGACATCGACATGAGCAAGG 57.694 50.000 0.00 0.00 33.72 3.61
841 1011 2.786027 CGTAGACATCGACATGAGCAAG 59.214 50.000 0.00 0.00 33.72 4.01
842 1012 2.797491 CGTAGACATCGACATGAGCAA 58.203 47.619 0.00 0.00 33.72 3.91
843 1013 1.533965 GCGTAGACATCGACATGAGCA 60.534 52.381 0.00 0.00 33.72 4.26
844 1014 1.124462 GCGTAGACATCGACATGAGC 58.876 55.000 0.00 0.00 33.72 4.26
845 1015 1.003866 TCGCGTAGACATCGACATGAG 60.004 52.381 5.77 0.00 33.72 2.90
846 1016 1.011333 TCGCGTAGACATCGACATGA 58.989 50.000 5.77 0.00 33.72 3.07
847 1017 1.822581 TTCGCGTAGACATCGACATG 58.177 50.000 5.77 0.00 35.92 3.21
848 1018 2.032924 TGATTCGCGTAGACATCGACAT 59.967 45.455 5.77 0.00 31.48 3.06
849 1019 1.399089 TGATTCGCGTAGACATCGACA 59.601 47.619 5.77 0.00 31.48 4.35
850 1020 1.774085 GTGATTCGCGTAGACATCGAC 59.226 52.381 5.77 0.36 31.48 4.20
851 1021 1.593793 CGTGATTCGCGTAGACATCGA 60.594 52.381 5.77 0.00 32.40 3.59
852 1022 0.764801 CGTGATTCGCGTAGACATCG 59.235 55.000 5.77 4.98 32.40 3.84
861 1031 0.163788 AGTTGCTTTCGTGATTCGCG 59.836 50.000 13.26 13.26 39.67 5.87
870 1040 5.377358 CACTAAGACAATCAGTTGCTTTCG 58.623 41.667 0.00 0.00 38.96 3.46
912 1097 0.906775 AAAATGGCCAGGAAGCATGG 59.093 50.000 13.05 0.00 41.04 3.66
920 1105 0.817013 ATGCGTGTAAAATGGCCAGG 59.183 50.000 13.05 0.00 0.00 4.45
924 1109 0.991344 GCACATGCGTGTAAAATGGC 59.009 50.000 12.10 6.13 45.50 4.40
964 1166 2.575694 AGAGACGAGCAGCACATAAG 57.424 50.000 0.00 0.00 0.00 1.73
965 1167 2.231235 TGAAGAGACGAGCAGCACATAA 59.769 45.455 0.00 0.00 0.00 1.90
971 1173 1.392853 CACAATGAAGAGACGAGCAGC 59.607 52.381 0.00 0.00 0.00 5.25
973 1175 1.270252 TGCACAATGAAGAGACGAGCA 60.270 47.619 0.00 0.00 0.00 4.26
974 1176 1.392853 CTGCACAATGAAGAGACGAGC 59.607 52.381 0.00 0.00 0.00 5.03
975 1177 2.681706 ACTGCACAATGAAGAGACGAG 58.318 47.619 0.00 0.00 0.00 4.18
976 1178 2.820059 ACTGCACAATGAAGAGACGA 57.180 45.000 0.00 0.00 0.00 4.20
1065 1267 7.308229 CCAAAGATCTTCTTGTCAGAAACGATT 60.308 37.037 8.78 0.00 38.63 3.34
1160 1367 3.924144 AGAAGCAGCGATTAGATGGATC 58.076 45.455 0.00 0.00 36.61 3.36
1384 1602 5.833667 AGGAACTTCAAAACCCTAGAAAAGG 59.166 40.000 0.00 0.00 40.29 3.11
1464 1682 0.040958 CACCTCAAAGTTGCTCACGC 60.041 55.000 0.00 0.00 0.00 5.34
1546 1765 9.848172 GAAACAACAATGCAGTTATTTTTACTG 57.152 29.630 0.00 0.00 44.55 2.74
1547 1766 9.040939 GGAAACAACAATGCAGTTATTTTTACT 57.959 29.630 0.00 0.00 29.06 2.24
1549 1768 7.306866 GCGGAAACAACAATGCAGTTATTTTTA 60.307 33.333 0.00 0.00 29.06 1.52
1550 1769 6.510960 GCGGAAACAACAATGCAGTTATTTTT 60.511 34.615 0.00 0.00 29.06 1.94
1650 1879 5.010012 AGTCCACCATGCTAAAAGTCAAAAG 59.990 40.000 0.00 0.00 0.00 2.27
1681 1910 7.596248 CAGCACAAGCAAAAAGAATTATAGTGT 59.404 33.333 0.00 0.00 45.49 3.55
1747 1977 7.414222 AGGATTGCAAATAACAACAGATGAT 57.586 32.000 1.71 0.00 0.00 2.45
1751 1981 8.177119 AGTTTAGGATTGCAAATAACAACAGA 57.823 30.769 1.71 0.00 0.00 3.41
1830 2119 1.471684 GAGTCCAGCATTTTCAGCAGG 59.528 52.381 0.00 0.00 39.73 4.85
1892 2182 8.444010 TTGTACTAGTGTTGGGCCATATATAT 57.556 34.615 7.26 0.00 0.00 0.86
1896 2186 4.473559 ACTTGTACTAGTGTTGGGCCATAT 59.526 41.667 7.26 0.00 0.00 1.78
1897 2187 3.841845 ACTTGTACTAGTGTTGGGCCATA 59.158 43.478 7.26 0.00 0.00 2.74
1898 2188 2.642807 ACTTGTACTAGTGTTGGGCCAT 59.357 45.455 7.26 0.00 0.00 4.40
1899 2189 2.051692 ACTTGTACTAGTGTTGGGCCA 58.948 47.619 9.25 0.00 0.00 5.36
1900 2190 2.853235 ACTTGTACTAGTGTTGGGCC 57.147 50.000 9.25 0.00 0.00 5.80
1901 2191 5.109903 CAGATACTTGTACTAGTGTTGGGC 58.890 45.833 18.57 2.14 0.00 5.36
1902 2192 6.100004 CACAGATACTTGTACTAGTGTTGGG 58.900 44.000 18.57 11.40 0.00 4.12
1903 2193 5.577164 GCACAGATACTTGTACTAGTGTTGG 59.423 44.000 18.57 10.97 0.00 3.77
1904 2194 6.156519 TGCACAGATACTTGTACTAGTGTTG 58.843 40.000 18.57 14.98 0.00 3.33
1905 2195 6.340962 TGCACAGATACTTGTACTAGTGTT 57.659 37.500 18.57 7.23 0.00 3.32
1906 2196 5.977489 TGCACAGATACTTGTACTAGTGT 57.023 39.130 18.57 12.77 0.00 3.55
1907 2197 6.254373 CACATGCACAGATACTTGTACTAGTG 59.746 42.308 18.57 5.80 0.00 2.74
1908 2198 6.152831 TCACATGCACAGATACTTGTACTAGT 59.847 38.462 14.36 14.36 0.00 2.57
1909 2199 6.564328 TCACATGCACAGATACTTGTACTAG 58.436 40.000 2.56 2.56 0.00 2.57
1910 2200 6.524101 TCACATGCACAGATACTTGTACTA 57.476 37.500 0.00 0.00 0.00 1.82
1911 2201 5.405935 TCACATGCACAGATACTTGTACT 57.594 39.130 0.00 0.00 0.00 2.73
1912 2202 6.045318 AGATCACATGCACAGATACTTGTAC 58.955 40.000 0.00 0.00 0.00 2.90
1913 2203 6.225981 AGATCACATGCACAGATACTTGTA 57.774 37.500 0.00 0.00 0.00 2.41
1914 2204 5.095145 AGATCACATGCACAGATACTTGT 57.905 39.130 0.00 0.00 0.00 3.16
1915 2205 5.583457 TGAAGATCACATGCACAGATACTTG 59.417 40.000 0.00 0.00 0.00 3.16
1916 2206 5.737860 TGAAGATCACATGCACAGATACTT 58.262 37.500 0.00 0.00 0.00 2.24
1917 2207 5.349061 TGAAGATCACATGCACAGATACT 57.651 39.130 0.00 0.00 0.00 2.12
1918 2208 7.719778 TTATGAAGATCACATGCACAGATAC 57.280 36.000 13.27 0.00 0.00 2.24
1919 2209 7.935210 ACATTATGAAGATCACATGCACAGATA 59.065 33.333 13.27 0.00 0.00 1.98
1920 2210 6.771267 ACATTATGAAGATCACATGCACAGAT 59.229 34.615 13.27 0.00 0.00 2.90
1921 2211 6.117488 ACATTATGAAGATCACATGCACAGA 58.883 36.000 13.27 0.00 0.00 3.41
1922 2212 6.373186 ACATTATGAAGATCACATGCACAG 57.627 37.500 13.27 0.00 0.00 3.66
1923 2213 6.762702 AACATTATGAAGATCACATGCACA 57.237 33.333 13.27 0.00 0.00 4.57
1924 2214 8.470040 AAAAACATTATGAAGATCACATGCAC 57.530 30.769 13.27 0.00 0.00 4.57
1925 2215 7.485595 CGAAAAACATTATGAAGATCACATGCA 59.514 33.333 13.27 0.00 0.00 3.96
1926 2216 7.485913 ACGAAAAACATTATGAAGATCACATGC 59.514 33.333 13.27 0.00 0.00 4.06
1927 2217 8.900511 ACGAAAAACATTATGAAGATCACATG 57.099 30.769 13.27 0.00 0.00 3.21
1928 2218 9.912634 AAACGAAAAACATTATGAAGATCACAT 57.087 25.926 0.00 9.65 0.00 3.21
1929 2219 9.743057 AAAACGAAAAACATTATGAAGATCACA 57.257 25.926 0.00 0.00 0.00 3.58
1934 2224 9.574458 TGTCAAAAACGAAAAACATTATGAAGA 57.426 25.926 0.00 0.00 0.00 2.87
1937 2227 9.574458 TCTTGTCAAAAACGAAAAACATTATGA 57.426 25.926 0.00 0.00 0.00 2.15
1940 2230 9.413048 AGTTCTTGTCAAAAACGAAAAACATTA 57.587 25.926 0.00 0.00 0.00 1.90
1941 2231 8.220434 CAGTTCTTGTCAAAAACGAAAAACATT 58.780 29.630 0.00 0.00 0.00 2.71
1942 2232 7.383843 ACAGTTCTTGTCAAAAACGAAAAACAT 59.616 29.630 0.00 0.00 33.87 2.71
1943 2233 6.697892 ACAGTTCTTGTCAAAAACGAAAAACA 59.302 30.769 0.00 0.00 33.87 2.83
1944 2234 7.001347 CACAGTTCTTGTCAAAAACGAAAAAC 58.999 34.615 0.00 0.00 38.16 2.43
1945 2235 6.346199 GCACAGTTCTTGTCAAAAACGAAAAA 60.346 34.615 0.00 0.00 38.16 1.94
1946 2236 5.117897 GCACAGTTCTTGTCAAAAACGAAAA 59.882 36.000 0.00 0.00 38.16 2.29
1947 2237 4.619336 GCACAGTTCTTGTCAAAAACGAAA 59.381 37.500 0.00 0.00 38.16 3.46
1948 2238 4.162812 GCACAGTTCTTGTCAAAAACGAA 58.837 39.130 0.00 0.00 38.16 3.85
1949 2239 3.726486 CGCACAGTTCTTGTCAAAAACGA 60.726 43.478 0.00 0.00 38.16 3.85
1950 2240 2.525891 CGCACAGTTCTTGTCAAAAACG 59.474 45.455 0.00 0.00 38.16 3.60
1951 2241 3.753842 TCGCACAGTTCTTGTCAAAAAC 58.246 40.909 0.00 0.00 38.16 2.43
1952 2242 3.730662 GCTCGCACAGTTCTTGTCAAAAA 60.731 43.478 0.00 0.00 38.16 1.94
1953 2243 2.223249 GCTCGCACAGTTCTTGTCAAAA 60.223 45.455 0.00 0.00 38.16 2.44
1954 2244 1.330521 GCTCGCACAGTTCTTGTCAAA 59.669 47.619 0.00 0.00 38.16 2.69
1955 2245 0.937304 GCTCGCACAGTTCTTGTCAA 59.063 50.000 0.00 0.00 38.16 3.18
1956 2246 0.179086 TGCTCGCACAGTTCTTGTCA 60.179 50.000 0.00 0.00 38.16 3.58
1957 2247 0.510359 CTGCTCGCACAGTTCTTGTC 59.490 55.000 0.00 0.00 38.16 3.18
1958 2248 1.502163 GCTGCTCGCACAGTTCTTGT 61.502 55.000 6.41 0.00 41.94 3.16
1959 2249 1.206072 GCTGCTCGCACAGTTCTTG 59.794 57.895 6.41 0.00 39.96 3.02
1960 2250 1.226686 CTGCTGCTCGCACAGTTCTT 61.227 55.000 0.00 0.00 45.47 2.52
1961 2251 1.667191 CTGCTGCTCGCACAGTTCT 60.667 57.895 0.00 0.00 45.47 3.01
1962 2252 1.224069 TTCTGCTGCTCGCACAGTTC 61.224 55.000 15.73 0.00 45.47 3.01
1963 2253 1.227645 TTCTGCTGCTCGCACAGTT 60.228 52.632 15.73 0.00 45.47 3.16
1964 2254 1.958205 GTTCTGCTGCTCGCACAGT 60.958 57.895 15.73 0.00 45.47 3.55
1965 2255 1.226686 AAGTTCTGCTGCTCGCACAG 61.227 55.000 0.00 12.27 45.47 3.66
1966 2256 0.815213 AAAGTTCTGCTGCTCGCACA 60.815 50.000 0.00 0.00 45.47 4.57
1967 2257 0.385223 CAAAGTTCTGCTGCTCGCAC 60.385 55.000 0.00 0.00 45.47 5.34
1969 2259 0.385223 CACAAAGTTCTGCTGCTCGC 60.385 55.000 0.00 0.00 39.77 5.03
1970 2260 0.940126 ACACAAAGTTCTGCTGCTCG 59.060 50.000 0.00 0.00 0.00 5.03
1971 2261 3.427161 AAACACAAAGTTCTGCTGCTC 57.573 42.857 0.00 0.00 40.26 4.26
1976 2266 6.073276 ACCTTTTTCAAAACACAAAGTTCTGC 60.073 34.615 0.00 0.00 40.26 4.26
2032 2402 4.340894 TTCAGCAGATCAATAACGTTGC 57.659 40.909 11.99 3.47 0.00 4.17
2040 2412 6.839124 TGTAAACCATTTCAGCAGATCAAT 57.161 33.333 0.00 0.00 0.00 2.57
2047 2419 3.825585 TCTGCATGTAAACCATTTCAGCA 59.174 39.130 0.00 0.00 34.19 4.41
2073 2445 6.095440 CCAGTTACCATCTCCCAATTTTACAG 59.905 42.308 0.00 0.00 0.00 2.74
2124 2496 4.156739 CCTTTCTTGTGCTTCCCATAGAAC 59.843 45.833 0.00 0.00 31.13 3.01
2127 2499 3.019564 CCCTTTCTTGTGCTTCCCATAG 58.980 50.000 0.00 0.00 0.00 2.23
2141 2515 2.224670 TGTGTTATGTTCGCCCCTTTCT 60.225 45.455 0.00 0.00 0.00 2.52
2156 2530 6.514870 GCTTGTCCTTTTGTCATCATGTGTTA 60.515 38.462 0.00 0.00 0.00 2.41
2191 2566 2.285834 CGCATAACCGCAGAATTCTGTC 60.286 50.000 30.88 22.73 45.45 3.51
2192 2567 1.665679 CGCATAACCGCAGAATTCTGT 59.334 47.619 30.88 17.09 45.45 3.41
2193 2568 2.373735 CGCATAACCGCAGAATTCTG 57.626 50.000 27.82 27.82 46.40 3.02
2212 2587 9.855361 GATATAATTATGATAGTGTGCGAATGC 57.145 33.333 8.28 0.00 43.20 3.56
2215 2590 9.087424 GCTGATATAATTATGATAGTGTGCGAA 57.913 33.333 8.28 0.00 0.00 4.70
2216 2591 7.706607 GGCTGATATAATTATGATAGTGTGCGA 59.293 37.037 8.28 0.00 0.00 5.10
2217 2592 7.042456 GGGCTGATATAATTATGATAGTGTGCG 60.042 40.741 8.28 0.00 0.00 5.34
2218 2593 7.227512 GGGGCTGATATAATTATGATAGTGTGC 59.772 40.741 8.28 2.45 0.00 4.57
2219 2594 8.489489 AGGGGCTGATATAATTATGATAGTGTG 58.511 37.037 8.28 0.00 0.00 3.82
2220 2595 8.629821 AGGGGCTGATATAATTATGATAGTGT 57.370 34.615 8.28 0.00 0.00 3.55
2221 2596 8.932610 AGAGGGGCTGATATAATTATGATAGTG 58.067 37.037 8.28 0.00 0.00 2.74
2222 2597 9.153479 GAGAGGGGCTGATATAATTATGATAGT 57.847 37.037 8.28 0.00 0.00 2.12
2223 2598 9.378504 AGAGAGGGGCTGATATAATTATGATAG 57.621 37.037 8.28 4.65 0.00 2.08
2225 2600 9.378504 CTAGAGAGGGGCTGATATAATTATGAT 57.621 37.037 8.28 0.00 0.00 2.45
2226 2601 8.569596 TCTAGAGAGGGGCTGATATAATTATGA 58.430 37.037 8.28 0.00 0.00 2.15
2227 2602 8.774546 TCTAGAGAGGGGCTGATATAATTATG 57.225 38.462 8.28 0.00 0.00 1.90
2244 2619 7.673641 ATAAATGATATGCCCCTCTAGAGAG 57.326 40.000 21.76 7.94 41.71 3.20
2245 2620 8.454859 AAATAAATGATATGCCCCTCTAGAGA 57.545 34.615 21.76 0.88 0.00 3.10
2248 2623 9.401058 CCTAAAATAAATGATATGCCCCTCTAG 57.599 37.037 0.00 0.00 0.00 2.43
2249 2624 7.834181 GCCTAAAATAAATGATATGCCCCTCTA 59.166 37.037 0.00 0.00 0.00 2.43
2250 2625 6.665248 GCCTAAAATAAATGATATGCCCCTCT 59.335 38.462 0.00 0.00 0.00 3.69
2251 2626 6.665248 AGCCTAAAATAAATGATATGCCCCTC 59.335 38.462 0.00 0.00 0.00 4.30
2252 2627 6.565036 AGCCTAAAATAAATGATATGCCCCT 58.435 36.000 0.00 0.00 0.00 4.79
2253 2628 6.437162 TGAGCCTAAAATAAATGATATGCCCC 59.563 38.462 0.00 0.00 0.00 5.80
2254 2629 7.466746 TGAGCCTAAAATAAATGATATGCCC 57.533 36.000 0.00 0.00 0.00 5.36
2255 2630 7.031975 GCTGAGCCTAAAATAAATGATATGCC 58.968 38.462 0.00 0.00 0.00 4.40
2256 2631 7.754027 CAGCTGAGCCTAAAATAAATGATATGC 59.246 37.037 8.42 0.00 0.00 3.14
2257 2632 8.242053 CCAGCTGAGCCTAAAATAAATGATATG 58.758 37.037 17.39 0.00 0.00 1.78
2258 2633 8.166061 TCCAGCTGAGCCTAAAATAAATGATAT 58.834 33.333 17.39 0.00 0.00 1.63
2259 2634 7.517320 TCCAGCTGAGCCTAAAATAAATGATA 58.483 34.615 17.39 0.00 0.00 2.15
2260 2635 6.367983 TCCAGCTGAGCCTAAAATAAATGAT 58.632 36.000 17.39 0.00 0.00 2.45
2261 2636 5.754782 TCCAGCTGAGCCTAAAATAAATGA 58.245 37.500 17.39 0.00 0.00 2.57
2262 2637 5.591877 ACTCCAGCTGAGCCTAAAATAAATG 59.408 40.000 17.39 0.00 45.61 2.32
2263 2638 5.760131 ACTCCAGCTGAGCCTAAAATAAAT 58.240 37.500 17.39 0.00 45.61 1.40
2264 2639 5.045578 AGACTCCAGCTGAGCCTAAAATAAA 60.046 40.000 17.39 0.00 45.61 1.40
2265 2640 4.471386 AGACTCCAGCTGAGCCTAAAATAA 59.529 41.667 17.39 0.00 45.61 1.40
2266 2641 4.033709 AGACTCCAGCTGAGCCTAAAATA 58.966 43.478 17.39 0.00 45.61 1.40
2267 2642 2.843113 AGACTCCAGCTGAGCCTAAAAT 59.157 45.455 17.39 0.00 45.61 1.82
2268 2643 2.260822 AGACTCCAGCTGAGCCTAAAA 58.739 47.619 17.39 0.00 45.61 1.52
2269 2644 1.944177 AGACTCCAGCTGAGCCTAAA 58.056 50.000 17.39 0.00 45.61 1.85
2270 2645 1.552337 CAAGACTCCAGCTGAGCCTAA 59.448 52.381 17.39 0.00 45.61 2.69
2271 2646 1.189752 CAAGACTCCAGCTGAGCCTA 58.810 55.000 17.39 0.00 45.61 3.93
2272 2647 1.981636 CAAGACTCCAGCTGAGCCT 59.018 57.895 17.39 5.73 45.61 4.58
2273 2648 1.744741 GCAAGACTCCAGCTGAGCC 60.745 63.158 17.39 3.26 45.61 4.70
2274 2649 1.004080 TGCAAGACTCCAGCTGAGC 60.004 57.895 17.39 0.00 45.61 4.26
2275 2650 0.321021 ACTGCAAGACTCCAGCTGAG 59.679 55.000 17.39 13.13 42.04 3.35
2276 2651 1.273606 GTACTGCAAGACTCCAGCTGA 59.726 52.381 17.39 0.00 37.43 4.26
2277 2652 1.001293 TGTACTGCAAGACTCCAGCTG 59.999 52.381 6.78 6.78 37.43 4.24
2278 2653 1.001406 GTGTACTGCAAGACTCCAGCT 59.999 52.381 0.00 0.00 37.43 4.24
2279 2654 1.433534 GTGTACTGCAAGACTCCAGC 58.566 55.000 0.00 0.00 37.43 4.85
2280 2655 1.702886 CGTGTACTGCAAGACTCCAG 58.297 55.000 0.00 2.47 37.43 3.86
2281 2656 0.319555 GCGTGTACTGCAAGACTCCA 60.320 55.000 5.89 0.00 37.43 3.86
2282 2657 1.014564 GGCGTGTACTGCAAGACTCC 61.015 60.000 11.80 0.00 37.43 3.85
2283 2658 0.038159 AGGCGTGTACTGCAAGACTC 60.038 55.000 11.80 0.00 41.08 3.36
2284 2659 0.393077 AAGGCGTGTACTGCAAGACT 59.607 50.000 11.80 0.00 46.96 3.24
2285 2660 0.790814 GAAGGCGTGTACTGCAAGAC 59.209 55.000 11.80 0.00 37.43 3.01
2286 2661 0.679505 AGAAGGCGTGTACTGCAAGA 59.320 50.000 11.80 0.00 37.43 3.02
2287 2662 1.195448 CAAGAAGGCGTGTACTGCAAG 59.805 52.381 11.80 0.00 42.29 4.01
2288 2663 1.202592 TCAAGAAGGCGTGTACTGCAA 60.203 47.619 11.80 0.00 0.00 4.08
2289 2664 0.391228 TCAAGAAGGCGTGTACTGCA 59.609 50.000 11.80 0.00 0.00 4.41
2290 2665 1.071605 CTCAAGAAGGCGTGTACTGC 58.928 55.000 0.00 0.00 0.00 4.40
2291 2666 1.071605 GCTCAAGAAGGCGTGTACTG 58.928 55.000 0.00 0.00 0.00 2.74
2292 2667 0.969894 AGCTCAAGAAGGCGTGTACT 59.030 50.000 0.00 0.00 0.00 2.73
2293 2668 1.351153 GAGCTCAAGAAGGCGTGTAC 58.649 55.000 9.40 0.00 0.00 2.90
2294 2669 0.246635 GGAGCTCAAGAAGGCGTGTA 59.753 55.000 17.19 0.00 0.00 2.90
2295 2670 1.004440 GGAGCTCAAGAAGGCGTGT 60.004 57.895 17.19 0.00 0.00 4.49
2296 2671 2.097038 CGGAGCTCAAGAAGGCGTG 61.097 63.158 17.19 0.00 0.00 5.34
2297 2672 2.262915 CGGAGCTCAAGAAGGCGT 59.737 61.111 17.19 0.00 0.00 5.68
2298 2673 1.807573 GTCGGAGCTCAAGAAGGCG 60.808 63.158 17.19 8.01 0.00 5.52
2299 2674 1.016653 GTGTCGGAGCTCAAGAAGGC 61.017 60.000 17.19 3.16 0.00 4.35
2300 2675 0.318441 TGTGTCGGAGCTCAAGAAGG 59.682 55.000 17.19 0.00 0.00 3.46
2301 2676 1.707632 CTGTGTCGGAGCTCAAGAAG 58.292 55.000 17.19 5.29 0.00 2.85
2302 2677 0.319900 GCTGTGTCGGAGCTCAAGAA 60.320 55.000 17.19 3.16 33.37 2.52
2303 2678 1.290324 GCTGTGTCGGAGCTCAAGA 59.710 57.895 17.19 11.54 33.37 3.02
2304 2679 2.091112 CGCTGTGTCGGAGCTCAAG 61.091 63.158 17.19 9.13 34.03 3.02
2305 2680 2.049156 CGCTGTGTCGGAGCTCAA 60.049 61.111 17.19 0.00 34.03 3.02


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

AutoCloner maintained by Alex Coulton.