Multiple sequence alignment - TraesCS5D01G536700

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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 TraesCS5D01G536700 chr5D 100.000 7573 0 0 1 7573 549848526 549856098 0.000000e+00 13985
1 TraesCS5D01G536700 chr5D 94.859 603 26 3 1 602 549826993 549827591 0.000000e+00 937
2 TraesCS5D01G536700 chr4A 93.993 4112 195 31 1554 5644 617950292 617946212 0.000000e+00 6178
3 TraesCS5D01G536700 chr4A 92.921 1003 49 12 6447 7433 617945700 617944704 0.000000e+00 1439
4 TraesCS5D01G536700 chr4A 96.607 501 17 0 1056 1556 617950851 617950351 0.000000e+00 832
5 TraesCS5D01G536700 chr4A 95.417 480 16 2 5728 6207 617946221 617945748 0.000000e+00 760
6 TraesCS5D01G536700 chr4A 84.053 301 16 18 775 1062 617951428 617951147 2.100000e-65 261
7 TraesCS5D01G536700 chr4A 87.586 145 10 2 7437 7573 617944615 617944471 2.190000e-35 161
8 TraesCS5D01G536700 chr5B 95.231 3418 109 23 2904 6283 701456377 701459778 0.000000e+00 5360
9 TraesCS5D01G536700 chr5B 89.650 2087 127 55 805 2836 701454327 701456379 0.000000e+00 2575
10 TraesCS5D01G536700 chr5B 91.278 1158 51 21 6305 7437 701459767 701460899 0.000000e+00 1533
11 TraesCS5D01G536700 chr5B 88.980 245 25 2 1749 1992 165765612 165765855 1.230000e-77 302
12 TraesCS5D01G536700 chr5B 88.980 245 25 2 1749 1992 166157225 166157468 1.230000e-77 302
13 TraesCS5D01G536700 chr5B 93.827 81 3 1 607 687 701454217 701454295 3.710000e-23 121
14 TraesCS5D01G536700 chr4D 92.699 589 34 6 18 602 311632048 311631465 0.000000e+00 841
15 TraesCS5D01G536700 chr4D 93.092 579 30 4 31 604 311625314 311624741 0.000000e+00 839
16 TraesCS5D01G536700 chr3D 92.013 601 35 10 4 602 522408492 522407903 0.000000e+00 832
17 TraesCS5D01G536700 chr3D 91.196 602 41 8 1 598 400903034 400903627 0.000000e+00 808
18 TraesCS5D01G536700 chr3D 91.167 600 41 9 1 598 406357036 406357625 0.000000e+00 804
19 TraesCS5D01G536700 chr3D 84.807 362 46 6 4205 4558 23086396 23086756 9.350000e-94 355
20 TraesCS5D01G536700 chr3D 87.037 108 10 3 2808 2914 555598221 555598325 1.330000e-22 119
21 TraesCS5D01G536700 chr7D 91.820 599 39 9 4 598 262836176 262835584 0.000000e+00 826
22 TraesCS5D01G536700 chr7D 91.542 603 41 9 4 602 262840346 262839750 0.000000e+00 822
23 TraesCS5D01G536700 chr6A 92.281 583 37 6 18 598 307874720 307874144 0.000000e+00 821
24 TraesCS5D01G536700 chr6A 86.047 258 20 5 1749 1992 34546565 34546310 5.830000e-66 263
25 TraesCS5D01G536700 chr6A 91.011 89 7 1 2832 2919 509279056 509279144 1.330000e-22 119
26 TraesCS5D01G536700 chr3A 85.271 387 45 9 4179 4557 32177531 32177913 9.220000e-104 388
27 TraesCS5D01G536700 chr1D 95.000 100 4 1 1581 1680 460325971 460325873 1.020000e-33 156
28 TraesCS5D01G536700 chr2A 97.333 75 1 1 2834 2907 754039015 754039089 7.980000e-25 126
29 TraesCS5D01G536700 chr2D 96.053 76 2 1 2831 2905 347465708 347465783 1.030000e-23 122
30 TraesCS5D01G536700 chr6D 93.827 81 4 1 2834 2913 469492411 469492331 3.710000e-23 121
31 TraesCS5D01G536700 chr6D 93.827 81 4 1 2834 2913 469511219 469511139 3.710000e-23 121
32 TraesCS5D01G536700 chr6D 91.011 89 7 1 2832 2919 368365283 368365371 1.330000e-22 119
33 TraesCS5D01G536700 chr6B 91.011 89 7 1 2832 2919 553057204 553057116 1.330000e-22 119
34 TraesCS5D01G536700 chr4B 93.750 80 3 1 2830 2907 269174154 269174075 1.330000e-22 119


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 TraesCS5D01G536700 chr5D 549848526 549856098 7572 False 13985.000000 13985 100.000000 1 7573 1 chr5D.!!$F2 7572
1 TraesCS5D01G536700 chr5D 549826993 549827591 598 False 937.000000 937 94.859000 1 602 1 chr5D.!!$F1 601
2 TraesCS5D01G536700 chr4A 617944471 617951428 6957 True 1605.166667 6178 91.762833 775 7573 6 chr4A.!!$R1 6798
3 TraesCS5D01G536700 chr5B 701454217 701460899 6682 False 2397.250000 5360 92.496500 607 7437 4 chr5B.!!$F3 6830
4 TraesCS5D01G536700 chr4D 311631465 311632048 583 True 841.000000 841 92.699000 18 602 1 chr4D.!!$R2 584
5 TraesCS5D01G536700 chr4D 311624741 311625314 573 True 839.000000 839 93.092000 31 604 1 chr4D.!!$R1 573
6 TraesCS5D01G536700 chr3D 522407903 522408492 589 True 832.000000 832 92.013000 4 602 1 chr3D.!!$R1 598
7 TraesCS5D01G536700 chr3D 400903034 400903627 593 False 808.000000 808 91.196000 1 598 1 chr3D.!!$F2 597
8 TraesCS5D01G536700 chr3D 406357036 406357625 589 False 804.000000 804 91.167000 1 598 1 chr3D.!!$F3 597
9 TraesCS5D01G536700 chr7D 262835584 262840346 4762 True 824.000000 826 91.681000 4 602 2 chr7D.!!$R1 598
10 TraesCS5D01G536700 chr6A 307874144 307874720 576 True 821.000000 821 92.281000 18 598 1 chr6A.!!$R2 580

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
944 969 0.250553 CCGCTAGATCTCCTCCGTCT 60.251 60.000 0.00 0.00 0.00 4.18 F
995 1020 0.264359 CTCCCCTCAGATCCACCTCT 59.736 60.000 0.00 0.00 0.00 3.69 F
2010 2410 0.863799 CCGATGAATCTGACCGCATG 59.136 55.000 0.00 0.00 0.00 4.06 F
3709 6546 1.270907 ATGGAAGGAGTCGTTGCTCT 58.729 50.000 16.49 3.45 35.89 4.09 F
4302 7139 0.690192 TCCTCCGATTGTCCTTGCAA 59.310 50.000 0.00 0.00 0.00 4.08 F
5901 8758 1.211709 CGCCCGCCTTCGAAATTTT 59.788 52.632 0.00 0.00 38.10 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2277 2677 0.745845 AATCAGATGGTGCTGTCGGC 60.746 55.000 0.00 0.0 42.22 5.54 R
2280 2680 3.538591 TGATGAATCAGATGGTGCTGTC 58.461 45.455 0.00 0.0 37.20 3.51 R
3757 6594 0.036164 ACACCGTTGCCAGCTGATTA 59.964 50.000 17.39 0.0 0.00 1.75 R
4850 7701 1.303317 GGACGGGCCAAGACAACAT 60.303 57.895 4.39 0.0 36.34 2.71 R
6283 9152 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.0 0.00 3.82 R
6727 9608 1.264749 TGGATTCTGGAGGTGACCGG 61.265 60.000 0.00 0.0 37.63 5.28 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
279 286 9.948964 TCTTCTCTCATGAAAATCATTGAGTTA 57.051 29.630 0.00 0.00 34.28 2.24
463 478 7.669089 AAGTTTGGGAAAGTCCTTTTATTCA 57.331 32.000 0.00 0.00 36.57 2.57
503 518 6.750039 TCGAAAAGTTTTGAATTTCACTCACC 59.250 34.615 5.36 0.00 33.68 4.02
533 548 7.980662 AGTCAATCAATCACACAACAATCAAAA 59.019 29.630 0.00 0.00 0.00 2.44
534 549 8.602328 GTCAATCAATCACACAACAATCAAAAA 58.398 29.630 0.00 0.00 0.00 1.94
603 619 6.748132 AGATTTTTGGGATGTTACACAACTG 58.252 36.000 0.00 0.00 32.68 3.16
605 621 1.518325 TGGGATGTTACACAACTGCG 58.482 50.000 0.00 0.00 35.56 5.18
649 665 0.312729 CCCTGGTTTTTCCGGTTTCG 59.687 55.000 0.00 0.00 40.86 3.46
672 688 6.361768 GGGAACCCTCTAGAAGGTTATATG 57.638 45.833 23.05 3.01 46.38 1.78
673 689 5.248705 GGGAACCCTCTAGAAGGTTATATGG 59.751 48.000 23.05 4.02 46.38 2.74
751 767 8.749841 TGAAGAAAAATCAGAAAAACGTTTGA 57.250 26.923 15.46 8.65 0.00 2.69
752 768 9.197694 TGAAGAAAAATCAGAAAAACGTTTGAA 57.802 25.926 15.46 0.00 0.00 2.69
762 778 9.364989 TCAGAAAAACGTTTGAAAATTTCATCT 57.635 25.926 15.46 4.07 39.84 2.90
763 779 9.971744 CAGAAAAACGTTTGAAAATTTCATCTT 57.028 25.926 15.46 0.00 39.84 2.40
838 857 7.359595 TCATGAGAAGTTCGGTTTTGTAAATG 58.640 34.615 0.00 0.00 0.00 2.32
839 858 5.516090 TGAGAAGTTCGGTTTTGTAAATGC 58.484 37.500 0.00 0.00 0.00 3.56
841 860 3.276882 AGTTCGGTTTTGTAAATGCCG 57.723 42.857 11.89 11.89 43.32 5.69
844 863 3.546002 TCGGTTTTGTAAATGCCGAAG 57.454 42.857 15.94 0.00 46.81 3.79
855 874 2.185608 GCCGAAGAGCAGGAGGAC 59.814 66.667 0.00 0.00 0.00 3.85
857 876 2.046864 CCGAAGAGCAGGAGGACGA 61.047 63.158 0.00 0.00 0.00 4.20
858 877 1.431440 CGAAGAGCAGGAGGACGAG 59.569 63.158 0.00 0.00 0.00 4.18
859 878 1.309499 CGAAGAGCAGGAGGACGAGT 61.309 60.000 0.00 0.00 0.00 4.18
890 912 3.075005 GGTCCAGCCTCCGTAGCA 61.075 66.667 0.00 0.00 0.00 3.49
891 913 2.496817 GTCCAGCCTCCGTAGCAG 59.503 66.667 0.00 0.00 0.00 4.24
893 915 1.304962 TCCAGCCTCCGTAGCAGAA 60.305 57.895 0.00 0.00 0.00 3.02
894 916 1.142748 CCAGCCTCCGTAGCAGAAG 59.857 63.158 0.00 0.00 0.00 2.85
896 918 0.532573 CAGCCTCCGTAGCAGAAGAA 59.467 55.000 0.00 0.00 0.00 2.52
898 920 1.834263 AGCCTCCGTAGCAGAAGAAAT 59.166 47.619 0.00 0.00 0.00 2.17
938 963 0.606944 CGCTACCCGCTAGATCTCCT 60.607 60.000 0.00 0.00 36.13 3.69
939 964 1.170442 GCTACCCGCTAGATCTCCTC 58.830 60.000 0.00 0.00 35.14 3.71
940 965 1.828979 CTACCCGCTAGATCTCCTCC 58.171 60.000 0.00 0.00 0.00 4.30
942 967 1.228306 CCCGCTAGATCTCCTCCGT 60.228 63.158 0.00 0.00 0.00 4.69
943 968 1.238625 CCCGCTAGATCTCCTCCGTC 61.239 65.000 0.00 0.00 0.00 4.79
944 969 0.250553 CCGCTAGATCTCCTCCGTCT 60.251 60.000 0.00 0.00 0.00 4.18
945 970 1.002201 CCGCTAGATCTCCTCCGTCTA 59.998 57.143 0.00 0.00 0.00 2.59
946 971 2.343101 CGCTAGATCTCCTCCGTCTAG 58.657 57.143 0.00 4.67 42.65 2.43
947 972 2.289195 CGCTAGATCTCCTCCGTCTAGT 60.289 54.545 0.00 0.00 42.07 2.57
948 973 3.332034 GCTAGATCTCCTCCGTCTAGTC 58.668 54.545 0.00 0.96 42.07 2.59
949 974 2.943036 AGATCTCCTCCGTCTAGTCC 57.057 55.000 0.00 0.00 0.00 3.85
977 1002 3.700350 CACTCCCTCCCCTCCCCT 61.700 72.222 0.00 0.00 0.00 4.79
979 1004 4.179599 CTCCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
985 1010 4.505970 CCCCTCCCCTCCCCTCAG 62.506 77.778 0.00 0.00 0.00 3.35
986 1011 3.368501 CCCTCCCCTCCCCTCAGA 61.369 72.222 0.00 0.00 0.00 3.27
987 1012 2.731461 CCCTCCCCTCCCCTCAGAT 61.731 68.421 0.00 0.00 0.00 2.90
989 1014 1.152139 CTCCCCTCCCCTCAGATCC 60.152 68.421 0.00 0.00 0.00 3.36
990 1015 1.946707 TCCCCTCCCCTCAGATCCA 60.947 63.158 0.00 0.00 0.00 3.41
993 1018 1.316266 CCTCCCCTCAGATCCACCT 59.684 63.158 0.00 0.00 0.00 4.00
994 1019 0.762461 CCTCCCCTCAGATCCACCTC 60.762 65.000 0.00 0.00 0.00 3.85
995 1020 0.264359 CTCCCCTCAGATCCACCTCT 59.736 60.000 0.00 0.00 0.00 3.69
997 1022 1.112315 CCCCTCAGATCCACCTCTCG 61.112 65.000 0.00 0.00 0.00 4.04
1485 1818 1.246056 CCCACGTCGTCTCCAAGGTA 61.246 60.000 0.00 0.00 0.00 3.08
1520 1853 1.901650 GCTCCCGCTTTGAACAGACG 61.902 60.000 0.00 0.00 0.00 4.18
1545 1878 2.840511 TGTGGCTAATTCACCCCTCTA 58.159 47.619 0.00 0.00 34.46 2.43
1546 1879 2.504175 TGTGGCTAATTCACCCCTCTAC 59.496 50.000 0.00 0.00 34.46 2.59
1594 1988 3.119459 GCTTCGTCTCATTCACCTCACTA 60.119 47.826 0.00 0.00 0.00 2.74
1634 2031 3.770263 AAATGATCACATGTCCTTGCG 57.230 42.857 0.00 0.00 36.79 4.85
1638 2035 2.028567 TGATCACATGTCCTTGCGTACA 60.029 45.455 0.00 0.00 0.00 2.90
1653 2050 3.431912 TGCGTACATATCATCGGAATTGC 59.568 43.478 0.00 0.00 0.00 3.56
1759 2156 8.727910 ACAAATGATCATATGCTCATATGTCAC 58.272 33.333 19.57 16.46 46.60 3.67
1761 2158 8.719560 AATGATCATATGCTCATATGTCACTC 57.280 34.615 19.57 16.49 46.60 3.51
1763 2160 6.211986 TGATCATATGCTCATATGTCACTCCA 59.788 38.462 22.19 12.85 46.60 3.86
1766 2163 8.137745 TCATATGCTCATATGTCACTCCATAA 57.862 34.615 22.19 4.09 46.60 1.90
1775 2172 9.807649 TCATATGTCACTCCATAATTATCATCG 57.192 33.333 1.90 0.00 31.44 3.84
1796 2193 3.436704 CGGAACACATTGTAATGCTGAGT 59.563 43.478 4.58 0.00 40.04 3.41
1828 2228 7.201884 CCATGTGATTAAAAAGATCTCTGCCAT 60.202 37.037 0.00 0.00 0.00 4.40
1836 2236 4.313020 AAGATCTCTGCCATTTGAACCT 57.687 40.909 0.00 0.00 0.00 3.50
1846 2246 3.617288 GCCATTTGAACCTTTGACCATCC 60.617 47.826 0.00 0.00 0.00 3.51
1850 2250 4.387026 TTGAACCTTTGACCATCCAGAT 57.613 40.909 0.00 0.00 0.00 2.90
1851 2251 4.387026 TGAACCTTTGACCATCCAGATT 57.613 40.909 0.00 0.00 0.00 2.40
1852 2252 4.739793 TGAACCTTTGACCATCCAGATTT 58.260 39.130 0.00 0.00 0.00 2.17
1886 2286 5.349824 CTTGGAACTAAAGCAAGTCTGAC 57.650 43.478 0.00 0.00 0.00 3.51
1891 2291 5.989777 GGAACTAAAGCAAGTCTGACAGTAA 59.010 40.000 10.88 0.00 0.00 2.24
1908 2308 9.528018 CTGACAGTAAATGTTTACCAATTTGTT 57.472 29.630 11.03 0.00 44.17 2.83
1911 2311 8.700973 ACAGTAAATGTTTACCAATTTGTTCCT 58.299 29.630 11.03 0.00 43.03 3.36
1915 2315 3.070302 TGTTTACCAATTTGTTCCTGCCC 59.930 43.478 0.00 0.00 0.00 5.36
1917 2317 2.990740 ACCAATTTGTTCCTGCCCTA 57.009 45.000 0.00 0.00 0.00 3.53
1928 2328 4.522789 TGTTCCTGCCCTAGTTTCATTTTC 59.477 41.667 0.00 0.00 0.00 2.29
1940 2340 9.103861 CCTAGTTTCATTTTCAGGTAGAGATTC 57.896 37.037 0.00 0.00 0.00 2.52
1943 2343 8.160106 AGTTTCATTTTCAGGTAGAGATTCTGT 58.840 33.333 0.00 0.00 0.00 3.41
1951 2351 5.485353 TCAGGTAGAGATTCTGTCCATTGTT 59.515 40.000 0.00 0.00 0.00 2.83
1952 2352 6.013379 TCAGGTAGAGATTCTGTCCATTGTTT 60.013 38.462 0.00 0.00 0.00 2.83
1978 2378 6.039717 TCTGAAATCTAAATGCCAATGTAGCC 59.960 38.462 0.00 0.00 0.00 3.93
1992 2392 5.393027 CCAATGTAGCCAGTTCATTAACACC 60.393 44.000 0.00 0.00 38.12 4.16
1994 2394 2.851263 AGCCAGTTCATTAACACCGA 57.149 45.000 0.00 0.00 38.12 4.69
1997 2397 3.006940 GCCAGTTCATTAACACCGATGA 58.993 45.455 0.00 0.00 38.12 2.92
1998 2398 3.438781 GCCAGTTCATTAACACCGATGAA 59.561 43.478 0.00 0.00 39.30 2.57
2010 2410 0.863799 CCGATGAATCTGACCGCATG 59.136 55.000 0.00 0.00 0.00 4.06
2012 2412 1.524355 CGATGAATCTGACCGCATGAC 59.476 52.381 0.00 0.00 0.00 3.06
2029 2429 7.769044 ACCGCATGACTAAATTACTGACTAAAT 59.231 33.333 0.00 0.00 0.00 1.40
2093 2493 1.732809 TCGAAATTTGCGGCGTATCAA 59.267 42.857 9.37 0.83 0.00 2.57
2150 2550 1.516386 CCTTGTCATCCGTCGACCG 60.516 63.158 10.58 3.37 32.15 4.79
2175 2575 6.690530 CCCAGAGTTATTTCATCAAAGCAAA 58.309 36.000 0.00 0.00 0.00 3.68
2213 2613 4.523943 ACCAAATTGCTTTAGCTCATGTCA 59.476 37.500 3.10 0.00 42.66 3.58
2221 2621 5.704978 TGCTTTAGCTCATGTCATGTTGTTA 59.295 36.000 12.54 6.83 42.66 2.41
2233 2633 9.689976 CATGTCATGTTGTTAATGAAACCTAAA 57.310 29.630 4.53 0.00 35.87 1.85
2277 2677 6.208204 AGGTTGAGAAACTGATCAAGGAATTG 59.792 38.462 0.00 0.00 36.16 2.32
2280 2680 3.441572 AGAAACTGATCAAGGAATTGCCG 59.558 43.478 0.00 0.00 43.43 5.69
2331 2731 5.186992 TGAAGATCGTTCAGTTGATAAGGGA 59.813 40.000 4.18 0.00 0.00 4.20
2352 2752 4.219944 GGATACTCCGGCAATGATACTACA 59.780 45.833 0.00 0.00 0.00 2.74
2524 2924 8.802267 GGGCATCTCTAGCTTCTAATATATAGG 58.198 40.741 0.00 0.00 0.00 2.57
2620 3023 7.027161 AGTTCACACGAAAATATTTGGTATGC 58.973 34.615 0.39 0.00 31.43 3.14
2861 3341 9.250624 CTCCCTCTGTAAAGAAATATAAGAACG 57.749 37.037 0.00 0.00 0.00 3.95
2863 3343 9.379791 CCCTCTGTAAAGAAATATAAGAACGTT 57.620 33.333 0.00 0.00 0.00 3.99
3027 3510 7.548075 GCTACAAAACTACTTGATGGTAGCTTA 59.452 37.037 11.88 0.00 45.37 3.09
3307 6136 9.717942 AAATATCTTCATCAGGTAGCTGTAATC 57.282 33.333 20.76 0.00 0.00 1.75
3318 6147 7.832685 TCAGGTAGCTGTAATCTCTGTTACTTA 59.167 37.037 20.76 0.00 35.94 2.24
3342 6171 7.828508 AATATTCTGATGAAGCCTAAATGCA 57.171 32.000 0.00 0.00 35.44 3.96
3343 6172 8.418597 AATATTCTGATGAAGCCTAAATGCAT 57.581 30.769 0.00 0.00 35.44 3.96
3344 6173 9.524496 AATATTCTGATGAAGCCTAAATGCATA 57.476 29.630 0.00 0.00 35.44 3.14
3345 6174 9.696572 ATATTCTGATGAAGCCTAAATGCATAT 57.303 29.630 0.00 0.00 35.44 1.78
3346 6175 6.812879 TCTGATGAAGCCTAAATGCATATG 57.187 37.500 0.00 0.00 0.00 1.78
3347 6176 5.708697 TCTGATGAAGCCTAAATGCATATGG 59.291 40.000 0.00 3.80 0.00 2.74
3348 6177 5.633117 TGATGAAGCCTAAATGCATATGGA 58.367 37.500 14.36 1.06 0.00 3.41
3349 6178 5.474532 TGATGAAGCCTAAATGCATATGGAC 59.525 40.000 14.36 7.43 0.00 4.02
3350 6179 5.052693 TGAAGCCTAAATGCATATGGACT 57.947 39.130 14.36 9.07 0.00 3.85
3365 6201 9.929180 TGCATATGGACTTAGATAACATCTTAC 57.071 33.333 4.56 0.00 40.76 2.34
3499 6335 5.374071 TGTTCTCCTGGAAAACCTAAAGAC 58.626 41.667 10.27 0.00 35.51 3.01
3567 6403 9.905713 TCTTGAAGGTATGCTTAATTATTCTGT 57.094 29.630 0.00 0.00 0.00 3.41
3605 6441 6.096141 TGTTTTCTGTGATTTGGTCTGCTAAA 59.904 34.615 0.00 0.00 0.00 1.85
3613 6449 7.981789 TGTGATTTGGTCTGCTAAATCTACTAG 59.018 37.037 14.33 0.00 46.30 2.57
3636 6472 2.205022 ACTATGCTTGCCTGCAAAGA 57.795 45.000 6.00 0.00 46.61 2.52
3637 6473 2.089980 ACTATGCTTGCCTGCAAAGAG 58.910 47.619 6.00 1.77 46.61 2.85
3660 6496 9.338622 AGAGTGCTATTGTATATTTTTGGTACC 57.661 33.333 4.43 4.43 0.00 3.34
3687 6523 8.911662 GTGTGTGTAATGACAATTAAATTGGTC 58.088 33.333 0.00 0.24 44.42 4.02
3697 6533 7.877097 TGACAATTAAATTGGTCAAATGGAAGG 59.123 33.333 0.00 0.00 44.42 3.46
3709 6546 1.270907 ATGGAAGGAGTCGTTGCTCT 58.729 50.000 16.49 3.45 35.89 4.09
3730 6567 2.255316 GCTGAGCAAGTAACGTCTCTC 58.745 52.381 0.00 0.00 0.00 3.20
3766 6603 6.422100 ACGTAATCAAGTGCTATAATCAGCTG 59.578 38.462 7.63 7.63 42.30 4.24
3771 6608 3.209410 AGTGCTATAATCAGCTGGCAAC 58.791 45.455 15.13 8.89 42.30 4.17
3835 6672 2.630098 TGTTACAGAGAGTTGCAGAGCT 59.370 45.455 0.00 0.00 0.00 4.09
4302 7139 0.690192 TCCTCCGATTGTCCTTGCAA 59.310 50.000 0.00 0.00 0.00 4.08
4465 7304 2.742856 CGTAATGCTTCTGATGGGAGCA 60.743 50.000 4.41 4.41 39.91 4.26
4578 7417 2.795329 ACCATGTCATTTCAGTGACCC 58.205 47.619 0.00 0.00 46.17 4.46
4592 7431 1.348036 GTGACCCAGACCTAGCACTTT 59.652 52.381 0.00 0.00 0.00 2.66
4672 7511 7.011576 TGAGTGTATGCTTTCGTTTCAAGTTAA 59.988 33.333 0.00 0.00 0.00 2.01
4751 7600 1.262683 GTGCTCAAGTCAGTGTGAAGC 59.737 52.381 0.00 0.00 0.00 3.86
4800 7651 4.707105 CTTACCAGCATCATACATGGTGA 58.293 43.478 13.94 1.16 46.89 4.02
4804 7655 3.136763 CAGCATCATACATGGTGAGGTC 58.863 50.000 6.65 8.28 46.89 3.85
4818 7669 3.941483 GGTGAGGTCCATATTGACAACTG 59.059 47.826 9.01 0.00 36.97 3.16
4819 7670 4.565652 GGTGAGGTCCATATTGACAACTGT 60.566 45.833 9.01 0.00 36.97 3.55
4858 7709 1.610522 GGTGCAGCTTTCATGTTGTCT 59.389 47.619 9.07 0.00 0.00 3.41
4872 7723 2.046217 GTCTTGGCCCGTCCTTCC 60.046 66.667 0.00 0.00 35.26 3.46
4890 7741 4.630069 CCTTCCGTAGTCCTTGTTACATTG 59.370 45.833 0.00 0.00 0.00 2.82
4940 7791 4.097437 CAGACCACGTAGCAGTTTATAGGA 59.903 45.833 0.00 0.00 0.00 2.94
4949 7800 7.148641 CGTAGCAGTTTATAGGATTGACAGAT 58.851 38.462 0.00 0.00 0.00 2.90
5307 8159 9.793252 AGAAGCTAATGTTGCATTTGTAAATAG 57.207 29.630 0.00 0.00 0.00 1.73
5310 8162 9.357652 AGCTAATGTTGCATTTGTAAATAGTTG 57.642 29.630 0.00 0.00 0.00 3.16
5521 8375 5.017294 TCCATGTTTGGTTTTCTGTTTCC 57.983 39.130 0.00 0.00 44.06 3.13
5593 8450 7.212976 TCTTCTGAGCAAGGTCATATTACATC 58.787 38.462 2.09 0.00 0.00 3.06
5643 8500 8.766994 AGTTATGGTCATATGCCTATTTTGTT 57.233 30.769 14.63 0.00 0.00 2.83
5676 8533 2.943036 TAGCCCCGTTTCAACTTCTT 57.057 45.000 0.00 0.00 0.00 2.52
5761 8618 4.982241 AGGTGTTTCTTGAAGGAGATCA 57.018 40.909 0.00 0.00 0.00 2.92
5849 8706 6.650807 CGGCAACTTATTATGACATGGTATCT 59.349 38.462 0.00 0.00 0.00 1.98
5901 8758 1.211709 CGCCCGCCTTCGAAATTTT 59.788 52.632 0.00 0.00 38.10 1.82
6128 8985 9.383519 TCTTTTTACGCTCATTCTCATAAATCT 57.616 29.630 0.00 0.00 0.00 2.40
6251 9120 1.592064 TTTCTGCATGCGACACTTGA 58.408 45.000 14.09 0.00 0.00 3.02
6258 9127 3.052036 GCATGCGACACTTGAAACATTT 58.948 40.909 0.00 0.00 0.00 2.32
6283 9152 3.917329 TCTCTGCTACACTACACACAC 57.083 47.619 0.00 0.00 0.00 3.82
6285 9154 3.004419 TCTCTGCTACACTACACACACAC 59.996 47.826 0.00 0.00 0.00 3.82
6287 9156 2.794910 CTGCTACACTACACACACACAC 59.205 50.000 0.00 0.00 0.00 3.82
6288 9157 2.166664 TGCTACACTACACACACACACA 59.833 45.455 0.00 0.00 0.00 3.72
6290 9159 2.753055 ACACTACACACACACACACA 57.247 45.000 0.00 0.00 0.00 3.72
6291 9160 2.343101 ACACTACACACACACACACAC 58.657 47.619 0.00 0.00 0.00 3.82
6292 9161 2.289133 ACACTACACACACACACACACA 60.289 45.455 0.00 0.00 0.00 3.72
6293 9162 2.093625 CACTACACACACACACACACAC 59.906 50.000 0.00 0.00 0.00 3.82
6295 9164 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6296 9165 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6297 9166 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6299 9168 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6300 9169 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6301 9170 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6302 9171 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6303 9172 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6304 9173 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6305 9174 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6306 9175 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6307 9176 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6308 9177 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6309 9178 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6310 9179 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6311 9180 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6312 9181 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6313 9182 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6314 9183 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6315 9184 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
6316 9185 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
6317 9186 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
6318 9187 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
6319 9188 2.031245 ACACACACACACACACACAAAG 60.031 45.455 0.00 0.00 0.00 2.77
6320 9189 1.539388 ACACACACACACACACAAAGG 59.461 47.619 0.00 0.00 0.00 3.11
6321 9190 1.809547 CACACACACACACACAAAGGA 59.190 47.619 0.00 0.00 0.00 3.36
6322 9191 2.423185 CACACACACACACACAAAGGAT 59.577 45.455 0.00 0.00 0.00 3.24
6323 9192 3.088532 ACACACACACACACAAAGGATT 58.911 40.909 0.00 0.00 0.00 3.01
6324 9193 3.119531 ACACACACACACACAAAGGATTG 60.120 43.478 0.00 0.00 42.46 2.67
6344 9213 9.362151 AGGATTGTACTTAGGAGAATAGAGAAG 57.638 37.037 0.00 0.00 0.00 2.85
6454 9325 6.093771 ACACATTGTTTCACATGCATTGTTTT 59.906 30.769 0.00 0.00 36.00 2.43
6655 9526 7.050377 AGATATGTCTGGTGTTGTTCATTAGG 58.950 38.462 0.00 0.00 32.13 2.69
6659 9530 4.023193 GTCTGGTGTTGTTCATTAGGTTGG 60.023 45.833 0.00 0.00 0.00 3.77
6660 9531 4.141287 CTGGTGTTGTTCATTAGGTTGGA 58.859 43.478 0.00 0.00 0.00 3.53
6661 9532 4.141287 TGGTGTTGTTCATTAGGTTGGAG 58.859 43.478 0.00 0.00 0.00 3.86
6662 9533 4.141367 TGGTGTTGTTCATTAGGTTGGAGA 60.141 41.667 0.00 0.00 0.00 3.71
6663 9534 5.010282 GGTGTTGTTCATTAGGTTGGAGAT 58.990 41.667 0.00 0.00 0.00 2.75
6664 9535 5.476945 GGTGTTGTTCATTAGGTTGGAGATT 59.523 40.000 0.00 0.00 0.00 2.40
6665 9536 6.349363 GGTGTTGTTCATTAGGTTGGAGATTC 60.349 42.308 0.00 0.00 0.00 2.52
6666 9537 5.411361 TGTTGTTCATTAGGTTGGAGATTCG 59.589 40.000 0.00 0.00 0.00 3.34
6667 9538 5.160607 TGTTCATTAGGTTGGAGATTCGT 57.839 39.130 0.00 0.00 0.00 3.85
6678 9558 7.210873 AGGTTGGAGATTCGTGAGATTTATAC 58.789 38.462 0.00 0.00 41.60 1.47
6681 9561 6.206498 TGGAGATTCGTGAGATTTATACGTG 58.794 40.000 0.00 0.00 41.60 4.49
6727 9608 6.249260 CGCTGTCATTGTTTGAATTTACTAGC 59.751 38.462 0.00 0.00 35.70 3.42
6729 9610 6.607689 TGTCATTGTTTGAATTTACTAGCCG 58.392 36.000 0.00 0.00 35.70 5.52
6827 9713 0.389817 TTCACCGGACAATCTGCTCG 60.390 55.000 9.46 0.00 0.00 5.03
6837 9723 2.283298 CAATCTGCTCGGCTGTTGTAT 58.717 47.619 0.00 0.00 0.00 2.29
6891 9777 5.471116 GCAAGGCCTTTTGATTCTTTTTCAT 59.529 36.000 17.61 0.00 0.00 2.57
6907 9793 7.577303 TCTTTTTCATGGCCTTCACTATATCT 58.423 34.615 3.32 0.00 0.00 1.98
6920 9806 6.239217 TCACTATATCTGTTGGCTTGTGAT 57.761 37.500 0.00 0.00 0.00 3.06
6934 9820 9.040939 GTTGGCTTGTGATAAGTTTTACAAATT 57.959 29.630 0.00 0.00 33.19 1.82
6971 9857 2.027385 CTGCTTCCCCTTTAATCCAGC 58.973 52.381 0.00 0.00 0.00 4.85
7083 9969 1.928152 GCTCCGATACATGTCTCGCTG 60.928 57.143 23.81 18.77 33.63 5.18
7216 10112 0.243095 GAGCAGCCCTGAAAAAGCAG 59.757 55.000 0.00 0.00 35.66 4.24
7267 10169 5.255710 TCAACACATTTTCAATGAACCGT 57.744 34.783 0.00 0.00 0.00 4.83
7279 10181 0.039798 TGAACCGTACACGACAGAGC 60.040 55.000 2.76 0.00 43.02 4.09
7307 10209 6.394025 GCTACCATAAGCAACTACTCTACT 57.606 41.667 0.00 0.00 42.30 2.57
7350 10260 2.795329 CCAGAAGTAACATTGCTGGGT 58.205 47.619 0.00 0.00 41.81 4.51
7408 10318 5.376854 AACTGTAGATTGCAATGTTGGAC 57.623 39.130 18.59 8.81 0.00 4.02
7433 10343 6.441093 TGAAGCAAGCAATTATCTTAGGTG 57.559 37.500 0.00 0.00 0.00 4.00
7442 10437 6.708054 AGCAATTATCTTAGGTGTCTGTATGC 59.292 38.462 0.00 0.00 0.00 3.14
7492 10495 1.526575 AAACATGGCGGAACTGCTGG 61.527 55.000 0.00 0.00 34.52 4.85
7493 10496 3.136123 CATGGCGGAACTGCTGGG 61.136 66.667 5.60 0.00 34.52 4.45
7500 10503 0.872388 CGGAACTGCTGGGTTTGTAC 59.128 55.000 0.00 0.00 0.00 2.90
7512 10515 6.266558 TGCTGGGTTTGTACTCAATATTTTGT 59.733 34.615 0.00 0.00 33.42 2.83
7516 10519 6.799925 GGGTTTGTACTCAATATTTTGTGACG 59.200 38.462 5.18 0.00 34.32 4.35
7541 10544 9.367444 CGATTATTCTAAGGAACTGTAGTTTGT 57.633 33.333 0.00 0.00 40.86 2.83
7548 10551 2.991866 GGAACTGTAGTTTGTACCGCTC 59.008 50.000 0.00 0.00 38.56 5.03
7565 10568 4.021719 ACCGCTCAAAGTAACTAGTGCTTA 60.022 41.667 11.79 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.941325 TGATTTTATGAGGTTTTATTGCAACAT 57.059 25.926 0.00 0.29 0.00 2.71
503 518 6.063640 TGTTGTGTGATTGATTGACTGAAG 57.936 37.500 0.00 0.00 0.00 3.02
598 614 1.092921 TAAATAGGCCGGCGCAGTTG 61.093 55.000 22.54 0.00 36.38 3.16
600 616 1.227556 CTAAATAGGCCGGCGCAGT 60.228 57.895 22.54 6.71 36.38 4.40
603 619 0.669625 CCTACTAAATAGGCCGGCGC 60.670 60.000 22.54 13.90 44.36 6.53
649 665 5.248705 CCATATAACCTTCTAGAGGGTTCCC 59.751 48.000 35.09 0.00 45.88 3.97
725 741 9.364989 TCAAACGTTTTTCTGATTTTTCTTCAT 57.635 25.926 11.66 0.00 0.00 2.57
726 742 8.749841 TCAAACGTTTTTCTGATTTTTCTTCA 57.250 26.923 11.66 0.00 0.00 3.02
736 752 9.364989 AGATGAAATTTTCAAACGTTTTTCTGA 57.635 25.926 11.66 3.26 43.95 3.27
797 813 9.702494 ACTTCTCATGAAATTTTCAATTTCCTC 57.298 29.630 15.34 0.00 43.95 3.71
802 818 8.143835 ACCGAACTTCTCATGAAATTTTCAATT 58.856 29.630 15.34 0.00 43.95 2.32
817 836 4.915667 GGCATTTACAAAACCGAACTTCTC 59.084 41.667 0.00 0.00 0.00 2.87
838 857 2.185608 GTCCTCCTGCTCTTCGGC 59.814 66.667 0.00 0.00 0.00 5.54
839 858 1.999071 CTCGTCCTCCTGCTCTTCGG 61.999 65.000 0.00 0.00 0.00 4.30
841 860 1.752683 TACTCGTCCTCCTGCTCTTC 58.247 55.000 0.00 0.00 0.00 2.87
842 861 1.819903 GTTACTCGTCCTCCTGCTCTT 59.180 52.381 0.00 0.00 0.00 2.85
843 862 1.465794 GTTACTCGTCCTCCTGCTCT 58.534 55.000 0.00 0.00 0.00 4.09
844 863 0.456628 GGTTACTCGTCCTCCTGCTC 59.543 60.000 0.00 0.00 0.00 4.26
848 867 1.379576 CCGGGTTACTCGTCCTCCT 60.380 63.158 3.32 0.00 0.00 3.69
849 868 2.421399 CCCGGGTTACTCGTCCTCC 61.421 68.421 14.18 0.00 0.00 4.30
850 869 3.073742 GCCCGGGTTACTCGTCCTC 62.074 68.421 24.63 0.00 0.00 3.71
851 870 3.073101 GCCCGGGTTACTCGTCCT 61.073 66.667 24.63 0.00 0.00 3.85
852 871 4.152964 GGCCCGGGTTACTCGTCC 62.153 72.222 24.63 8.21 0.00 4.79
853 872 4.503314 CGGCCCGGGTTACTCGTC 62.503 72.222 24.63 1.42 0.00 4.20
855 874 4.503314 GTCGGCCCGGGTTACTCG 62.503 72.222 24.63 17.65 0.00 4.18
887 909 3.462021 GACGCTCCATATTTCTTCTGCT 58.538 45.455 0.00 0.00 0.00 4.24
888 910 2.219674 CGACGCTCCATATTTCTTCTGC 59.780 50.000 0.00 0.00 0.00 4.26
890 912 3.381908 AGACGACGCTCCATATTTCTTCT 59.618 43.478 0.00 0.00 0.00 2.85
891 913 3.707793 AGACGACGCTCCATATTTCTTC 58.292 45.455 0.00 0.00 0.00 2.87
893 915 2.287069 CGAGACGACGCTCCATATTTCT 60.287 50.000 11.82 0.00 0.00 2.52
894 916 2.044860 CGAGACGACGCTCCATATTTC 58.955 52.381 11.82 0.00 0.00 2.17
896 918 1.002684 GACGAGACGACGCTCCATATT 60.003 52.381 11.82 0.00 36.70 1.28
898 920 1.759293 CGACGAGACGACGCTCCATA 61.759 60.000 11.82 0.00 38.14 2.74
938 963 0.971386 GTGGGTTTGGACTAGACGGA 59.029 55.000 0.00 0.00 0.00 4.69
939 964 0.036671 GGTGGGTTTGGACTAGACGG 60.037 60.000 0.00 0.00 0.00 4.79
940 965 0.389426 CGGTGGGTTTGGACTAGACG 60.389 60.000 0.00 0.00 0.00 4.18
942 967 1.122632 TGCGGTGGGTTTGGACTAGA 61.123 55.000 0.00 0.00 0.00 2.43
943 968 0.953960 GTGCGGTGGGTTTGGACTAG 60.954 60.000 0.00 0.00 0.00 2.57
944 969 1.071814 GTGCGGTGGGTTTGGACTA 59.928 57.895 0.00 0.00 0.00 2.59
945 970 2.203294 GTGCGGTGGGTTTGGACT 60.203 61.111 0.00 0.00 0.00 3.85
946 971 2.203294 AGTGCGGTGGGTTTGGAC 60.203 61.111 0.00 0.00 0.00 4.02
947 972 2.112297 GAGTGCGGTGGGTTTGGA 59.888 61.111 0.00 0.00 0.00 3.53
948 973 2.983592 GGAGTGCGGTGGGTTTGG 60.984 66.667 0.00 0.00 0.00 3.28
949 974 2.983592 GGGAGTGCGGTGGGTTTG 60.984 66.667 0.00 0.00 0.00 2.93
971 996 1.152139 GGATCTGAGGGGAGGGGAG 60.152 68.421 0.00 0.00 0.00 4.30
972 997 1.946707 TGGATCTGAGGGGAGGGGA 60.947 63.158 0.00 0.00 0.00 4.81
977 1002 0.263172 GAGAGGTGGATCTGAGGGGA 59.737 60.000 0.00 0.00 0.00 4.81
979 1004 1.743321 GCGAGAGGTGGATCTGAGGG 61.743 65.000 0.00 0.00 0.00 4.30
980 1005 1.739049 GCGAGAGGTGGATCTGAGG 59.261 63.158 0.00 0.00 0.00 3.86
981 1006 1.039785 TGGCGAGAGGTGGATCTGAG 61.040 60.000 0.00 0.00 0.00 3.35
984 1009 1.406065 CCATGGCGAGAGGTGGATCT 61.406 60.000 0.00 0.00 33.53 2.75
985 1010 1.070445 CCATGGCGAGAGGTGGATC 59.930 63.158 0.00 0.00 33.53 3.36
986 1011 3.112205 GCCATGGCGAGAGGTGGAT 62.112 63.158 23.48 0.00 33.53 3.41
987 1012 3.785859 GCCATGGCGAGAGGTGGA 61.786 66.667 23.48 0.00 33.53 4.02
1455 1788 2.989824 ACGTGGGAGGTGTCGAGG 60.990 66.667 0.00 0.00 0.00 4.63
1537 1870 2.633481 GACAACTGAAGTGTAGAGGGGT 59.367 50.000 0.00 0.00 0.00 4.95
1545 1878 0.546122 TGCAGGGACAACTGAAGTGT 59.454 50.000 0.00 0.00 40.97 3.55
1546 1879 1.901591 ATGCAGGGACAACTGAAGTG 58.098 50.000 0.00 0.00 40.97 3.16
1574 1968 3.824443 TGTAGTGAGGTGAATGAGACGAA 59.176 43.478 0.00 0.00 0.00 3.85
1577 1971 4.792521 ACTGTAGTGAGGTGAATGAGAC 57.207 45.455 0.00 0.00 0.00 3.36
1594 1988 7.620880 TCATTTATACTAGGTGCTGAAACTGT 58.379 34.615 0.00 0.00 0.00 3.55
1634 2031 4.684242 TGTCGCAATTCCGATGATATGTAC 59.316 41.667 0.00 0.00 39.67 2.90
1638 2035 6.340522 TGATATGTCGCAATTCCGATGATAT 58.659 36.000 0.00 0.62 39.67 1.63
1759 2156 7.912056 ATGTGTTCCGATGATAATTATGGAG 57.088 36.000 1.78 0.00 0.00 3.86
1761 2158 7.874940 ACAATGTGTTCCGATGATAATTATGG 58.125 34.615 1.78 0.00 0.00 2.74
1766 2163 7.229306 AGCATTACAATGTGTTCCGATGATAAT 59.771 33.333 0.00 0.00 38.65 1.28
1775 2172 5.376854 AACTCAGCATTACAATGTGTTCC 57.623 39.130 0.00 0.00 38.65 3.62
1802 2199 6.095860 TGGCAGAGATCTTTTTAATCACATGG 59.904 38.462 0.00 0.00 0.00 3.66
1803 2200 7.092137 TGGCAGAGATCTTTTTAATCACATG 57.908 36.000 0.00 0.00 0.00 3.21
1804 2201 7.893124 ATGGCAGAGATCTTTTTAATCACAT 57.107 32.000 0.00 0.00 0.00 3.21
1806 2203 8.246180 TCAAATGGCAGAGATCTTTTTAATCAC 58.754 33.333 0.00 0.00 0.00 3.06
1817 2217 4.460382 TCAAAGGTTCAAATGGCAGAGATC 59.540 41.667 0.00 0.00 0.00 2.75
1823 2223 2.392662 TGGTCAAAGGTTCAAATGGCA 58.607 42.857 0.00 0.00 0.00 4.92
1828 2228 4.177537 TCTGGATGGTCAAAGGTTCAAA 57.822 40.909 0.00 0.00 0.00 2.69
1851 2251 9.908152 GCTTTAGTTCCAAGCTTAATAGAAAAA 57.092 29.630 0.00 0.00 42.95 1.94
1852 2252 9.073475 TGCTTTAGTTCCAAGCTTAATAGAAAA 57.927 29.630 0.00 0.00 45.90 2.29
1860 2260 5.470098 CAGACTTGCTTTAGTTCCAAGCTTA 59.530 40.000 0.00 0.00 45.90 3.09
1866 2266 4.141711 ACTGTCAGACTTGCTTTAGTTCCA 60.142 41.667 6.91 0.00 0.00 3.53
1868 2268 7.478520 TTTACTGTCAGACTTGCTTTAGTTC 57.521 36.000 6.91 0.00 0.00 3.01
1869 2269 7.499232 ACATTTACTGTCAGACTTGCTTTAGTT 59.501 33.333 6.91 0.00 29.94 2.24
1886 2286 8.977505 CAGGAACAAATTGGTAAACATTTACTG 58.022 33.333 12.90 6.76 42.00 2.74
1891 2291 5.304778 GGCAGGAACAAATTGGTAAACATT 58.695 37.500 0.00 0.00 0.00 2.71
1908 2308 4.335416 CTGAAAATGAAACTAGGGCAGGA 58.665 43.478 0.00 0.00 0.00 3.86
1911 2311 4.112634 ACCTGAAAATGAAACTAGGGCA 57.887 40.909 0.00 0.00 0.00 5.36
1915 2315 9.883142 AGAATCTCTACCTGAAAATGAAACTAG 57.117 33.333 0.00 0.00 0.00 2.57
1917 2317 8.160106 ACAGAATCTCTACCTGAAAATGAAACT 58.840 33.333 0.00 0.00 0.00 2.66
1928 2328 5.350504 ACAATGGACAGAATCTCTACCTG 57.649 43.478 0.00 0.00 0.00 4.00
1940 2340 9.918630 ATTTAGATTTCAGAAAACAATGGACAG 57.081 29.630 0.00 0.00 0.00 3.51
1943 2343 7.818930 GGCATTTAGATTTCAGAAAACAATGGA 59.181 33.333 13.59 0.00 0.00 3.41
1951 2351 7.975616 GCTACATTGGCATTTAGATTTCAGAAA 59.024 33.333 0.00 0.00 0.00 2.52
1952 2352 7.416664 GGCTACATTGGCATTTAGATTTCAGAA 60.417 37.037 0.00 0.00 0.00 3.02
1978 2378 6.313658 TCAGATTCATCGGTGTTAATGAACTG 59.686 38.462 0.00 14.53 42.82 3.16
1992 2392 1.524355 GTCATGCGGTCAGATTCATCG 59.476 52.381 0.00 0.00 0.00 3.84
1994 2394 2.996249 AGTCATGCGGTCAGATTCAT 57.004 45.000 0.00 0.00 0.00 2.57
1997 2397 6.258727 CAGTAATTTAGTCATGCGGTCAGATT 59.741 38.462 0.00 0.00 0.00 2.40
1998 2398 5.755375 CAGTAATTTAGTCATGCGGTCAGAT 59.245 40.000 0.00 0.00 0.00 2.90
2033 2433 9.104965 GCATGTTACCATTTGTACTAAGTGATA 57.895 33.333 0.00 0.00 0.00 2.15
2035 2435 6.373216 GGCATGTTACCATTTGTACTAAGTGA 59.627 38.462 0.00 0.00 0.00 3.41
2045 2445 2.609350 GCAGTGGCATGTTACCATTTG 58.391 47.619 0.00 0.00 39.95 2.32
2093 2493 6.605995 TCATTGGAAGAAAATCTCAGCATCAT 59.394 34.615 0.00 0.00 0.00 2.45
2150 2550 4.158394 TGCTTTGATGAAATAACTCTGGGC 59.842 41.667 0.00 0.00 0.00 5.36
2175 2575 9.723601 AAGCAATTTGGTAAACACATATCAAAT 57.276 25.926 0.82 0.86 44.50 2.32
2233 2633 5.675684 ACCTGAATGAACAAAACAAACCT 57.324 34.783 0.00 0.00 0.00 3.50
2277 2677 0.745845 AATCAGATGGTGCTGTCGGC 60.746 55.000 0.00 0.00 42.22 5.54
2280 2680 3.538591 TGATGAATCAGATGGTGCTGTC 58.461 45.455 0.00 0.00 37.20 3.51
2331 2731 5.480422 TGATGTAGTATCATTGCCGGAGTAT 59.520 40.000 5.05 0.00 0.00 2.12
2870 3350 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2871 3351 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2872 3352 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2873 3353 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2874 3354 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2876 3356 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2877 3357 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2880 3360 8.636213 TGTACTCCCTCCGTAAAGAAATATAAG 58.364 37.037 0.00 0.00 0.00 1.73
3027 3510 0.381801 CAACCACAAAGCAACGCTCT 59.618 50.000 0.00 0.00 38.25 4.09
3318 6147 7.828508 TGCATTTAGGCTTCATCAGAATATT 57.171 32.000 0.00 0.00 32.31 1.28
3365 6201 6.050454 TGCTGCAAATGAAACAAAAATCAG 57.950 33.333 0.00 0.00 0.00 2.90
3366 6202 6.432607 TTGCTGCAAATGAAACAAAAATCA 57.567 29.167 13.51 0.00 0.00 2.57
3499 6335 4.307432 TCGCTTTGTAGTTTCTCAGGAAG 58.693 43.478 0.00 0.00 32.61 3.46
3605 6441 6.432783 CAGGCAAGCATAGTACTCTAGTAGAT 59.567 42.308 0.00 0.00 0.00 1.98
3613 6449 2.315925 TGCAGGCAAGCATAGTACTC 57.684 50.000 0.00 0.00 40.11 2.59
3636 6472 7.771826 ACGGTACCAAAAATATACAATAGCACT 59.228 33.333 13.54 0.00 0.00 4.40
3637 6473 7.853929 CACGGTACCAAAAATATACAATAGCAC 59.146 37.037 13.54 0.00 0.00 4.40
3649 6485 5.531659 TCATTACACACACGGTACCAAAAAT 59.468 36.000 13.54 0.00 0.00 1.82
3656 6492 5.600908 AATTGTCATTACACACACGGTAC 57.399 39.130 0.00 0.00 34.61 3.34
3658 6494 6.621316 TTTAATTGTCATTACACACACGGT 57.379 33.333 0.00 0.00 34.61 4.83
3659 6495 7.061673 CCAATTTAATTGTCATTACACACACGG 59.938 37.037 15.40 0.00 38.59 4.94
3660 6496 7.593273 ACCAATTTAATTGTCATTACACACACG 59.407 33.333 15.40 0.00 38.59 4.49
3687 6523 2.154462 AGCAACGACTCCTTCCATTTG 58.846 47.619 0.00 0.00 0.00 2.32
3691 6527 0.318441 CAGAGCAACGACTCCTTCCA 59.682 55.000 0.00 0.00 37.39 3.53
3697 6533 2.735634 CTCAGCAGAGCAACGACTC 58.264 57.895 0.00 0.00 34.61 3.36
3709 6546 1.613925 AGAGACGTTACTTGCTCAGCA 59.386 47.619 0.00 0.00 36.47 4.41
3723 6560 1.828832 GTATCAAGGTGCGAGAGACG 58.171 55.000 0.00 0.00 45.66 4.18
3757 6594 0.036164 ACACCGTTGCCAGCTGATTA 59.964 50.000 17.39 0.00 0.00 1.75
3766 6603 1.664333 CAATGCCAACACCGTTGCC 60.664 57.895 1.26 0.00 0.00 4.52
3771 6608 2.126467 CAAACTTCAATGCCAACACCG 58.874 47.619 0.00 0.00 0.00 4.94
3835 6672 7.453393 AGAACTTAGAAATGGAGATGTGTTGA 58.547 34.615 0.00 0.00 0.00 3.18
4342 7180 8.338259 CCGAATGATAAGTCATGAAAAGTAAGG 58.662 37.037 0.00 0.00 44.20 2.69
4357 7196 2.366916 AGGTCAGCCTCCGAATGATAAG 59.633 50.000 0.00 0.00 42.67 1.73
4465 7304 2.094286 CAGAATCTGCAGGAGAACTCGT 60.094 50.000 15.13 0.00 33.12 4.18
4503 7342 8.542926 CATACATATATGAAATCCTCCACAGGA 58.457 37.037 19.63 0.00 45.62 3.86
4545 7384 8.859090 TGAAATGACATGGTAAGACTTCAAATT 58.141 29.630 0.00 0.00 0.00 1.82
4578 7417 4.636249 ACTGAGAAAAAGTGCTAGGTCTG 58.364 43.478 0.00 0.00 0.00 3.51
4751 7600 3.508012 AGTACAAGTAGTCAGCCAGTCAG 59.492 47.826 0.00 0.00 0.00 3.51
4800 7651 4.323792 CCTCACAGTTGTCAATATGGACCT 60.324 45.833 7.81 0.00 36.97 3.85
4804 7655 3.346315 TGCCTCACAGTTGTCAATATGG 58.654 45.455 5.91 0.00 0.00 2.74
4818 7669 2.094026 CCTTGCCCTTTTATTGCCTCAC 60.094 50.000 0.00 0.00 0.00 3.51
4819 7670 2.178580 CCTTGCCCTTTTATTGCCTCA 58.821 47.619 0.00 0.00 0.00 3.86
4850 7701 1.303317 GGACGGGCCAAGACAACAT 60.303 57.895 4.39 0.00 36.34 2.71
4858 7709 2.604079 TACGGAAGGACGGGCCAA 60.604 61.111 4.39 0.00 40.02 4.52
4872 7723 6.721571 ATTCACAATGTAACAAGGACTACG 57.278 37.500 0.00 0.00 0.00 3.51
5310 8162 9.916397 CGTAGTCTTAAATGTTCCATTGAATAC 57.084 33.333 0.00 0.00 31.98 1.89
5334 8188 2.890808 TCAGAGAACAAGAGCAACGT 57.109 45.000 0.00 0.00 0.00 3.99
5335 8189 3.496130 ACAATCAGAGAACAAGAGCAACG 59.504 43.478 0.00 0.00 0.00 4.10
5339 8193 6.868864 TGTAGTTACAATCAGAGAACAAGAGC 59.131 38.462 0.00 0.00 32.40 4.09
5521 8375 3.908382 GCTAAAATGCTGTCAGTTGAACG 59.092 43.478 0.93 0.00 30.13 3.95
5593 8450 8.492673 TCAAATGCAGACCATAAAACTAGTAG 57.507 34.615 0.00 0.00 32.67 2.57
5643 8500 4.528920 ACGGGGCTAATAAATTACAGCAA 58.471 39.130 9.68 0.00 0.00 3.91
5658 8515 2.067365 AAAGAAGTTGAAACGGGGCT 57.933 45.000 0.00 0.00 0.00 5.19
5689 8546 9.453572 TGAAATAGCATAGAATGAAAACAGACT 57.546 29.630 0.00 0.00 0.00 3.24
5703 8560 9.228949 AGGAAAGCTCATAATGAAATAGCATAG 57.771 33.333 0.00 0.00 35.63 2.23
5893 8750 9.433153 AGGTAGAAAGGTAGAACTAAAATTTCG 57.567 33.333 0.00 0.00 32.02 3.46
6283 9152 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6285 9154 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6287 9156 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6288 9157 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6290 9159 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6291 9160 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6292 9161 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6293 9162 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6295 9164 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6296 9165 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
6297 9166 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
6299 9168 2.583739 CTTTGTGTGTGTGTGTGTGTG 58.416 47.619 0.00 0.00 0.00 3.82
6300 9169 1.539388 CCTTTGTGTGTGTGTGTGTGT 59.461 47.619 0.00 0.00 0.00 3.72
6301 9170 1.809547 TCCTTTGTGTGTGTGTGTGTG 59.190 47.619 0.00 0.00 0.00 3.82
6302 9171 2.192664 TCCTTTGTGTGTGTGTGTGT 57.807 45.000 0.00 0.00 0.00 3.72
6303 9172 3.119531 ACAATCCTTTGTGTGTGTGTGTG 60.120 43.478 0.00 0.00 44.36 3.82
6304 9173 3.088532 ACAATCCTTTGTGTGTGTGTGT 58.911 40.909 0.00 0.00 44.36 3.72
6305 9174 3.781079 ACAATCCTTTGTGTGTGTGTG 57.219 42.857 0.00 0.00 44.36 3.82
6306 9175 4.523083 AGTACAATCCTTTGTGTGTGTGT 58.477 39.130 0.00 0.00 45.56 3.72
6307 9176 5.499139 AAGTACAATCCTTTGTGTGTGTG 57.501 39.130 0.00 0.00 45.56 3.82
6308 9177 5.763204 CCTAAGTACAATCCTTTGTGTGTGT 59.237 40.000 0.00 0.00 45.56 3.72
6309 9178 5.995282 TCCTAAGTACAATCCTTTGTGTGTG 59.005 40.000 0.00 0.00 45.56 3.82
6310 9179 6.042781 TCTCCTAAGTACAATCCTTTGTGTGT 59.957 38.462 0.00 0.00 45.56 3.72
6311 9180 6.464222 TCTCCTAAGTACAATCCTTTGTGTG 58.536 40.000 0.00 0.00 45.56 3.82
6312 9181 6.681729 TCTCCTAAGTACAATCCTTTGTGT 57.318 37.500 0.00 0.00 45.56 3.72
6313 9182 9.319143 CTATTCTCCTAAGTACAATCCTTTGTG 57.681 37.037 0.00 0.00 45.56 3.33
6315 9184 9.757227 CTCTATTCTCCTAAGTACAATCCTTTG 57.243 37.037 0.00 0.00 38.86 2.77
6316 9185 9.716556 TCTCTATTCTCCTAAGTACAATCCTTT 57.283 33.333 0.00 0.00 0.00 3.11
6317 9186 9.716556 TTCTCTATTCTCCTAAGTACAATCCTT 57.283 33.333 0.00 0.00 0.00 3.36
6318 9187 9.362151 CTTCTCTATTCTCCTAAGTACAATCCT 57.638 37.037 0.00 0.00 0.00 3.24
6319 9188 9.357161 TCTTCTCTATTCTCCTAAGTACAATCC 57.643 37.037 0.00 0.00 0.00 3.01
6323 9192 9.509956 GCTATCTTCTCTATTCTCCTAAGTACA 57.490 37.037 0.00 0.00 0.00 2.90
6324 9193 9.509956 TGCTATCTTCTCTATTCTCCTAAGTAC 57.490 37.037 0.00 0.00 0.00 2.73
6325 9194 9.733556 CTGCTATCTTCTCTATTCTCCTAAGTA 57.266 37.037 0.00 0.00 0.00 2.24
6326 9195 8.444783 TCTGCTATCTTCTCTATTCTCCTAAGT 58.555 37.037 0.00 0.00 0.00 2.24
6327 9196 8.730680 GTCTGCTATCTTCTCTATTCTCCTAAG 58.269 40.741 0.00 0.00 0.00 2.18
6328 9197 8.221251 TGTCTGCTATCTTCTCTATTCTCCTAA 58.779 37.037 0.00 0.00 0.00 2.69
6329 9198 7.750655 TGTCTGCTATCTTCTCTATTCTCCTA 58.249 38.462 0.00 0.00 0.00 2.94
6330 9199 6.609876 TGTCTGCTATCTTCTCTATTCTCCT 58.390 40.000 0.00 0.00 0.00 3.69
6331 9200 6.892658 TGTCTGCTATCTTCTCTATTCTCC 57.107 41.667 0.00 0.00 0.00 3.71
6332 9201 8.413229 ACTTTGTCTGCTATCTTCTCTATTCTC 58.587 37.037 0.00 0.00 0.00 2.87
6337 9206 6.403746 CGACACTTTGTCTGCTATCTTCTCTA 60.404 42.308 4.87 0.00 44.85 2.43
6344 9213 3.061429 GCTTCGACACTTTGTCTGCTATC 59.939 47.826 4.87 0.00 44.85 2.08
6364 9233 6.764308 ACATGTTTAATCACATAAGCTGCT 57.236 33.333 0.00 0.00 35.51 4.24
6454 9325 1.153269 TTCCGCGCATATTCCTGCA 60.153 52.632 8.75 0.00 42.40 4.41
6600 9471 3.117512 CCCAAGGACCTATAGGCAACATT 60.118 47.826 19.25 11.26 39.32 2.71
6655 9526 6.696148 ACGTATAAATCTCACGAATCTCCAAC 59.304 38.462 0.00 0.00 38.96 3.77
6659 9530 6.207213 ACCACGTATAAATCTCACGAATCTC 58.793 40.000 0.00 0.00 38.96 2.75
6660 9531 6.145338 ACCACGTATAAATCTCACGAATCT 57.855 37.500 0.00 0.00 38.96 2.40
6661 9532 7.358066 TCTACCACGTATAAATCTCACGAATC 58.642 38.462 0.00 0.00 38.96 2.52
6662 9533 7.268199 TCTACCACGTATAAATCTCACGAAT 57.732 36.000 0.00 0.00 38.96 3.34
6663 9534 6.682423 TCTACCACGTATAAATCTCACGAA 57.318 37.500 0.00 0.00 38.96 3.85
6664 9535 5.277683 GCTCTACCACGTATAAATCTCACGA 60.278 44.000 0.00 0.00 38.96 4.35
6665 9536 4.910456 GCTCTACCACGTATAAATCTCACG 59.090 45.833 0.00 0.00 41.32 4.35
6666 9537 4.910456 CGCTCTACCACGTATAAATCTCAC 59.090 45.833 0.00 0.00 0.00 3.51
6667 9538 4.556104 GCGCTCTACCACGTATAAATCTCA 60.556 45.833 0.00 0.00 0.00 3.27
6678 9558 2.202623 GTCCAGCGCTCTACCACG 60.203 66.667 7.13 0.00 0.00 4.94
6681 9561 1.153549 CAAGGTCCAGCGCTCTACC 60.154 63.158 24.09 24.09 0.00 3.18
6727 9608 1.264749 TGGATTCTGGAGGTGACCGG 61.265 60.000 0.00 0.00 37.63 5.28
6729 9610 1.573108 TCTGGATTCTGGAGGTGACC 58.427 55.000 0.00 0.00 0.00 4.02
6827 9713 7.443575 AGTTGATATTCTGATCATACAACAGCC 59.556 37.037 18.80 0.83 38.78 4.85
6837 9723 8.298729 ACAGACACTAGTTGATATTCTGATCA 57.701 34.615 13.97 0.00 34.41 2.92
6855 9741 2.162681 AGGCCTTGCATTTACAGACAC 58.837 47.619 0.00 0.00 0.00 3.67
6891 9777 3.433598 GCCAACAGATATAGTGAAGGCCA 60.434 47.826 5.01 0.00 34.48 5.36
6907 9793 6.701145 TGTAAAACTTATCACAAGCCAACA 57.299 33.333 0.00 0.00 0.00 3.33
6934 9820 4.591321 AGCAGATTGGGAAATAAGGACA 57.409 40.909 0.00 0.00 0.00 4.02
6950 9836 2.357154 GCTGGATTAAAGGGGAAGCAGA 60.357 50.000 0.00 0.00 0.00 4.26
6971 9857 7.631822 TGAATTTTGCAACAATTGTCTCATTG 58.368 30.769 12.39 7.20 0.00 2.82
7083 9969 9.509855 TGTTGTTTTGTTGAGATGTTATGTTAC 57.490 29.630 0.00 0.00 0.00 2.50
7247 10143 5.974751 GTGTACGGTTCATTGAAAATGTGTT 59.025 36.000 0.00 0.00 0.00 3.32
7307 10209 3.833732 TGTTAAGGGGTTGTGTTATGCA 58.166 40.909 0.00 0.00 0.00 3.96
7408 10318 6.916387 CACCTAAGATAATTGCTTGCTTCATG 59.084 38.462 5.85 0.00 0.00 3.07
7433 10343 3.255642 ACCACAAATGTTGGCATACAGAC 59.744 43.478 8.15 0.00 34.39 3.51
7442 10437 3.533606 TGGTTTCACCACAAATGTTGG 57.466 42.857 0.00 0.00 44.79 3.77
7492 10495 7.577979 TCGTCACAAAATATTGAGTACAAACC 58.422 34.615 0.00 0.00 38.94 3.27
7493 10496 9.607285 AATCGTCACAAAATATTGAGTACAAAC 57.393 29.630 0.00 0.00 38.94 2.93
7512 10515 8.289939 ACTACAGTTCCTTAGAATAATCGTCA 57.710 34.615 0.00 0.00 33.67 4.35
7524 10527 4.281688 AGCGGTACAAACTACAGTTCCTTA 59.718 41.667 0.00 0.00 37.25 2.69
7541 10544 3.508793 AGCACTAGTTACTTTGAGCGGTA 59.491 43.478 0.00 0.00 0.00 4.02
7548 10551 6.743575 ATTGGCTAAGCACTAGTTACTTTG 57.256 37.500 12.03 11.26 0.00 2.77


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

AutoCloner maintained by Alex Coulton.