Multiple sequence alignment - TraesCS5B01G355300

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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 TraesCS5B01G355300 chr5B 100.000 3149 0 0 1 3149 534824055 534827203 0.000000e+00 5816.0
1 TraesCS5B01G355300 chr5B 95.671 1871 61 8 318 2181 534992517 534994374 0.000000e+00 2988.0
2 TraesCS5B01G355300 chr5B 90.615 650 59 1 910 1557 535004840 535005489 0.000000e+00 861.0
3 TraesCS5B01G355300 chr5B 85.500 600 55 14 389 974 534604575 534605156 5.810000e-167 597.0
4 TraesCS5B01G355300 chr5B 85.333 600 58 13 389 974 534643962 534644545 7.520000e-166 593.0
5 TraesCS5B01G355300 chr5B 83.725 510 45 19 389 861 535001569 535002077 6.200000e-122 448.0
6 TraesCS5B01G355300 chr5B 90.087 343 33 1 924 1266 534679722 534680063 8.010000e-121 444.0
7 TraesCS5B01G355300 chr5B 95.149 268 13 0 5 272 534990916 534991183 1.040000e-114 424.0
8 TraesCS5B01G355300 chr5B 76.712 657 114 27 943 1569 535063113 535063760 2.340000e-86 329.0
9 TraesCS5B01G355300 chr5B 82.645 363 31 10 534 889 534679384 534679721 3.070000e-75 292.0
10 TraesCS5B01G355300 chr5B 91.549 213 11 4 2307 2517 535022132 535022339 1.430000e-73 287.0
11 TraesCS5B01G355300 chr5B 83.630 281 34 9 28 306 534601155 534601425 1.450000e-63 254.0
12 TraesCS5B01G355300 chr5B 83.274 281 35 9 28 306 534640594 534640864 6.740000e-62 248.0
13 TraesCS5B01G355300 chr5B 85.141 249 28 5 28 274 534676180 534676421 2.430000e-61 246.0
14 TraesCS5B01G355300 chr5B 89.937 159 12 2 2403 2559 534994685 534994841 5.330000e-48 202.0
15 TraesCS5B01G355300 chr5B 89.844 128 11 2 424 549 534679242 534679369 2.510000e-36 163.0
16 TraesCS5B01G355300 chr5B 95.890 73 3 0 1933 2005 535005487 535005559 5.520000e-23 119.0
17 TraesCS5B01G355300 chr5D 89.981 2136 144 35 455 2556 439744976 439747075 0.000000e+00 2695.0
18 TraesCS5B01G355300 chr5D 86.506 704 59 14 389 1064 440067805 440068500 0.000000e+00 741.0
19 TraesCS5B01G355300 chr5D 93.047 489 31 3 1405 1893 440069424 440069909 0.000000e+00 712.0
20 TraesCS5B01G355300 chr5D 76.642 685 114 33 920 1569 440116557 440117230 1.400000e-88 337.0
21 TraesCS5B01G355300 chr5D 90.114 263 17 6 2896 3149 439772667 439772929 1.810000e-87 333.0
22 TraesCS5B01G355300 chr5D 91.080 213 17 2 2687 2898 439747632 439747843 1.430000e-73 287.0
23 TraesCS5B01G355300 chr5D 88.115 244 22 4 28 269 439734769 439735007 1.850000e-72 283.0
24 TraesCS5B01G355300 chr5D 87.705 244 23 4 28 269 440061759 440061997 8.600000e-71 278.0
25 TraesCS5B01G355300 chr5D 80.000 185 36 1 2963 3146 439998095 439998279 5.480000e-28 135.0
26 TraesCS5B01G355300 chr5A 88.385 2247 166 40 389 2559 555638158 555640385 0.000000e+00 2615.0
27 TraesCS5B01G355300 chr5A 83.755 554 51 14 32 550 555636342 555636891 3.650000e-134 488.0
28 TraesCS5B01G355300 chr5A 76.754 684 115 31 920 1569 555651961 555652634 3.010000e-90 342.0
29 TraesCS5B01G355300 chr5A 81.868 182 33 0 2963 3144 555598834 555599015 1.510000e-33 154.0
30 TraesCS5B01G355300 chr3D 77.536 138 20 7 2752 2882 599006483 599006350 4.360000e-09 73.1


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 TraesCS5B01G355300 chr5B 534824055 534827203 3148 False 5816.000000 5816 100.000000 1 3149 1 chr5B.!!$F1 3148
1 TraesCS5B01G355300 chr5B 534990916 534994841 3925 False 1204.666667 2988 93.585667 5 2559 3 chr5B.!!$F7 2554
2 TraesCS5B01G355300 chr5B 535001569 535005559 3990 False 476.000000 861 90.076667 389 2005 3 chr5B.!!$F8 1616
3 TraesCS5B01G355300 chr5B 534601155 534605156 4001 False 425.500000 597 84.565000 28 974 2 chr5B.!!$F4 946
4 TraesCS5B01G355300 chr5B 534640594 534644545 3951 False 420.500000 593 84.303500 28 974 2 chr5B.!!$F5 946
5 TraesCS5B01G355300 chr5B 535063113 535063760 647 False 329.000000 329 76.712000 943 1569 1 chr5B.!!$F3 626
6 TraesCS5B01G355300 chr5B 534676180 534680063 3883 False 286.250000 444 86.929250 28 1266 4 chr5B.!!$F6 1238
7 TraesCS5B01G355300 chr5D 439744976 439747843 2867 False 1491.000000 2695 90.530500 455 2898 2 chr5D.!!$F6 2443
8 TraesCS5B01G355300 chr5D 440067805 440069909 2104 False 726.500000 741 89.776500 389 1893 2 chr5D.!!$F7 1504
9 TraesCS5B01G355300 chr5D 440116557 440117230 673 False 337.000000 337 76.642000 920 1569 1 chr5D.!!$F5 649
10 TraesCS5B01G355300 chr5A 555636342 555640385 4043 False 1551.500000 2615 86.070000 32 2559 2 chr5A.!!$F3 2527
11 TraesCS5B01G355300 chr5A 555651961 555652634 673 False 342.000000 342 76.754000 920 1569 1 chr5A.!!$F2 649

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
784 4838 0.175760 TACCATCAGCTCTTCCACGC 59.824 55.0 0.0 0.0 0.0 5.34 F
1153 8158 0.031585 CGTCACCTTCTTCACACCGA 59.968 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 9328 0.391130 GGTACAGCTCGCCATTCACA 60.391 55.0 0.0 0.0 0.0 3.58 R
2919 11021 0.105593 TCGTAGGTCTATCGTCGGCT 59.894 55.0 0.0 0.0 0.0 5.52 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
30 31 4.424626 GCGTGATCTTGATCTAGTGTTCA 58.575 43.478 11.31 4.18 0.00 3.18
137 143 4.380761 GGTGAATAATTGATGTGTGCTGCA 60.381 41.667 0.00 0.00 0.00 4.41
199 205 0.550914 ACCCAACTCAGGTGAAGCAA 59.449 50.000 0.00 0.00 35.85 3.91
211 217 2.604462 GGTGAAGCAAACAACAAAGCAG 59.396 45.455 0.00 0.00 0.00 4.24
231 239 1.276989 GTCAACCCTAACCACCGATGA 59.723 52.381 0.00 0.00 0.00 2.92
296 1965 6.769134 AAAAAGAAGGTTTTTCTCCGAAGA 57.231 33.333 0.00 0.00 30.33 2.87
382 2052 5.766222 TCTCTTTACGAACCTGAACAGTAC 58.234 41.667 0.00 0.00 0.00 2.73
652 4684 1.657094 GGAAGAATTAAACGCGAGCGA 59.343 47.619 24.72 1.34 42.83 4.93
784 4838 0.175760 TACCATCAGCTCTTCCACGC 59.824 55.000 0.00 0.00 0.00 5.34
903 7696 0.530431 CGACGATGATGACCATGGCA 60.530 55.000 13.04 11.62 34.76 4.92
1034 7830 2.048222 CGACGCCTTCAGCTTCCA 60.048 61.111 0.00 0.00 36.41 3.53
1045 7841 0.322277 CAGCTTCCAGTCCATGTGCT 60.322 55.000 0.00 0.00 0.00 4.40
1093 7889 1.374252 AAGTTCTTCGCGCCGATGT 60.374 52.632 0.00 0.00 35.23 3.06
1100 8105 1.692148 TTCGCGCCGATGTTGATGAC 61.692 55.000 0.00 0.00 35.23 3.06
1150 8155 1.557443 CGCCGTCACCTTCTTCACAC 61.557 60.000 0.00 0.00 0.00 3.82
1153 8158 0.031585 CGTCACCTTCTTCACACCGA 59.968 55.000 0.00 0.00 0.00 4.69
1569 9106 2.640302 ATGGACGCTGCTCGACACT 61.640 57.895 5.98 0.00 41.67 3.55
1645 9182 2.386661 AGCGATCTTCAACGGACATT 57.613 45.000 0.00 0.00 0.00 2.71
1686 9223 3.391382 GTGGCGGTAGTGGGAGCT 61.391 66.667 0.00 0.00 0.00 4.09
1927 9464 0.676782 CCCCGGATTGACACTGTTCC 60.677 60.000 0.73 0.00 0.00 3.62
1984 9521 2.809601 CAAGCGTCTCCGGGTTCG 60.810 66.667 0.00 5.10 33.68 3.95
2005 9542 3.648009 GAGGAGAATTCCATCTACTGCG 58.352 50.000 0.65 0.00 46.64 5.18
2116 9656 2.550277 TCAGGATTCAGCTGGGACTA 57.450 50.000 15.13 0.00 0.00 2.59
2158 9698 6.677781 ATCATTGGAAATAAGGTACGTGTG 57.322 37.500 0.00 0.00 0.00 3.82
2159 9699 5.553123 TCATTGGAAATAAGGTACGTGTGT 58.447 37.500 0.00 0.00 0.00 3.72
2160 9700 5.410132 TCATTGGAAATAAGGTACGTGTGTG 59.590 40.000 0.00 0.00 0.00 3.82
2163 9703 5.472148 TGGAAATAAGGTACGTGTGTGTAG 58.528 41.667 0.00 0.00 0.00 2.74
2181 9721 5.186198 GTGTAGAGGTTATTCCATGTTGCT 58.814 41.667 0.00 0.00 39.02 3.91
2182 9722 5.294552 GTGTAGAGGTTATTCCATGTTGCTC 59.705 44.000 0.00 0.00 39.02 4.26
2184 9724 5.121380 AGAGGTTATTCCATGTTGCTCAT 57.879 39.130 0.00 0.00 39.02 2.90
2185 9725 5.513233 AGAGGTTATTCCATGTTGCTCATT 58.487 37.500 0.00 0.00 39.02 2.57
2187 9727 5.513233 AGGTTATTCCATGTTGCTCATTCT 58.487 37.500 0.00 0.00 39.02 2.40
2188 9728 5.359009 AGGTTATTCCATGTTGCTCATTCTG 59.641 40.000 0.00 0.00 39.02 3.02
2191 9731 3.421919 TCCATGTTGCTCATTCTGTGA 57.578 42.857 0.00 0.00 34.09 3.58
2192 9732 3.959293 TCCATGTTGCTCATTCTGTGAT 58.041 40.909 0.00 0.00 35.97 3.06
2197 9740 6.293462 CCATGTTGCTCATTCTGTGATCTATG 60.293 42.308 0.00 0.00 35.97 2.23
2206 9749 4.574674 TCTGTGATCTATGCAGGGTTTT 57.425 40.909 0.00 0.00 0.00 2.43
2235 9874 5.738619 TCGCTATTTATCAAGGGCTATGA 57.261 39.130 0.00 0.00 0.00 2.15
2251 9890 2.875094 ATGAAGCCTAGGCCATCATC 57.125 50.000 32.22 22.55 41.31 2.92
2253 9892 2.130193 TGAAGCCTAGGCCATCATCTT 58.870 47.619 30.42 15.88 43.17 2.40
2260 9899 6.852404 AGCCTAGGCCATCATCTTATTTTTA 58.148 36.000 30.42 0.00 43.17 1.52
2265 9904 6.809869 AGGCCATCATCTTATTTTTACTTGC 58.190 36.000 5.01 0.00 0.00 4.01
2267 9906 5.687285 GCCATCATCTTATTTTTACTTGCGG 59.313 40.000 0.00 0.00 0.00 5.69
2274 9913 5.475564 TCTTATTTTTACTTGCGGCCTCTTT 59.524 36.000 0.00 0.00 0.00 2.52
2374 10038 1.227527 CAGACGTGTGGAAGGTGCA 60.228 57.895 4.46 0.00 0.00 4.57
2375 10039 1.227556 AGACGTGTGGAAGGTGCAC 60.228 57.895 8.80 8.80 39.30 4.57
2376 10040 1.522806 GACGTGTGGAAGGTGCACA 60.523 57.895 20.43 0.00 46.44 4.57
2408 10072 1.532868 GAAGCATATTAGGCGGTGCTG 59.467 52.381 0.00 0.00 46.37 4.41
2426 10090 1.607467 GGTGCAACAGATGGGGCTT 60.607 57.895 0.00 0.00 39.98 4.35
2492 10156 3.435566 TGCGCTTTGTATCTTCTACTCG 58.564 45.455 9.73 0.00 0.00 4.18
2525 10189 5.705441 GTCCTCTATTTTGTGTGGATGTTCA 59.295 40.000 0.00 0.00 0.00 3.18
2536 10200 5.411361 TGTGTGGATGTTCATTACTGTAAGC 59.589 40.000 6.40 0.00 37.60 3.09
2543 10207 6.968131 TGTTCATTACTGTAAGCTGATGAC 57.032 37.500 6.40 3.54 37.60 3.06
2559 10223 2.017138 TGACGTTCTCAGCACAAACA 57.983 45.000 0.00 0.00 0.00 2.83
2560 10224 1.933181 TGACGTTCTCAGCACAAACAG 59.067 47.619 0.00 0.00 0.00 3.16
2561 10225 2.201732 GACGTTCTCAGCACAAACAGA 58.798 47.619 0.00 0.00 0.00 3.41
2562 10226 2.607635 GACGTTCTCAGCACAAACAGAA 59.392 45.455 0.00 0.00 0.00 3.02
2565 10229 3.060003 CGTTCTCAGCACAAACAGAAGAG 60.060 47.826 0.00 0.00 0.00 2.85
2566 10230 4.122776 GTTCTCAGCACAAACAGAAGAGA 58.877 43.478 0.00 0.00 0.00 3.10
2569 10233 6.101650 TCTCAGCACAAACAGAAGAGATAA 57.898 37.500 0.00 0.00 0.00 1.75
2570 10234 6.524734 TCTCAGCACAAACAGAAGAGATAAA 58.475 36.000 0.00 0.00 0.00 1.40
2571 10235 6.992123 TCTCAGCACAAACAGAAGAGATAAAA 59.008 34.615 0.00 0.00 0.00 1.52
2573 10237 8.846943 TCAGCACAAACAGAAGAGATAAAATA 57.153 30.769 0.00 0.00 0.00 1.40
2574 10238 9.283768 TCAGCACAAACAGAAGAGATAAAATAA 57.716 29.630 0.00 0.00 0.00 1.40
2575 10239 9.897744 CAGCACAAACAGAAGAGATAAAATAAA 57.102 29.630 0.00 0.00 0.00 1.40
2615 10454 9.691362 AAATAAAATAAAACAAGCTGATGACGT 57.309 25.926 0.00 0.00 0.00 4.34
2617 10456 7.623268 AAAATAAAACAAGCTGATGACGTTC 57.377 32.000 0.00 0.00 0.00 3.95
2629 10672 6.072286 AGCTGATGACGTTCTGATTTTTGAAT 60.072 34.615 0.00 0.00 0.00 2.57
2630 10673 7.119699 AGCTGATGACGTTCTGATTTTTGAATA 59.880 33.333 0.00 0.00 0.00 1.75
2632 10675 9.611284 CTGATGACGTTCTGATTTTTGAATAAA 57.389 29.630 0.00 0.00 0.00 1.40
2633 10676 9.958234 TGATGACGTTCTGATTTTTGAATAAAA 57.042 25.926 0.00 0.00 34.13 1.52
2665 10766 9.434275 AGAAGAGATAAAAGGGGAAAAAGAAAA 57.566 29.630 0.00 0.00 0.00 2.29
2744 10845 3.230976 AGGGTTCCTAAAACTGGCAAAG 58.769 45.455 0.00 0.00 28.47 2.77
2750 10851 3.634910 TCCTAAAACTGGCAAAGAACCAC 59.365 43.478 0.00 0.00 32.49 4.16
2762 10863 4.578928 GCAAAGAACCACCTAGAAAGTTCA 59.421 41.667 16.19 0.00 40.82 3.18
2783 10884 4.638421 TCATAAAACCGGGATGTGATGAAC 59.362 41.667 6.32 0.00 0.00 3.18
2828 10929 2.678336 CCCATCTTACCTTTGTTCGCTC 59.322 50.000 0.00 0.00 0.00 5.03
2838 10939 2.048127 GTTCGCTCGGCTCCTGTT 60.048 61.111 0.00 0.00 0.00 3.16
2839 10940 2.048222 TTCGCTCGGCTCCTGTTG 60.048 61.111 0.00 0.00 0.00 3.33
2858 10959 2.176889 TGGGAACAGCTACTACCTGAC 58.823 52.381 0.00 0.00 34.47 3.51
2890 10992 5.338822 GTCCAATAAGTTTTTCGAGCGAAAC 59.661 40.000 16.59 8.21 42.88 2.78
2891 10993 4.317291 CCAATAAGTTTTTCGAGCGAAACG 59.683 41.667 16.59 0.00 42.88 3.60
2892 10994 4.977741 ATAAGTTTTTCGAGCGAAACGA 57.022 36.364 16.59 6.97 42.88 3.85
2893 10995 2.640375 AGTTTTTCGAGCGAAACGAC 57.360 45.000 16.59 16.65 42.88 4.34
2894 10996 1.071698 AGTTTTTCGAGCGAAACGACG 60.072 47.619 16.59 0.00 42.88 5.12
2895 10997 0.922717 TTTTTCGAGCGAAACGACGT 59.077 45.000 16.59 0.00 42.88 4.34
2896 10998 0.499761 TTTTCGAGCGAAACGACGTC 59.500 50.000 16.59 5.18 42.88 4.34
2897 10999 0.317269 TTTCGAGCGAAACGACGTCT 60.317 50.000 14.70 0.00 38.95 4.18
2898 11000 0.995234 TTCGAGCGAAACGACGTCTG 60.995 55.000 14.70 9.79 39.46 3.51
2899 11001 2.763881 GAGCGAAACGACGTCTGC 59.236 61.111 14.70 5.94 35.59 4.26
2900 11002 1.729838 GAGCGAAACGACGTCTGCT 60.730 57.895 17.85 17.85 35.59 4.24
2901 11003 1.935065 GAGCGAAACGACGTCTGCTG 61.935 60.000 21.36 0.00 35.59 4.41
2902 11004 2.465920 CGAAACGACGTCTGCTGC 59.534 61.111 14.70 0.00 0.00 5.25
2903 11005 2.016704 CGAAACGACGTCTGCTGCT 61.017 57.895 14.70 0.00 0.00 4.24
2904 11006 1.488957 GAAACGACGTCTGCTGCTG 59.511 57.895 14.70 0.00 0.00 4.41
2905 11007 2.486036 GAAACGACGTCTGCTGCTGC 62.486 60.000 14.70 8.89 40.20 5.25
2906 11008 2.978452 AAACGACGTCTGCTGCTGCT 62.978 55.000 17.00 0.00 40.48 4.24
2907 11009 3.476646 CGACGTCTGCTGCTGCTG 61.477 66.667 17.00 15.94 40.48 4.41
2908 11010 2.356793 GACGTCTGCTGCTGCTGT 60.357 61.111 17.00 9.65 40.48 4.40
2909 11011 2.356793 ACGTCTGCTGCTGCTGTC 60.357 61.111 17.00 12.49 40.48 3.51
2910 11012 3.117171 CGTCTGCTGCTGCTGTCC 61.117 66.667 17.00 10.10 40.48 4.02
2911 11013 2.745492 GTCTGCTGCTGCTGTCCC 60.745 66.667 17.00 5.66 40.48 4.46
2912 11014 4.025858 TCTGCTGCTGCTGTCCCC 62.026 66.667 17.00 0.00 40.48 4.81
2927 11029 2.904905 CCCCCAAATAGCCGACGA 59.095 61.111 0.00 0.00 0.00 4.20
2928 11030 1.450211 CCCCCAAATAGCCGACGAT 59.550 57.895 0.00 0.00 0.00 3.73
2929 11031 0.682852 CCCCCAAATAGCCGACGATA 59.317 55.000 0.00 0.00 0.00 2.92
2930 11032 1.337823 CCCCCAAATAGCCGACGATAG 60.338 57.143 0.00 0.00 46.19 2.08
2931 11033 1.616865 CCCCAAATAGCCGACGATAGA 59.383 52.381 0.00 0.00 41.38 1.98
2932 11034 2.609737 CCCCAAATAGCCGACGATAGAC 60.610 54.545 0.00 0.00 41.38 2.59
2933 11035 2.609737 CCCAAATAGCCGACGATAGACC 60.610 54.545 0.00 0.00 41.38 3.85
2934 11036 2.296471 CCAAATAGCCGACGATAGACCT 59.704 50.000 0.00 0.00 41.38 3.85
2935 11037 3.504906 CCAAATAGCCGACGATAGACCTA 59.495 47.826 0.00 0.00 41.38 3.08
2936 11038 4.474113 CAAATAGCCGACGATAGACCTAC 58.526 47.826 0.00 0.00 41.38 3.18
2937 11039 1.788258 TAGCCGACGATAGACCTACG 58.212 55.000 0.00 0.00 41.38 3.51
2938 11040 0.105593 AGCCGACGATAGACCTACGA 59.894 55.000 0.00 0.00 41.38 3.43
2939 11041 1.155042 GCCGACGATAGACCTACGAT 58.845 55.000 0.00 0.00 41.38 3.73
2940 11042 1.534595 GCCGACGATAGACCTACGATT 59.465 52.381 0.00 0.00 41.38 3.34
2941 11043 2.031333 GCCGACGATAGACCTACGATTT 60.031 50.000 0.00 0.00 41.38 2.17
2942 11044 3.549625 GCCGACGATAGACCTACGATTTT 60.550 47.826 0.00 0.00 41.38 1.82
2943 11045 4.604976 CCGACGATAGACCTACGATTTTT 58.395 43.478 0.00 0.00 41.38 1.94
2962 11064 5.789643 TTTTTCTGGATTTTGTCTCCCTG 57.210 39.130 0.00 0.00 31.32 4.45
2963 11065 4.722526 TTTCTGGATTTTGTCTCCCTGA 57.277 40.909 0.00 0.00 31.32 3.86
2964 11066 3.703001 TCTGGATTTTGTCTCCCTGAC 57.297 47.619 0.00 0.00 45.54 3.51
2965 11067 3.251484 TCTGGATTTTGTCTCCCTGACT 58.749 45.455 0.00 0.00 45.54 3.41
2966 11068 3.652869 TCTGGATTTTGTCTCCCTGACTT 59.347 43.478 0.00 0.00 45.54 3.01
2967 11069 4.844085 TCTGGATTTTGTCTCCCTGACTTA 59.156 41.667 0.00 0.00 45.54 2.24
2968 11070 5.309543 TCTGGATTTTGTCTCCCTGACTTAA 59.690 40.000 0.00 0.00 45.54 1.85
2969 11071 5.947663 TGGATTTTGTCTCCCTGACTTAAA 58.052 37.500 0.00 0.00 45.54 1.52
2970 11072 6.552008 TGGATTTTGTCTCCCTGACTTAAAT 58.448 36.000 0.00 0.00 45.54 1.40
2971 11073 6.659242 TGGATTTTGTCTCCCTGACTTAAATC 59.341 38.462 17.78 17.78 44.69 2.17
2972 11074 6.659242 GGATTTTGTCTCCCTGACTTAAATCA 59.341 38.462 22.24 0.00 45.65 2.57
2973 11075 7.340487 GGATTTTGTCTCCCTGACTTAAATCAT 59.660 37.037 22.24 4.12 45.65 2.45
2974 11076 7.687941 TTTTGTCTCCCTGACTTAAATCATC 57.312 36.000 0.00 0.00 45.54 2.92
2975 11077 6.373005 TTGTCTCCCTGACTTAAATCATCA 57.627 37.500 0.00 0.00 45.54 3.07
2976 11078 6.566079 TGTCTCCCTGACTTAAATCATCAT 57.434 37.500 0.00 0.00 45.54 2.45
2977 11079 7.675161 TGTCTCCCTGACTTAAATCATCATA 57.325 36.000 0.00 0.00 45.54 2.15
2978 11080 8.089625 TGTCTCCCTGACTTAAATCATCATAA 57.910 34.615 0.00 0.00 45.54 1.90
2979 11081 7.987458 TGTCTCCCTGACTTAAATCATCATAAC 59.013 37.037 0.00 0.00 45.54 1.89
2980 11082 8.207545 GTCTCCCTGACTTAAATCATCATAACT 58.792 37.037 0.00 0.00 42.21 2.24
2981 11083 8.772250 TCTCCCTGACTTAAATCATCATAACTT 58.228 33.333 0.00 0.00 0.00 2.66
3001 11103 9.860898 ATAACTTAATTTCAATTCAGAAGGTGC 57.139 29.630 1.32 0.00 0.00 5.01
3002 11104 7.530426 ACTTAATTTCAATTCAGAAGGTGCT 57.470 32.000 1.32 0.00 0.00 4.40
3003 11105 7.955918 ACTTAATTTCAATTCAGAAGGTGCTT 58.044 30.769 1.32 0.00 0.00 3.91
3004 11106 9.077885 ACTTAATTTCAATTCAGAAGGTGCTTA 57.922 29.630 1.32 0.00 0.00 3.09
3005 11107 9.912634 CTTAATTTCAATTCAGAAGGTGCTTAA 57.087 29.630 0.00 0.00 0.00 1.85
3006 11108 9.691362 TTAATTTCAATTCAGAAGGTGCTTAAC 57.309 29.630 0.00 0.00 0.00 2.01
3007 11109 6.707440 TTTCAATTCAGAAGGTGCTTAACA 57.293 33.333 0.00 0.00 0.00 2.41
3031 11133 4.609301 ACATAATGTGTGGTAATTGCCCT 58.391 39.130 10.34 0.00 40.28 5.19
3032 11134 4.402155 ACATAATGTGTGGTAATTGCCCTG 59.598 41.667 10.34 0.00 40.28 4.45
3033 11135 2.603075 ATGTGTGGTAATTGCCCTGT 57.397 45.000 10.34 0.00 0.00 4.00
3034 11136 2.373335 TGTGTGGTAATTGCCCTGTT 57.627 45.000 10.34 0.00 0.00 3.16
3035 11137 3.510531 TGTGTGGTAATTGCCCTGTTA 57.489 42.857 10.34 0.00 0.00 2.41
3036 11138 3.150767 TGTGTGGTAATTGCCCTGTTAC 58.849 45.455 10.34 1.69 0.00 2.50
3037 11139 3.181438 TGTGTGGTAATTGCCCTGTTACT 60.181 43.478 10.34 0.00 32.70 2.24
3038 11140 3.439129 GTGTGGTAATTGCCCTGTTACTC 59.561 47.826 10.34 0.00 32.70 2.59
3039 11141 2.676342 GTGGTAATTGCCCTGTTACTCG 59.324 50.000 10.34 0.00 32.70 4.18
3040 11142 2.568062 TGGTAATTGCCCTGTTACTCGA 59.432 45.455 10.34 0.00 32.70 4.04
3041 11143 2.934553 GGTAATTGCCCTGTTACTCGAC 59.065 50.000 0.16 0.00 32.70 4.20
3042 11144 3.369157 GGTAATTGCCCTGTTACTCGACT 60.369 47.826 0.16 0.00 32.70 4.18
3043 11145 2.674796 ATTGCCCTGTTACTCGACTC 57.325 50.000 0.00 0.00 0.00 3.36
3044 11146 0.606604 TTGCCCTGTTACTCGACTCC 59.393 55.000 0.00 0.00 0.00 3.85
3045 11147 0.541063 TGCCCTGTTACTCGACTCCA 60.541 55.000 0.00 0.00 0.00 3.86
3046 11148 0.824759 GCCCTGTTACTCGACTCCAT 59.175 55.000 0.00 0.00 0.00 3.41
3047 11149 1.471676 GCCCTGTTACTCGACTCCATG 60.472 57.143 0.00 0.00 0.00 3.66
3048 11150 1.137086 CCCTGTTACTCGACTCCATGG 59.863 57.143 4.97 4.97 0.00 3.66
3049 11151 1.825474 CCTGTTACTCGACTCCATGGT 59.175 52.381 12.58 0.00 0.00 3.55
3050 11152 2.233922 CCTGTTACTCGACTCCATGGTT 59.766 50.000 12.58 0.00 0.00 3.67
3051 11153 3.512680 CTGTTACTCGACTCCATGGTTC 58.487 50.000 12.58 8.77 0.00 3.62
3052 11154 3.162666 TGTTACTCGACTCCATGGTTCT 58.837 45.455 12.58 0.00 0.00 3.01
3053 11155 4.338012 TGTTACTCGACTCCATGGTTCTA 58.662 43.478 12.58 1.10 0.00 2.10
3054 11156 4.398358 TGTTACTCGACTCCATGGTTCTAG 59.602 45.833 12.58 12.79 0.00 2.43
3055 11157 3.088789 ACTCGACTCCATGGTTCTAGT 57.911 47.619 12.58 13.40 0.00 2.57
3056 11158 3.432378 ACTCGACTCCATGGTTCTAGTT 58.568 45.455 12.58 0.63 0.00 2.24
3057 11159 3.193691 ACTCGACTCCATGGTTCTAGTTG 59.806 47.826 12.58 11.59 0.00 3.16
3058 11160 3.162666 TCGACTCCATGGTTCTAGTTGT 58.837 45.455 12.58 0.00 0.00 3.32
3059 11161 3.576982 TCGACTCCATGGTTCTAGTTGTT 59.423 43.478 12.58 0.00 0.00 2.83
3060 11162 3.927142 CGACTCCATGGTTCTAGTTGTTC 59.073 47.826 12.58 0.00 0.00 3.18
3061 11163 3.926616 ACTCCATGGTTCTAGTTGTTCG 58.073 45.455 12.58 0.00 0.00 3.95
3062 11164 3.262420 CTCCATGGTTCTAGTTGTTCGG 58.738 50.000 12.58 0.00 0.00 4.30
3063 11165 2.027561 TCCATGGTTCTAGTTGTTCGGG 60.028 50.000 12.58 0.00 0.00 5.14
3064 11166 2.027561 CCATGGTTCTAGTTGTTCGGGA 60.028 50.000 2.57 0.00 0.00 5.14
3065 11167 3.558321 CCATGGTTCTAGTTGTTCGGGAA 60.558 47.826 2.57 0.00 0.00 3.97
3066 11168 4.261801 CATGGTTCTAGTTGTTCGGGAAT 58.738 43.478 0.00 0.00 0.00 3.01
3067 11169 4.360951 TGGTTCTAGTTGTTCGGGAATT 57.639 40.909 0.00 0.00 0.00 2.17
3068 11170 4.721132 TGGTTCTAGTTGTTCGGGAATTT 58.279 39.130 0.00 0.00 0.00 1.82
3069 11171 5.134661 TGGTTCTAGTTGTTCGGGAATTTT 58.865 37.500 0.00 0.00 0.00 1.82
3070 11172 5.009210 TGGTTCTAGTTGTTCGGGAATTTTG 59.991 40.000 0.00 0.00 0.00 2.44
3071 11173 5.009310 GGTTCTAGTTGTTCGGGAATTTTGT 59.991 40.000 0.00 0.00 0.00 2.83
3072 11174 6.205270 GGTTCTAGTTGTTCGGGAATTTTGTA 59.795 38.462 0.00 0.00 0.00 2.41
3073 11175 7.094506 GGTTCTAGTTGTTCGGGAATTTTGTAT 60.095 37.037 0.00 0.00 0.00 2.29
3074 11176 7.989416 TCTAGTTGTTCGGGAATTTTGTATT 57.011 32.000 0.00 0.00 0.00 1.89
3075 11177 8.398878 TCTAGTTGTTCGGGAATTTTGTATTT 57.601 30.769 0.00 0.00 0.00 1.40
3076 11178 9.504708 TCTAGTTGTTCGGGAATTTTGTATTTA 57.495 29.630 0.00 0.00 0.00 1.40
3077 11179 9.769093 CTAGTTGTTCGGGAATTTTGTATTTAG 57.231 33.333 0.00 0.00 0.00 1.85
3078 11180 8.398878 AGTTGTTCGGGAATTTTGTATTTAGA 57.601 30.769 0.00 0.00 0.00 2.10
3079 11181 8.852135 AGTTGTTCGGGAATTTTGTATTTAGAA 58.148 29.630 0.00 0.00 0.00 2.10
3080 11182 9.124807 GTTGTTCGGGAATTTTGTATTTAGAAG 57.875 33.333 0.00 0.00 0.00 2.85
3081 11183 8.398878 TGTTCGGGAATTTTGTATTTAGAAGT 57.601 30.769 0.00 0.00 0.00 3.01
3082 11184 8.852135 TGTTCGGGAATTTTGTATTTAGAAGTT 58.148 29.630 0.00 0.00 0.00 2.66
3083 11185 9.338291 GTTCGGGAATTTTGTATTTAGAAGTTC 57.662 33.333 0.00 0.00 0.00 3.01
3084 11186 8.857694 TCGGGAATTTTGTATTTAGAAGTTCT 57.142 30.769 10.87 10.87 0.00 3.01
3085 11187 8.943002 TCGGGAATTTTGTATTTAGAAGTTCTC 58.057 33.333 9.12 0.00 0.00 2.87
3086 11188 8.726988 CGGGAATTTTGTATTTAGAAGTTCTCA 58.273 33.333 9.12 0.00 0.00 3.27
3101 11203 8.066612 AGAAGTTCTCAAAATTTCCTGAAACA 57.933 30.769 0.00 0.00 32.51 2.83
3102 11204 8.531146 AGAAGTTCTCAAAATTTCCTGAAACAA 58.469 29.630 0.00 1.05 32.51 2.83
3103 11205 9.317936 GAAGTTCTCAAAATTTCCTGAAACAAT 57.682 29.630 13.91 7.50 32.51 2.71
3104 11206 9.671279 AAGTTCTCAAAATTTCCTGAAACAATT 57.329 25.926 13.91 0.00 32.51 2.32
3105 11207 9.317936 AGTTCTCAAAATTTCCTGAAACAATTC 57.682 29.630 13.91 0.00 36.04 2.17
3106 11208 9.317936 GTTCTCAAAATTTCCTGAAACAATTCT 57.682 29.630 0.00 0.00 36.48 2.40
3108 11210 9.965824 TCTCAAAATTTCCTGAAACAATTCTAC 57.034 29.630 0.00 0.00 36.48 2.59
3109 11211 9.748708 CTCAAAATTTCCTGAAACAATTCTACA 57.251 29.630 0.00 0.00 36.48 2.74
3113 11215 9.480053 AAATTTCCTGAAACAATTCTACATGTG 57.520 29.630 9.11 0.00 36.48 3.21
3114 11216 7.581213 TTTCCTGAAACAATTCTACATGTGT 57.419 32.000 9.11 0.00 36.48 3.72
3115 11217 6.558771 TCCTGAAACAATTCTACATGTGTG 57.441 37.500 9.11 1.17 36.48 3.82
3116 11218 5.048782 TCCTGAAACAATTCTACATGTGTGC 60.049 40.000 9.11 0.00 36.48 4.57
3117 11219 4.782156 TGAAACAATTCTACATGTGTGCG 58.218 39.130 9.11 0.00 36.48 5.34
3118 11220 3.829886 AACAATTCTACATGTGTGCGG 57.170 42.857 9.11 0.00 0.00 5.69
3119 11221 2.083774 ACAATTCTACATGTGTGCGGG 58.916 47.619 9.11 0.00 0.00 6.13
3120 11222 2.083774 CAATTCTACATGTGTGCGGGT 58.916 47.619 9.11 0.00 0.00 5.28
3121 11223 1.737838 ATTCTACATGTGTGCGGGTG 58.262 50.000 9.11 0.00 0.00 4.61
3122 11224 0.394938 TTCTACATGTGTGCGGGTGT 59.605 50.000 9.11 0.00 0.00 4.16
3123 11225 1.258676 TCTACATGTGTGCGGGTGTA 58.741 50.000 9.11 0.00 0.00 2.90
3124 11226 1.828595 TCTACATGTGTGCGGGTGTAT 59.171 47.619 9.11 0.00 0.00 2.29
3125 11227 2.235155 TCTACATGTGTGCGGGTGTATT 59.765 45.455 9.11 0.00 0.00 1.89
3126 11228 1.448985 ACATGTGTGCGGGTGTATTC 58.551 50.000 0.00 0.00 0.00 1.75
3127 11229 1.003118 ACATGTGTGCGGGTGTATTCT 59.997 47.619 0.00 0.00 0.00 2.40
3128 11230 2.235155 ACATGTGTGCGGGTGTATTCTA 59.765 45.455 0.00 0.00 0.00 2.10
3129 11231 3.118408 ACATGTGTGCGGGTGTATTCTAT 60.118 43.478 0.00 0.00 0.00 1.98
3130 11232 2.899976 TGTGTGCGGGTGTATTCTATG 58.100 47.619 0.00 0.00 0.00 2.23
3131 11233 2.235155 TGTGTGCGGGTGTATTCTATGT 59.765 45.455 0.00 0.00 0.00 2.29
3132 11234 3.447944 TGTGTGCGGGTGTATTCTATGTA 59.552 43.478 0.00 0.00 0.00 2.29
3133 11235 4.081586 TGTGTGCGGGTGTATTCTATGTAA 60.082 41.667 0.00 0.00 0.00 2.41
3134 11236 4.269363 GTGTGCGGGTGTATTCTATGTAAC 59.731 45.833 0.00 0.00 0.00 2.50
3135 11237 3.488310 GTGCGGGTGTATTCTATGTAACG 59.512 47.826 0.00 0.00 0.00 3.18
3136 11238 3.130869 TGCGGGTGTATTCTATGTAACGT 59.869 43.478 0.00 0.00 0.00 3.99
3137 11239 3.488310 GCGGGTGTATTCTATGTAACGTG 59.512 47.826 0.00 0.00 0.00 4.49
3138 11240 3.488310 CGGGTGTATTCTATGTAACGTGC 59.512 47.826 0.00 0.00 0.00 5.34
3139 11241 4.435425 GGGTGTATTCTATGTAACGTGCA 58.565 43.478 0.00 0.00 0.00 4.57
3140 11242 4.871557 GGGTGTATTCTATGTAACGTGCAA 59.128 41.667 0.00 0.00 0.00 4.08
3141 11243 5.526111 GGGTGTATTCTATGTAACGTGCAAT 59.474 40.000 0.00 0.00 0.00 3.56
3142 11244 6.418956 GGTGTATTCTATGTAACGTGCAATG 58.581 40.000 0.00 0.00 0.00 2.82
3143 11245 6.036735 GGTGTATTCTATGTAACGTGCAATGT 59.963 38.462 0.00 0.00 38.00 2.71
3145 11247 7.960738 GTGTATTCTATGTAACGTGCAATGTTT 59.039 33.333 10.48 0.00 45.42 2.83
3146 11248 8.172484 TGTATTCTATGTAACGTGCAATGTTTC 58.828 33.333 10.48 6.79 45.42 2.78
3147 11249 6.795098 TTCTATGTAACGTGCAATGTTTCT 57.205 33.333 10.48 0.60 45.42 2.52
3148 11250 6.795098 TCTATGTAACGTGCAATGTTTCTT 57.205 33.333 10.48 7.00 45.42 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.372582 TCAAGATCACGCCTTGATGC 58.627 50.000 0.00 0.00 45.67 3.91
11 12 9.376075 GAATCTTTGAACACTAGATCAAGATCA 57.624 33.333 12.21 0.00 37.74 2.92
137 143 4.202567 ACACACCTAGGAATGGACACAAAT 60.203 41.667 17.98 0.00 0.00 2.32
199 205 2.456577 AGGGTTGACTGCTTTGTTGTT 58.543 42.857 0.00 0.00 0.00 2.83
211 217 1.276989 TCATCGGTGGTTAGGGTTGAC 59.723 52.381 0.00 0.00 0.00 3.18
286 1955 1.809619 CGCGCCATTCTTCGGAGAA 60.810 57.895 9.01 9.01 45.90 2.87
287 1956 2.202743 CGCGCCATTCTTCGGAGA 60.203 61.111 0.00 0.00 0.00 3.71
354 2023 5.302568 TGTTCAGGTTCGTAAAGAGAGGTTA 59.697 40.000 0.00 0.00 0.00 2.85
382 2052 5.728471 AGAATAATGCCTCCATCGAGTATG 58.272 41.667 0.00 0.00 33.93 2.39
652 4684 2.661866 GGCGTGCGTGAGTGAACT 60.662 61.111 0.00 0.00 0.00 3.01
784 4838 2.094597 GGAGATGAGCAGATGGATCGAG 60.095 54.545 0.00 0.00 33.60 4.04
1034 7830 3.005539 AGGCCGAGCACATGGACT 61.006 61.111 0.00 0.00 39.40 3.85
1093 7889 0.674581 CAGAAGGGCAGCGTCATCAA 60.675 55.000 0.00 0.00 0.00 2.57
1569 9106 0.317436 CGCAGCTTTTTGGCACGTTA 60.317 50.000 0.00 0.00 34.17 3.18
1626 9163 2.002586 CAATGTCCGTTGAAGATCGCT 58.997 47.619 0.00 0.00 0.00 4.93
1645 9182 2.281484 GGAGACAAACCTGCCGCA 60.281 61.111 0.00 0.00 0.00 5.69
1686 9223 2.031069 GGCAACGTCGCAGATAGAGATA 60.031 50.000 0.00 0.00 40.67 1.98
1711 9248 3.094062 ATGTCGCCGTGGGAGATGG 62.094 63.158 0.00 0.00 33.47 3.51
1791 9328 0.391130 GGTACAGCTCGCCATTCACA 60.391 55.000 0.00 0.00 0.00 3.58
1927 9464 3.612860 CCCTTCGTGAAATTAGTCGACAG 59.387 47.826 19.50 1.11 32.14 3.51
1984 9521 3.068873 ACGCAGTAGATGGAATTCTCCTC 59.931 47.826 5.23 0.32 41.94 3.71
2116 9656 3.839490 TGATTGGGTTGAATCCAGCAAAT 59.161 39.130 0.00 0.00 35.48 2.32
2158 9698 5.186198 AGCAACATGGAATAACCTCTACAC 58.814 41.667 0.00 0.00 39.86 2.90
2159 9699 5.045942 TGAGCAACATGGAATAACCTCTACA 60.046 40.000 0.00 0.00 39.86 2.74
2160 9700 5.428253 TGAGCAACATGGAATAACCTCTAC 58.572 41.667 0.00 0.00 39.86 2.59
2163 9703 5.591877 AGAATGAGCAACATGGAATAACCTC 59.408 40.000 0.00 0.00 39.39 3.85
2181 9721 3.713248 ACCCTGCATAGATCACAGAATGA 59.287 43.478 0.00 0.00 43.13 2.57
2182 9722 4.082665 ACCCTGCATAGATCACAGAATG 57.917 45.455 0.00 0.00 46.00 2.67
2184 9724 4.574674 AAACCCTGCATAGATCACAGAA 57.425 40.909 0.00 0.00 33.10 3.02
2185 9725 4.574674 AAAACCCTGCATAGATCACAGA 57.425 40.909 0.00 0.00 33.10 3.41
2187 9727 7.118723 AGAATAAAAACCCTGCATAGATCACA 58.881 34.615 0.00 0.00 0.00 3.58
2188 9728 7.573968 AGAATAAAAACCCTGCATAGATCAC 57.426 36.000 0.00 0.00 0.00 3.06
2191 9731 6.238759 GCGAAGAATAAAAACCCTGCATAGAT 60.239 38.462 0.00 0.00 0.00 1.98
2192 9732 5.065988 GCGAAGAATAAAAACCCTGCATAGA 59.934 40.000 0.00 0.00 0.00 1.98
2197 9740 3.850122 AGCGAAGAATAAAAACCCTGC 57.150 42.857 0.00 0.00 0.00 4.85
2206 9749 7.224297 AGCCCTTGATAAATAGCGAAGAATAA 58.776 34.615 0.00 0.00 0.00 1.40
2235 9874 5.330648 AAATAAGATGATGGCCTAGGCTT 57.669 39.130 32.18 20.41 41.60 4.35
2251 9890 4.965119 AGAGGCCGCAAGTAAAAATAAG 57.035 40.909 9.88 0.00 0.00 1.73
2253 9892 4.617298 GCAAAGAGGCCGCAAGTAAAAATA 60.617 41.667 9.88 0.00 0.00 1.40
2260 9899 0.674895 CTAGCAAAGAGGCCGCAAGT 60.675 55.000 9.88 0.00 0.00 3.16
2311 9973 7.233553 TGAAGATAGAATCAGTCGGGTGATTAT 59.766 37.037 11.65 11.33 45.32 1.28
2374 10038 2.264005 TGCTTCCGTTTGGTGTATGT 57.736 45.000 0.00 0.00 36.30 2.29
2375 10039 5.499139 AATATGCTTCCGTTTGGTGTATG 57.501 39.130 0.00 0.00 36.30 2.39
2376 10040 5.763204 CCTAATATGCTTCCGTTTGGTGTAT 59.237 40.000 0.00 0.00 36.30 2.29
2377 10041 5.120399 CCTAATATGCTTCCGTTTGGTGTA 58.880 41.667 0.00 0.00 36.30 2.90
2408 10072 1.598701 GAAGCCCCATCTGTTGCACC 61.599 60.000 0.00 0.00 0.00 5.01
2426 10090 3.036819 AGCTGCATGGATGTCTCTAAGA 58.963 45.455 1.02 0.00 0.00 2.10
2492 10156 7.064728 CCACACAAAATAGAGGACTAGCTAAAC 59.935 40.741 0.00 0.00 31.78 2.01
2525 10189 5.967088 AGAACGTCATCAGCTTACAGTAAT 58.033 37.500 0.00 0.00 0.00 1.89
2536 10200 2.070262 TGTGCTGAGAACGTCATCAG 57.930 50.000 20.20 20.20 44.70 2.90
2543 10207 2.866156 TCTTCTGTTTGTGCTGAGAACG 59.134 45.455 0.00 0.00 0.00 3.95
2589 10428 9.691362 ACGTCATCAGCTTGTTTTATTTTATTT 57.309 25.926 0.00 0.00 0.00 1.40
2592 10431 8.564574 AGAACGTCATCAGCTTGTTTTATTTTA 58.435 29.630 0.00 0.00 0.00 1.52
2598 10437 3.876914 TCAGAACGTCATCAGCTTGTTTT 59.123 39.130 0.00 0.00 0.00 2.43
2604 10443 4.756642 TCAAAAATCAGAACGTCATCAGCT 59.243 37.500 0.00 0.00 0.00 4.24
2605 10444 5.034554 TCAAAAATCAGAACGTCATCAGC 57.965 39.130 0.00 0.00 0.00 4.26
2606 10445 9.611284 TTTATTCAAAAATCAGAACGTCATCAG 57.389 29.630 0.00 0.00 0.00 2.90
2607 10446 9.958234 TTTTATTCAAAAATCAGAACGTCATCA 57.042 25.926 0.00 0.00 30.69 3.07
2637 10680 9.434275 TTCTTTTTCCCCTTTTATCTCTTCTTT 57.566 29.630 0.00 0.00 0.00 2.52
2639 10682 9.434275 TTTTCTTTTTCCCCTTTTATCTCTTCT 57.566 29.630 0.00 0.00 0.00 2.85
2682 10783 8.925700 GCCGATTTTTCATTTCTATTTTTCTGT 58.074 29.630 0.00 0.00 0.00 3.41
2683 10784 8.382875 GGCCGATTTTTCATTTCTATTTTTCTG 58.617 33.333 0.00 0.00 0.00 3.02
2685 10786 8.250538 TGGCCGATTTTTCATTTCTATTTTTC 57.749 30.769 0.00 0.00 0.00 2.29
2686 10787 8.614469 TTGGCCGATTTTTCATTTCTATTTTT 57.386 26.923 0.00 0.00 0.00 1.94
2691 10792 5.393027 GCTCTTGGCCGATTTTTCATTTCTA 60.393 40.000 0.00 0.00 34.27 2.10
2693 10794 3.614176 GCTCTTGGCCGATTTTTCATTTC 59.386 43.478 0.00 0.00 34.27 2.17
2694 10795 3.588955 GCTCTTGGCCGATTTTTCATTT 58.411 40.909 0.00 0.00 34.27 2.32
2695 10796 3.236632 GCTCTTGGCCGATTTTTCATT 57.763 42.857 0.00 0.00 34.27 2.57
2696 10797 2.947448 GCTCTTGGCCGATTTTTCAT 57.053 45.000 0.00 0.00 34.27 2.57
2733 10834 2.159179 AGGTGGTTCTTTGCCAGTTT 57.841 45.000 0.00 0.00 36.57 2.66
2744 10845 7.572539 CGGTTTTATGAACTTTCTAGGTGGTTC 60.573 40.741 12.38 12.38 38.64 3.62
2750 10851 5.493809 TCCCGGTTTTATGAACTTTCTAGG 58.506 41.667 0.00 0.00 0.00 3.02
2762 10863 3.625764 CGTTCATCACATCCCGGTTTTAT 59.374 43.478 0.00 0.00 0.00 1.40
2783 10884 4.447724 CCGGTCCATGTAAGATGTTATTCG 59.552 45.833 0.00 0.00 0.00 3.34
2838 10939 2.176889 GTCAGGTAGTAGCTGTTCCCA 58.823 52.381 24.70 6.45 43.70 4.37
2839 10940 1.134560 CGTCAGGTAGTAGCTGTTCCC 59.865 57.143 24.70 12.73 43.70 3.97
2846 10947 0.179134 CCACTGCGTCAGGTAGTAGC 60.179 60.000 10.80 0.00 39.81 3.58
2858 10959 1.821216 AACTTATTGGACCCACTGCG 58.179 50.000 0.00 0.00 0.00 5.18
2869 10971 5.056449 GTCGTTTCGCTCGAAAAACTTATTG 59.944 40.000 17.50 3.27 44.40 1.90
2874 10976 1.071698 CGTCGTTTCGCTCGAAAAACT 60.072 47.619 17.50 0.00 44.40 2.66
2890 10992 3.476646 CAGCAGCAGCAGACGTCG 61.477 66.667 10.46 6.47 45.49 5.12
2891 10993 2.356793 ACAGCAGCAGCAGACGTC 60.357 61.111 7.70 7.70 45.49 4.34
2892 10994 2.356793 GACAGCAGCAGCAGACGT 60.357 61.111 3.17 0.00 45.49 4.34
2893 10995 3.117171 GGACAGCAGCAGCAGACG 61.117 66.667 3.17 0.00 45.49 4.18
2894 10996 2.745492 GGGACAGCAGCAGCAGAC 60.745 66.667 3.17 0.00 45.49 3.51
2895 10997 4.025858 GGGGACAGCAGCAGCAGA 62.026 66.667 3.17 0.00 45.49 4.26
2910 11012 0.682852 TATCGTCGGCTATTTGGGGG 59.317 55.000 0.00 0.00 0.00 5.40
2911 11013 1.616865 TCTATCGTCGGCTATTTGGGG 59.383 52.381 0.00 0.00 0.00 4.96
2912 11014 2.609737 GGTCTATCGTCGGCTATTTGGG 60.610 54.545 0.00 0.00 0.00 4.12
2913 11015 2.296471 AGGTCTATCGTCGGCTATTTGG 59.704 50.000 0.00 0.00 0.00 3.28
2914 11016 3.644884 AGGTCTATCGTCGGCTATTTG 57.355 47.619 0.00 0.00 0.00 2.32
2915 11017 3.188048 CGTAGGTCTATCGTCGGCTATTT 59.812 47.826 0.00 0.00 0.00 1.40
2916 11018 2.740981 CGTAGGTCTATCGTCGGCTATT 59.259 50.000 0.00 0.00 0.00 1.73
2917 11019 2.028658 TCGTAGGTCTATCGTCGGCTAT 60.029 50.000 0.00 0.00 0.00 2.97
2918 11020 1.341209 TCGTAGGTCTATCGTCGGCTA 59.659 52.381 0.00 0.00 0.00 3.93
2919 11021 0.105593 TCGTAGGTCTATCGTCGGCT 59.894 55.000 0.00 0.00 0.00 5.52
2920 11022 1.155042 ATCGTAGGTCTATCGTCGGC 58.845 55.000 0.00 0.00 0.00 5.54
2921 11023 3.892918 AAATCGTAGGTCTATCGTCGG 57.107 47.619 0.00 0.00 0.00 4.79
2940 11042 5.301805 GTCAGGGAGACAAAATCCAGAAAAA 59.698 40.000 0.00 0.00 46.77 1.94
2941 11043 4.827284 GTCAGGGAGACAAAATCCAGAAAA 59.173 41.667 0.00 0.00 46.77 2.29
2942 11044 4.398319 GTCAGGGAGACAAAATCCAGAAA 58.602 43.478 0.00 0.00 46.77 2.52
2943 11045 4.021102 GTCAGGGAGACAAAATCCAGAA 57.979 45.455 0.00 0.00 46.77 3.02
2944 11046 3.703001 GTCAGGGAGACAAAATCCAGA 57.297 47.619 0.00 0.00 46.77 3.86
2955 11057 8.324191 AGTTATGATGATTTAAGTCAGGGAGA 57.676 34.615 6.81 0.00 0.00 3.71
2956 11058 8.970859 AAGTTATGATGATTTAAGTCAGGGAG 57.029 34.615 6.81 0.00 0.00 4.30
2975 11077 9.860898 GCACCTTCTGAATTGAAATTAAGTTAT 57.139 29.630 0.98 0.00 30.28 1.89
2976 11078 9.077885 AGCACCTTCTGAATTGAAATTAAGTTA 57.922 29.630 0.98 0.00 30.28 2.24
2977 11079 7.955918 AGCACCTTCTGAATTGAAATTAAGTT 58.044 30.769 0.98 0.00 30.28 2.66
2978 11080 7.530426 AGCACCTTCTGAATTGAAATTAAGT 57.470 32.000 0.98 0.00 30.28 2.24
2979 11081 9.912634 TTAAGCACCTTCTGAATTGAAATTAAG 57.087 29.630 3.93 0.00 0.00 1.85
2980 11082 9.691362 GTTAAGCACCTTCTGAATTGAAATTAA 57.309 29.630 3.93 3.57 0.00 1.40
2981 11083 8.855110 TGTTAAGCACCTTCTGAATTGAAATTA 58.145 29.630 3.93 0.00 0.00 1.40
2982 11084 7.653311 GTGTTAAGCACCTTCTGAATTGAAATT 59.347 33.333 3.93 0.00 42.10 1.82
2983 11085 7.147976 GTGTTAAGCACCTTCTGAATTGAAAT 58.852 34.615 3.93 0.00 42.10 2.17
2984 11086 6.503524 GTGTTAAGCACCTTCTGAATTGAAA 58.496 36.000 3.93 0.00 42.10 2.69
2985 11087 6.072112 GTGTTAAGCACCTTCTGAATTGAA 57.928 37.500 3.93 0.00 42.10 2.69
2986 11088 5.689383 GTGTTAAGCACCTTCTGAATTGA 57.311 39.130 3.93 0.00 42.10 2.57
3009 11111 4.402155 CAGGGCAATTACCACACATTATGT 59.598 41.667 0.00 0.00 44.81 2.29
3010 11112 4.402155 ACAGGGCAATTACCACACATTATG 59.598 41.667 0.00 0.00 0.00 1.90
3011 11113 4.609301 ACAGGGCAATTACCACACATTAT 58.391 39.130 0.00 0.00 0.00 1.28
3012 11114 4.040936 ACAGGGCAATTACCACACATTA 57.959 40.909 0.00 0.00 0.00 1.90
3013 11115 2.888212 ACAGGGCAATTACCACACATT 58.112 42.857 0.00 0.00 0.00 2.71
3014 11116 2.603075 ACAGGGCAATTACCACACAT 57.397 45.000 0.00 0.00 0.00 3.21
3015 11117 2.373335 AACAGGGCAATTACCACACA 57.627 45.000 0.00 0.00 0.00 3.72
3016 11118 3.418047 AGTAACAGGGCAATTACCACAC 58.582 45.455 0.00 0.00 32.67 3.82
3017 11119 3.681593 GAGTAACAGGGCAATTACCACA 58.318 45.455 0.00 0.00 32.67 4.17
3018 11120 2.676342 CGAGTAACAGGGCAATTACCAC 59.324 50.000 0.00 0.00 32.67 4.16
3019 11121 2.568062 TCGAGTAACAGGGCAATTACCA 59.432 45.455 0.00 0.00 32.67 3.25
3020 11122 2.934553 GTCGAGTAACAGGGCAATTACC 59.065 50.000 0.00 0.00 32.67 2.85
3021 11123 3.858247 AGTCGAGTAACAGGGCAATTAC 58.142 45.455 0.00 0.00 0.00 1.89
3022 11124 3.118884 GGAGTCGAGTAACAGGGCAATTA 60.119 47.826 0.00 0.00 0.00 1.40
3023 11125 2.354805 GGAGTCGAGTAACAGGGCAATT 60.355 50.000 0.00 0.00 0.00 2.32
3024 11126 1.207329 GGAGTCGAGTAACAGGGCAAT 59.793 52.381 0.00 0.00 0.00 3.56
3025 11127 0.606604 GGAGTCGAGTAACAGGGCAA 59.393 55.000 0.00 0.00 0.00 4.52
3026 11128 0.541063 TGGAGTCGAGTAACAGGGCA 60.541 55.000 0.00 0.00 0.00 5.36
3027 11129 0.824759 ATGGAGTCGAGTAACAGGGC 59.175 55.000 0.00 0.00 0.00 5.19
3028 11130 1.137086 CCATGGAGTCGAGTAACAGGG 59.863 57.143 5.56 12.04 0.00 4.45
3029 11131 1.825474 ACCATGGAGTCGAGTAACAGG 59.175 52.381 21.47 0.00 0.00 4.00
3030 11132 3.193691 AGAACCATGGAGTCGAGTAACAG 59.806 47.826 21.47 0.00 0.00 3.16
3031 11133 3.162666 AGAACCATGGAGTCGAGTAACA 58.837 45.455 21.47 0.00 0.00 2.41
3032 11134 3.870633 AGAACCATGGAGTCGAGTAAC 57.129 47.619 21.47 0.00 0.00 2.50
3033 11135 4.597004 ACTAGAACCATGGAGTCGAGTAA 58.403 43.478 23.83 7.57 0.00 2.24
3034 11136 4.232188 ACTAGAACCATGGAGTCGAGTA 57.768 45.455 23.83 9.39 0.00 2.59
3035 11137 3.088789 ACTAGAACCATGGAGTCGAGT 57.911 47.619 21.47 21.41 0.00 4.18
3036 11138 3.193691 ACAACTAGAACCATGGAGTCGAG 59.806 47.826 21.47 20.79 0.00 4.04
3037 11139 3.162666 ACAACTAGAACCATGGAGTCGA 58.837 45.455 21.47 10.51 0.00 4.20
3038 11140 3.594603 ACAACTAGAACCATGGAGTCG 57.405 47.619 21.47 2.89 0.00 4.18
3039 11141 3.927142 CGAACAACTAGAACCATGGAGTC 59.073 47.826 21.47 15.15 0.00 3.36
3040 11142 3.306780 CCGAACAACTAGAACCATGGAGT 60.307 47.826 21.47 8.56 0.00 3.85
3041 11143 3.262420 CCGAACAACTAGAACCATGGAG 58.738 50.000 21.47 7.80 0.00 3.86
3042 11144 2.027561 CCCGAACAACTAGAACCATGGA 60.028 50.000 21.47 0.00 0.00 3.41
3043 11145 2.027561 TCCCGAACAACTAGAACCATGG 60.028 50.000 11.19 11.19 0.00 3.66
3044 11146 3.328382 TCCCGAACAACTAGAACCATG 57.672 47.619 0.00 0.00 0.00 3.66
3045 11147 4.569719 ATTCCCGAACAACTAGAACCAT 57.430 40.909 0.00 0.00 0.00 3.55
3046 11148 4.360951 AATTCCCGAACAACTAGAACCA 57.639 40.909 0.00 0.00 0.00 3.67
3047 11149 5.009310 ACAAAATTCCCGAACAACTAGAACC 59.991 40.000 0.00 0.00 0.00 3.62
3048 11150 6.068473 ACAAAATTCCCGAACAACTAGAAC 57.932 37.500 0.00 0.00 0.00 3.01
3049 11151 7.989416 ATACAAAATTCCCGAACAACTAGAA 57.011 32.000 0.00 0.00 0.00 2.10
3050 11152 7.989416 AATACAAAATTCCCGAACAACTAGA 57.011 32.000 0.00 0.00 0.00 2.43
3051 11153 9.769093 CTAAATACAAAATTCCCGAACAACTAG 57.231 33.333 0.00 0.00 0.00 2.57
3052 11154 9.504708 TCTAAATACAAAATTCCCGAACAACTA 57.495 29.630 0.00 0.00 0.00 2.24
3053 11155 8.398878 TCTAAATACAAAATTCCCGAACAACT 57.601 30.769 0.00 0.00 0.00 3.16
3054 11156 9.124807 CTTCTAAATACAAAATTCCCGAACAAC 57.875 33.333 0.00 0.00 0.00 3.32
3055 11157 8.852135 ACTTCTAAATACAAAATTCCCGAACAA 58.148 29.630 0.00 0.00 0.00 2.83
3056 11158 8.398878 ACTTCTAAATACAAAATTCCCGAACA 57.601 30.769 0.00 0.00 0.00 3.18
3057 11159 9.338291 GAACTTCTAAATACAAAATTCCCGAAC 57.662 33.333 0.00 0.00 0.00 3.95
3058 11160 9.292195 AGAACTTCTAAATACAAAATTCCCGAA 57.708 29.630 0.00 0.00 0.00 4.30
3059 11161 8.857694 AGAACTTCTAAATACAAAATTCCCGA 57.142 30.769 0.00 0.00 0.00 5.14
3060 11162 8.726988 TGAGAACTTCTAAATACAAAATTCCCG 58.273 33.333 0.00 0.00 0.00 5.14
3075 11177 9.184523 TGTTTCAGGAAATTTTGAGAACTTCTA 57.815 29.630 0.00 0.00 32.36 2.10
3076 11178 8.066612 TGTTTCAGGAAATTTTGAGAACTTCT 57.933 30.769 0.00 0.00 32.36 2.85
3077 11179 8.702163 TTGTTTCAGGAAATTTTGAGAACTTC 57.298 30.769 0.00 0.00 32.36 3.01
3078 11180 9.671279 AATTGTTTCAGGAAATTTTGAGAACTT 57.329 25.926 0.00 0.00 32.36 2.66
3079 11181 9.317936 GAATTGTTTCAGGAAATTTTGAGAACT 57.682 29.630 0.00 0.00 32.36 3.01
3080 11182 9.317936 AGAATTGTTTCAGGAAATTTTGAGAAC 57.682 29.630 0.00 2.57 34.08 3.01
3082 11184 9.965824 GTAGAATTGTTTCAGGAAATTTTGAGA 57.034 29.630 0.00 0.00 34.08 3.27
3083 11185 9.748708 TGTAGAATTGTTTCAGGAAATTTTGAG 57.251 29.630 0.00 0.00 34.08 3.02
3087 11189 9.480053 CACATGTAGAATTGTTTCAGGAAATTT 57.520 29.630 0.00 0.00 34.08 1.82
3088 11190 8.641541 ACACATGTAGAATTGTTTCAGGAAATT 58.358 29.630 0.00 0.00 34.08 1.82
3089 11191 8.084073 CACACATGTAGAATTGTTTCAGGAAAT 58.916 33.333 0.00 0.00 34.08 2.17
3090 11192 7.424803 CACACATGTAGAATTGTTTCAGGAAA 58.575 34.615 0.00 0.00 34.08 3.13
3091 11193 6.514870 GCACACATGTAGAATTGTTTCAGGAA 60.515 38.462 0.00 0.00 34.08 3.36
3092 11194 5.048782 GCACACATGTAGAATTGTTTCAGGA 60.049 40.000 0.00 0.00 34.08 3.86
3093 11195 5.156355 GCACACATGTAGAATTGTTTCAGG 58.844 41.667 0.00 0.00 34.08 3.86
3094 11196 4.847757 CGCACACATGTAGAATTGTTTCAG 59.152 41.667 0.00 0.00 34.08 3.02
3095 11197 4.320129 CCGCACACATGTAGAATTGTTTCA 60.320 41.667 0.00 0.00 34.08 2.69
3096 11198 4.158384 CCGCACACATGTAGAATTGTTTC 58.842 43.478 0.00 0.00 0.00 2.78
3097 11199 3.057596 CCCGCACACATGTAGAATTGTTT 60.058 43.478 0.00 0.00 0.00 2.83
3098 11200 2.487762 CCCGCACACATGTAGAATTGTT 59.512 45.455 0.00 0.00 0.00 2.83
3099 11201 2.083774 CCCGCACACATGTAGAATTGT 58.916 47.619 0.00 0.00 0.00 2.71
3100 11202 2.083774 ACCCGCACACATGTAGAATTG 58.916 47.619 0.00 0.00 0.00 2.32
3101 11203 2.083774 CACCCGCACACATGTAGAATT 58.916 47.619 0.00 0.00 0.00 2.17
3102 11204 1.003118 ACACCCGCACACATGTAGAAT 59.997 47.619 0.00 0.00 0.00 2.40
3103 11205 0.394938 ACACCCGCACACATGTAGAA 59.605 50.000 0.00 0.00 0.00 2.10
3104 11206 1.258676 TACACCCGCACACATGTAGA 58.741 50.000 0.00 0.00 0.00 2.59
3105 11207 2.309528 ATACACCCGCACACATGTAG 57.690 50.000 0.00 0.00 31.41 2.74
3106 11208 2.235155 AGAATACACCCGCACACATGTA 59.765 45.455 0.00 0.00 32.38 2.29
3107 11209 1.003118 AGAATACACCCGCACACATGT 59.997 47.619 0.00 0.00 0.00 3.21
3108 11210 1.737838 AGAATACACCCGCACACATG 58.262 50.000 0.00 0.00 0.00 3.21
3109 11211 3.118408 ACATAGAATACACCCGCACACAT 60.118 43.478 0.00 0.00 0.00 3.21
3110 11212 2.235155 ACATAGAATACACCCGCACACA 59.765 45.455 0.00 0.00 0.00 3.72
3111 11213 2.901249 ACATAGAATACACCCGCACAC 58.099 47.619 0.00 0.00 0.00 3.82
3112 11214 4.435425 GTTACATAGAATACACCCGCACA 58.565 43.478 0.00 0.00 0.00 4.57
3113 11215 3.488310 CGTTACATAGAATACACCCGCAC 59.512 47.826 0.00 0.00 0.00 5.34
3114 11216 3.130869 ACGTTACATAGAATACACCCGCA 59.869 43.478 0.00 0.00 0.00 5.69
3115 11217 3.488310 CACGTTACATAGAATACACCCGC 59.512 47.826 0.00 0.00 0.00 6.13
3116 11218 3.488310 GCACGTTACATAGAATACACCCG 59.512 47.826 0.00 0.00 0.00 5.28
3117 11219 4.435425 TGCACGTTACATAGAATACACCC 58.565 43.478 0.00 0.00 0.00 4.61
3118 11220 6.036735 ACATTGCACGTTACATAGAATACACC 59.963 38.462 0.00 0.00 0.00 4.16
3119 11221 7.000575 ACATTGCACGTTACATAGAATACAC 57.999 36.000 0.00 0.00 0.00 2.90
3120 11222 7.603963 AACATTGCACGTTACATAGAATACA 57.396 32.000 0.00 0.00 0.00 2.29
3121 11223 8.388103 AGAAACATTGCACGTTACATAGAATAC 58.612 33.333 1.29 0.00 0.00 1.89
3122 11224 8.487313 AGAAACATTGCACGTTACATAGAATA 57.513 30.769 1.29 0.00 0.00 1.75
3123 11225 7.377766 AGAAACATTGCACGTTACATAGAAT 57.622 32.000 1.29 0.00 0.00 2.40
3124 11226 6.795098 AGAAACATTGCACGTTACATAGAA 57.205 33.333 1.29 0.00 0.00 2.10
3125 11227 6.795098 AAGAAACATTGCACGTTACATAGA 57.205 33.333 1.29 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.