Multiple sequence alignment - TraesCS6A01G123400

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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 TraesCS6A01G123400 chr6A 100.000 6481 0 0 1 6481 96990666 96984186 0.000000e+00 11969.0
1 TraesCS6A01G123400 chr6A 90.961 1051 69 12 2347 3392 20767291 20768320 0.000000e+00 1391.0
2 TraesCS6A01G123400 chr6A 90.961 1051 69 12 2347 3392 20800008 20801037 0.000000e+00 1391.0
3 TraesCS6A01G123400 chr6A 89.692 1038 94 5 3792 4829 20768829 20769853 0.000000e+00 1312.0
4 TraesCS6A01G123400 chr6A 89.595 1038 95 5 3792 4829 20801546 20802570 0.000000e+00 1306.0
5 TraesCS6A01G123400 chr6A 80.056 356 40 15 1641 1969 20799655 20800006 1.090000e-57 235.0
6 TraesCS6A01G123400 chr6A 79.944 354 42 15 1641 1969 20766940 20767289 3.910000e-57 233.0
7 TraesCS6A01G123400 chr6A 97.778 135 2 1 2068 2202 434530624 434530491 1.410000e-56 231.0
8 TraesCS6A01G123400 chr6A 87.578 161 11 3 3542 3700 20768652 20768805 1.860000e-40 178.0
9 TraesCS6A01G123400 chr6A 87.578 161 11 3 3542 3700 20801369 20801522 1.860000e-40 178.0
10 TraesCS6A01G123400 chr6A 77.068 266 41 16 5451 5715 96820792 96820546 1.130000e-27 135.0
11 TraesCS6A01G123400 chr6A 81.884 138 11 9 1287 1413 20766793 20766927 3.200000e-18 104.0
12 TraesCS6A01G123400 chr6D 94.338 4274 165 38 2196 6434 80524303 80520072 0.000000e+00 6481.0
13 TraesCS6A01G123400 chr6D 85.028 2164 161 67 9 2069 80526405 80524302 0.000000e+00 2050.0
14 TraesCS6A01G123400 chr6D 91.860 172 11 3 5865 6036 80513055 80512887 3.020000e-58 237.0
15 TraesCS6A01G123400 chr6D 93.878 49 2 1 6434 6481 80520032 80519984 9.010000e-09 73.1
16 TraesCS6A01G123400 chr6D 77.444 133 13 9 5714 5846 80520752 80520637 5.430000e-06 63.9
17 TraesCS6A01G123400 chr6B 95.639 2568 71 11 3702 6262 153958372 153955839 0.000000e+00 4084.0
18 TraesCS6A01G123400 chr6B 95.944 1652 54 7 2196 3842 153960195 153958552 0.000000e+00 2667.0
19 TraesCS6A01G123400 chr6B 84.792 2137 151 64 9 2021 153962466 153960380 0.000000e+00 1986.0
20 TraesCS6A01G123400 chr6B 86.776 1036 115 15 2232 3249 73892199 73893230 0.000000e+00 1134.0
21 TraesCS6A01G123400 chr6B 87.424 827 95 6 2232 3052 73732143 73732966 0.000000e+00 942.0
22 TraesCS6A01G123400 chr6B 87.304 827 96 6 2232 3052 73587975 73588798 0.000000e+00 937.0
23 TraesCS6A01G123400 chr6B 86.957 828 97 8 2232 3052 73656751 73657574 0.000000e+00 920.0
24 TraesCS6A01G123400 chr6B 86.699 827 97 8 2232 3052 73628198 73629017 0.000000e+00 905.0
25 TraesCS6A01G123400 chr6B 84.505 626 61 19 5837 6434 153685823 153685206 2.600000e-163 586.0
26 TraesCS6A01G123400 chr6B 84.295 624 62 20 5839 6434 153757425 153756810 1.570000e-160 577.0
27 TraesCS6A01G123400 chr6B 86.013 479 53 5 2775 3249 73738483 73738951 9.700000e-138 501.0
28 TraesCS6A01G123400 chr6B 86.564 454 46 6 2800 3249 73745518 73745960 2.720000e-133 486.0
29 TraesCS6A01G123400 chr6B 84.742 485 54 6 2775 3249 73596396 73596870 9.840000e-128 468.0
30 TraesCS6A01G123400 chr6B 81.019 432 48 17 6030 6434 153400980 153400556 4.880000e-81 313.0
31 TraesCS6A01G123400 chr6B 92.529 174 10 2 5865 6036 153676477 153676305 5.020000e-61 246.0
32 TraesCS6A01G123400 chr6B 91.954 174 11 2 5865 6036 153747789 153747617 2.340000e-59 241.0
33 TraesCS6A01G123400 chr6B 93.750 160 9 1 3672 3831 153958558 153958400 8.400000e-59 239.0
34 TraesCS6A01G123400 chr6B 98.450 129 2 0 2069 2197 706167392 706167520 1.820000e-55 228.0
35 TraesCS6A01G123400 chr6B 89.326 178 15 2 6260 6433 153955812 153955635 3.040000e-53 220.0
36 TraesCS6A01G123400 chr6B 94.000 50 3 0 2020 2069 153960243 153960194 6.970000e-10 76.8
37 TraesCS6A01G123400 chr6B 95.238 42 2 0 5805 5846 153685815 153685774 4.190000e-07 67.6
38 TraesCS6A01G123400 chr6B 90.909 44 2 2 5805 5846 153956240 153956197 2.520000e-04 58.4
39 TraesCS6A01G123400 chr7B 98.496 133 2 0 2068 2200 567591994 567591862 1.090000e-57 235.0
40 TraesCS6A01G123400 chr1A 97.794 136 3 0 2070 2205 170109750 170109615 1.090000e-57 235.0
41 TraesCS6A01G123400 chr4A 99.213 127 1 0 2071 2197 179174946 179174820 5.050000e-56 230.0
42 TraesCS6A01G123400 chr2B 97.727 132 3 0 2070 2201 11084201 11084332 1.820000e-55 228.0
43 TraesCS6A01G123400 chrUn 97.692 130 3 0 2071 2200 88590237 88590108 2.350000e-54 224.0
44 TraesCS6A01G123400 chr5B 97.692 130 3 0 2071 2200 621230362 621230233 2.350000e-54 224.0
45 TraesCS6A01G123400 chr2A 96.850 127 4 0 2071 2197 444077728 444077854 5.090000e-51 213.0


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 TraesCS6A01G123400 chr6A 96984186 96990666 6480 True 11969.000000 11969 100.000000 1 6481 1 chr6A.!!$R2 6480
1 TraesCS6A01G123400 chr6A 20799655 20802570 2915 False 777.500000 1391 87.047500 1641 4829 4 chr6A.!!$F2 3188
2 TraesCS6A01G123400 chr6A 20766793 20769853 3060 False 643.600000 1391 86.011800 1287 4829 5 chr6A.!!$F1 3542
3 TraesCS6A01G123400 chr6D 80519984 80526405 6421 True 2167.000000 6481 87.672000 9 6481 4 chr6D.!!$R2 6472
4 TraesCS6A01G123400 chr6B 153955635 153962466 6831 True 1333.028571 4084 92.051429 9 6433 7 chr6B.!!$R6 6424
5 TraesCS6A01G123400 chr6B 73892199 73893230 1031 False 1134.000000 1134 86.776000 2232 3249 1 chr6B.!!$F8 1017
6 TraesCS6A01G123400 chr6B 73732143 73732966 823 False 942.000000 942 87.424000 2232 3052 1 chr6B.!!$F5 820
7 TraesCS6A01G123400 chr6B 73587975 73588798 823 False 937.000000 937 87.304000 2232 3052 1 chr6B.!!$F1 820
8 TraesCS6A01G123400 chr6B 73656751 73657574 823 False 920.000000 920 86.957000 2232 3052 1 chr6B.!!$F4 820
9 TraesCS6A01G123400 chr6B 73628198 73629017 819 False 905.000000 905 86.699000 2232 3052 1 chr6B.!!$F3 820
10 TraesCS6A01G123400 chr6B 153756810 153757425 615 True 577.000000 577 84.295000 5839 6434 1 chr6B.!!$R4 595
11 TraesCS6A01G123400 chr6B 153685206 153685823 617 True 326.800000 586 89.871500 5805 6434 2 chr6B.!!$R5 629

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
949 1022 0.033504 GAGTCCACGTGAAGCCAAGA 59.966 55.000 19.3 0.0 0.00 3.02 F
2087 2407 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.0 0.0 0.00 4.30 F
2088 2408 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.0 0.0 0.00 3.34 F
3764 4702 0.529378 GCCCATTGCTCTGTTTCCTG 59.471 55.000 0.0 0.0 36.87 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2215 2535 1.275291 TGGCACTGACTACAAGGCTAC 59.725 52.381 0.00 0.00 0.00 3.58 R
3011 3343 1.199789 TGCGGATTGTTGACAGCAATC 59.800 47.619 27.64 27.64 46.76 2.67 R
4029 4967 1.484653 TCCACGACCCATACTTCCATG 59.515 52.381 0.00 0.00 0.00 3.66 R
5500 6438 1.537889 TCCCCGGAAAGAGAAGGCA 60.538 57.895 0.73 0.00 0.00 4.75 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
42 43 0.038251 TATTAGCCGCGGATCAGCAG 60.038 55.000 33.48 7.70 36.85 4.24
66 67 5.213891 ACAAGCCAACCCTGAAAAATAAG 57.786 39.130 0.00 0.00 0.00 1.73
101 103 2.128507 CCTAGGGAGTCTCGCACCC 61.129 68.421 18.26 3.00 46.86 4.61
112 114 0.462759 CTCGCACCCCAATCCTTCTC 60.463 60.000 0.00 0.00 0.00 2.87
114 116 1.299976 GCACCCCAATCCTTCTCGT 59.700 57.895 0.00 0.00 0.00 4.18
125 127 1.218047 CTTCTCGTTGGGCCGATGA 59.782 57.895 15.02 15.02 36.08 2.92
159 161 0.036010 CACTCTGGCAACCTTCCGAT 60.036 55.000 0.00 0.00 0.00 4.18
162 164 2.435938 TGGCAACCTTCCGATCGC 60.436 61.111 10.32 0.00 0.00 4.58
197 199 2.025898 TCTTGTACACTGACACGGTCA 58.974 47.619 0.00 6.57 40.50 4.02
208 210 0.243907 ACACGGTCAGGAAGTCATCG 59.756 55.000 0.00 0.00 0.00 3.84
209 211 0.458543 CACGGTCAGGAAGTCATCGG 60.459 60.000 0.00 0.00 0.00 4.18
210 212 0.898789 ACGGTCAGGAAGTCATCGGT 60.899 55.000 0.00 0.00 0.00 4.69
224 227 2.091541 CATCGGTGCCAAACAACCTAT 58.908 47.619 0.00 0.00 29.21 2.57
233 236 5.007332 GTGCCAAACAACCTATAGGATAACG 59.993 44.000 26.01 10.32 38.94 3.18
234 237 5.104859 TGCCAAACAACCTATAGGATAACGA 60.105 40.000 26.01 0.00 38.94 3.85
236 239 6.018180 GCCAAACAACCTATAGGATAACGAAG 60.018 42.308 26.01 8.40 38.94 3.79
237 240 7.046033 CCAAACAACCTATAGGATAACGAAGT 58.954 38.462 26.01 3.78 40.63 3.01
238 241 7.224167 CCAAACAACCTATAGGATAACGAAGTC 59.776 40.741 26.01 0.00 38.33 3.01
239 242 6.069684 ACAACCTATAGGATAACGAAGTCG 57.930 41.667 26.01 0.00 38.33 4.18
240 243 5.591877 ACAACCTATAGGATAACGAAGTCGT 59.408 40.000 26.01 0.00 46.62 4.34
266 272 4.840911 TCCGAAACTAACGATGACGATAG 58.159 43.478 0.00 0.00 45.68 2.08
322 333 8.771920 TCTTTCAAACATATGAACTCGTACAT 57.228 30.769 10.38 0.00 38.95 2.29
378 401 5.834169 TGTATGCAATGCAACTATCATTGG 58.166 37.500 13.45 1.23 43.62 3.16
458 488 9.833182 CTGACATATCATAGTATAGACACACAC 57.167 37.037 0.00 0.00 33.22 3.82
486 517 6.874134 AGGTTAGATGAGTAACACACAATGAC 59.126 38.462 0.00 0.00 35.00 3.06
487 518 6.874134 GGTTAGATGAGTAACACACAATGACT 59.126 38.462 0.00 0.00 35.00 3.41
490 521 9.586435 TTAGATGAGTAACACACAATGACTATG 57.414 33.333 0.00 0.00 0.00 2.23
495 526 5.762711 AGTAACACACAATGACTATGCACAA 59.237 36.000 0.00 0.00 0.00 3.33
525 556 1.962807 CCTTTTGTGCATGTGGAAGGA 59.037 47.619 10.12 0.00 36.59 3.36
526 557 2.364970 CCTTTTGTGCATGTGGAAGGAA 59.635 45.455 10.12 0.00 36.59 3.36
527 558 3.553508 CCTTTTGTGCATGTGGAAGGAAG 60.554 47.826 10.12 0.00 36.59 3.46
528 559 1.619654 TTGTGCATGTGGAAGGAAGG 58.380 50.000 0.00 0.00 0.00 3.46
543 574 7.393515 GTGGAAGGAAGGTTACACAATCTTATT 59.606 37.037 0.00 0.00 40.53 1.40
605 637 4.505808 TGTCTACGTCCAAAGTGTGAAAA 58.494 39.130 0.00 0.00 0.00 2.29
653 695 2.081462 CCTACCCAAAACCAGCTAACG 58.919 52.381 0.00 0.00 0.00 3.18
656 698 0.958822 CCCAAAACCAGCTAACGCTT 59.041 50.000 0.00 0.00 46.47 4.68
657 699 2.156098 CCCAAAACCAGCTAACGCTTA 58.844 47.619 0.00 0.00 46.47 3.09
658 700 2.554893 CCCAAAACCAGCTAACGCTTAA 59.445 45.455 0.00 0.00 46.47 1.85
659 701 3.561503 CCAAAACCAGCTAACGCTTAAC 58.438 45.455 0.00 0.00 46.47 2.01
661 703 4.219033 CAAAACCAGCTAACGCTTAACTG 58.781 43.478 0.00 0.00 46.47 3.16
662 704 1.439679 ACCAGCTAACGCTTAACTGC 58.560 50.000 0.00 0.00 46.47 4.40
663 705 1.002087 ACCAGCTAACGCTTAACTGCT 59.998 47.619 0.00 0.00 46.47 4.24
859 932 2.036387 GGGGGTAGAGAGAGAAAGAGC 58.964 57.143 0.00 0.00 0.00 4.09
889 962 2.370189 GAGGAGGAGAGAGAGAGAGAGG 59.630 59.091 0.00 0.00 0.00 3.69
891 964 1.421646 GAGGAGAGAGAGAGAGAGGGG 59.578 61.905 0.00 0.00 0.00 4.79
921 994 0.550914 GCAGAGGAGGAGAGAGGAGA 59.449 60.000 0.00 0.00 0.00 3.71
922 995 1.477558 GCAGAGGAGGAGAGAGGAGAG 60.478 61.905 0.00 0.00 0.00 3.20
923 996 1.143684 CAGAGGAGGAGAGAGGAGAGG 59.856 61.905 0.00 0.00 0.00 3.69
924 997 1.010793 AGAGGAGGAGAGAGGAGAGGA 59.989 57.143 0.00 0.00 0.00 3.71
925 998 1.421646 GAGGAGGAGAGAGGAGAGGAG 59.578 61.905 0.00 0.00 0.00 3.69
942 1015 1.816863 GAGGGCTGAGTCCACGTGAA 61.817 60.000 19.30 0.00 0.00 3.18
943 1016 1.374758 GGGCTGAGTCCACGTGAAG 60.375 63.158 19.30 7.40 0.00 3.02
947 1020 0.249868 CTGAGTCCACGTGAAGCCAA 60.250 55.000 19.30 0.00 0.00 4.52
948 1021 0.249868 TGAGTCCACGTGAAGCCAAG 60.250 55.000 19.30 0.00 0.00 3.61
949 1022 0.033504 GAGTCCACGTGAAGCCAAGA 59.966 55.000 19.30 0.00 0.00 3.02
951 1024 0.951040 GTCCACGTGAAGCCAAGAGG 60.951 60.000 19.30 0.00 34.82 3.69
1048 1129 3.151022 GCCGTCTCCCTCTCCCTG 61.151 72.222 0.00 0.00 0.00 4.45
1049 1130 2.360980 CCGTCTCCCTCTCCCTGT 59.639 66.667 0.00 0.00 0.00 4.00
1050 1131 1.755008 CCGTCTCCCTCTCCCTGTC 60.755 68.421 0.00 0.00 0.00 3.51
1052 1133 1.755008 GTCTCCCTCTCCCTGTCCG 60.755 68.421 0.00 0.00 0.00 4.79
1135 1228 2.024871 CTCGATCTGTCCGTCCGC 59.975 66.667 0.00 0.00 0.00 5.54
1281 1413 4.842091 CGTCCCGTCGGTTAGCGG 62.842 72.222 11.06 0.00 46.80 5.52
1311 1443 1.129326 CGGTGAATTCGATCGGTAGC 58.871 55.000 16.41 6.24 0.00 3.58
1504 1659 3.322466 CCGGGAACAGTGGCTCCT 61.322 66.667 11.99 0.00 31.88 3.69
1524 1679 1.228533 TGGCTTTACGTCGTTTTCCC 58.771 50.000 1.78 0.48 0.00 3.97
1634 1789 1.003839 CTGTGTTGAGCGGGGCTTA 60.004 57.895 0.00 0.00 39.88 3.09
1673 1828 4.082463 GGATGGTTTTATCTGTTTTGCGGA 60.082 41.667 0.00 0.00 36.82 5.54
1700 1860 2.436115 GACGGCAGGGGTTAGCAC 60.436 66.667 0.00 0.00 0.00 4.40
1715 1875 6.238293 GGGGTTAGCACGATTAAATCTGTTAC 60.238 42.308 0.00 0.00 0.00 2.50
1716 1876 6.537660 GGGTTAGCACGATTAAATCTGTTACT 59.462 38.462 0.00 0.00 0.00 2.24
1718 1878 8.753175 GGTTAGCACGATTAAATCTGTTACTAG 58.247 37.037 0.00 0.00 0.00 2.57
1719 1879 8.753175 GTTAGCACGATTAAATCTGTTACTAGG 58.247 37.037 0.00 0.00 0.00 3.02
1720 1880 7.108841 AGCACGATTAAATCTGTTACTAGGA 57.891 36.000 0.00 0.00 0.00 2.94
1721 1881 7.727181 AGCACGATTAAATCTGTTACTAGGAT 58.273 34.615 0.00 0.00 0.00 3.24
1722 1882 7.868415 AGCACGATTAAATCTGTTACTAGGATC 59.132 37.037 0.00 0.00 0.00 3.36
1727 1887 8.798975 ATTAAATCTGTTACTAGGATCCAGGA 57.201 34.615 15.82 3.09 0.00 3.86
1728 1888 6.739331 AAATCTGTTACTAGGATCCAGGAG 57.261 41.667 15.82 10.51 0.00 3.69
1729 1889 4.883021 TCTGTTACTAGGATCCAGGAGT 57.117 45.455 15.82 15.79 0.00 3.85
1730 1890 4.794334 TCTGTTACTAGGATCCAGGAGTC 58.206 47.826 15.82 4.19 0.00 3.36
1731 1891 3.552875 TGTTACTAGGATCCAGGAGTCG 58.447 50.000 15.82 0.00 0.00 4.18
1732 1892 3.053842 TGTTACTAGGATCCAGGAGTCGT 60.054 47.826 15.82 0.00 0.00 4.34
1734 1894 1.285373 ACTAGGATCCAGGAGTCGTGT 59.715 52.381 15.82 0.00 0.00 4.49
1793 1965 2.159517 GCGCAAGTAGATGGTTTCCTTG 60.160 50.000 0.30 0.00 41.68 3.61
1861 2041 3.701205 TGTACAATGCACATGTCTCCT 57.299 42.857 10.04 0.00 32.27 3.69
2022 2340 7.550551 TGCAAGATCTTCCTGAAAGTTACTATG 59.449 37.037 4.57 0.00 36.31 2.23
2074 2394 8.920509 GAAGATCTTCCTGAAAGTTACTACTC 57.079 38.462 22.68 0.00 36.31 2.59
2075 2395 7.412853 AGATCTTCCTGAAAGTTACTACTCC 57.587 40.000 0.00 0.00 36.31 3.85
2076 2396 5.997384 TCTTCCTGAAAGTTACTACTCCC 57.003 43.478 0.00 0.00 36.31 4.30
2077 2397 5.652324 TCTTCCTGAAAGTTACTACTCCCT 58.348 41.667 0.00 0.00 36.31 4.20
2078 2398 5.715753 TCTTCCTGAAAGTTACTACTCCCTC 59.284 44.000 0.00 0.00 36.31 4.30
2079 2399 4.351127 TCCTGAAAGTTACTACTCCCTCC 58.649 47.826 0.00 0.00 31.99 4.30
2080 2400 3.130693 CCTGAAAGTTACTACTCCCTCCG 59.869 52.174 0.00 0.00 31.99 4.63
2081 2401 3.762823 CTGAAAGTTACTACTCCCTCCGT 59.237 47.826 0.00 0.00 31.99 4.69
2082 2402 4.154942 TGAAAGTTACTACTCCCTCCGTT 58.845 43.478 0.00 0.00 31.99 4.44
2083 2403 4.219288 TGAAAGTTACTACTCCCTCCGTTC 59.781 45.833 0.00 0.00 31.99 3.95
2084 2404 2.732763 AGTTACTACTCCCTCCGTTCC 58.267 52.381 0.00 0.00 0.00 3.62
2085 2405 1.403323 GTTACTACTCCCTCCGTTCCG 59.597 57.143 0.00 0.00 0.00 4.30
2086 2406 0.911769 TACTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
2087 2407 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
2088 2408 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
2089 2409 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
2090 2410 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2091 2411 1.755380 ACTCCCTCCGTTCCGAATTAG 59.245 52.381 0.00 0.00 0.00 1.73
2092 2412 1.755380 CTCCCTCCGTTCCGAATTAGT 59.245 52.381 0.00 0.00 0.00 2.24
2093 2413 2.167900 CTCCCTCCGTTCCGAATTAGTT 59.832 50.000 0.00 0.00 0.00 2.24
2094 2414 2.093869 TCCCTCCGTTCCGAATTAGTTG 60.094 50.000 0.00 0.00 0.00 3.16
2095 2415 2.354403 CCCTCCGTTCCGAATTAGTTGT 60.354 50.000 0.00 0.00 0.00 3.32
2096 2416 2.928116 CCTCCGTTCCGAATTAGTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2097 2417 3.368116 CCTCCGTTCCGAATTAGTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2098 2418 4.243270 CTCCGTTCCGAATTAGTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2099 2419 5.389859 TCCGTTCCGAATTAGTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
2100 2420 5.404946 TCCGTTCCGAATTAGTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
2101 2421 5.183713 TCCGTTCCGAATTAGTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
2102 2422 6.040878 CCGTTCCGAATTAGTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
2103 2423 6.534079 CCGTTCCGAATTAGTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
2104 2424 7.064253 CCGTTCCGAATTAGTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
2105 2425 7.898309 CGTTCCGAATTAGTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
2106 2426 8.718734 GTTCCGAATTAGTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
2107 2427 8.475331 TCCGAATTAGTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
2108 2428 8.311836 TCCGAATTAGTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
2109 2429 9.582431 CCGAATTAGTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
2116 2436 8.407064 AGTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
2117 2437 8.404000 GTTGTCTTAGATTTGTCTAGATACGGA 58.596 37.037 0.00 0.00 0.00 4.69
2118 2438 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2119 2439 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2120 2440 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2121 2441 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2136 2456 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.00 36.56 2.32
2137 2457 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
2138 2458 7.148641 ACGGATGTATCTAGCACTAAAATGAG 58.851 38.462 0.00 0.00 0.00 2.90
2139 2459 7.148641 CGGATGTATCTAGCACTAAAATGAGT 58.851 38.462 0.00 0.00 0.00 3.41
2140 2460 7.327275 CGGATGTATCTAGCACTAAAATGAGTC 59.673 40.741 0.00 0.00 0.00 3.36
2141 2461 8.364142 GGATGTATCTAGCACTAAAATGAGTCT 58.636 37.037 0.00 0.00 0.00 3.24
2144 2464 9.185680 TGTATCTAGCACTAAAATGAGTCTACA 57.814 33.333 0.00 0.00 0.00 2.74
2148 2468 9.185680 TCTAGCACTAAAATGAGTCTACATACA 57.814 33.333 0.00 0.00 0.00 2.29
2149 2469 9.973450 CTAGCACTAAAATGAGTCTACATACAT 57.027 33.333 0.00 0.00 0.00 2.29
2150 2470 8.879342 AGCACTAAAATGAGTCTACATACATC 57.121 34.615 0.00 0.00 0.00 3.06
2151 2471 7.928706 AGCACTAAAATGAGTCTACATACATCC 59.071 37.037 0.00 0.00 0.00 3.51
2152 2472 7.096023 GCACTAAAATGAGTCTACATACATCCG 60.096 40.741 0.00 0.00 0.00 4.18
2153 2473 7.921214 CACTAAAATGAGTCTACATACATCCGT 59.079 37.037 0.00 0.00 0.00 4.69
2154 2474 9.128404 ACTAAAATGAGTCTACATACATCCGTA 57.872 33.333 0.00 0.00 0.00 4.02
2157 2477 8.410673 AAATGAGTCTACATACATCCGTATCT 57.589 34.615 0.00 0.00 36.11 1.98
2158 2478 9.516546 AAATGAGTCTACATACATCCGTATCTA 57.483 33.333 0.00 0.00 36.11 1.98
2159 2479 8.725405 ATGAGTCTACATACATCCGTATCTAG 57.275 38.462 0.00 0.00 36.11 2.43
2160 2480 7.904205 TGAGTCTACATACATCCGTATCTAGA 58.096 38.462 0.00 0.00 36.11 2.43
2161 2481 7.818446 TGAGTCTACATACATCCGTATCTAGAC 59.182 40.741 14.92 14.92 46.51 2.59
2162 2482 7.902387 GTCTACATACATCCGTATCTAGACA 57.098 40.000 16.59 0.00 46.00 3.41
2163 2483 8.320396 GTCTACATACATCCGTATCTAGACAA 57.680 38.462 16.59 0.00 46.00 3.18
2164 2484 8.781196 GTCTACATACATCCGTATCTAGACAAA 58.219 37.037 16.59 0.00 46.00 2.83
2165 2485 9.516546 TCTACATACATCCGTATCTAGACAAAT 57.483 33.333 0.00 0.00 36.11 2.32
2166 2486 9.776158 CTACATACATCCGTATCTAGACAAATC 57.224 37.037 0.00 0.00 36.11 2.17
2167 2487 7.603651 ACATACATCCGTATCTAGACAAATCC 58.396 38.462 0.00 0.00 36.11 3.01
2168 2488 7.232737 ACATACATCCGTATCTAGACAAATCCA 59.767 37.037 0.00 0.00 36.11 3.41
2169 2489 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
2170 2490 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
2171 2491 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
2172 2492 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
2173 2493 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
2174 2494 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
2175 2495 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
2176 2496 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
2177 2497 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
2178 2498 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2180 2500 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2181 2501 9.793259 TCTAGACAAATCCAAGACAAGTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
2184 2504 9.793259 AGACAAATCCAAGACAAGTAATTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
2187 2507 9.329913 CAAATCCAAGACAAGTAATTTAGAACG 57.670 33.333 0.00 0.00 0.00 3.95
2188 2508 7.611213 ATCCAAGACAAGTAATTTAGAACGG 57.389 36.000 0.00 0.00 0.00 4.44
2189 2509 6.761312 TCCAAGACAAGTAATTTAGAACGGA 58.239 36.000 0.00 0.00 0.00 4.69
2190 2510 6.872020 TCCAAGACAAGTAATTTAGAACGGAG 59.128 38.462 0.00 0.00 0.00 4.63
2191 2511 6.092259 CCAAGACAAGTAATTTAGAACGGAGG 59.908 42.308 0.00 0.00 0.00 4.30
2192 2512 5.731591 AGACAAGTAATTTAGAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
2193 2513 5.482878 AGACAAGTAATTTAGAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2194 2514 5.731591 ACAAGTAATTTAGAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2195 2515 5.247792 ACAAGTAATTTAGAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2196 2516 6.438425 ACAAGTAATTTAGAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2197 2517 7.125356 ACAAGTAATTTAGAACGGAGGGAGTAT 59.875 37.037 0.00 0.00 0.00 2.12
2198 2518 8.636213 CAAGTAATTTAGAACGGAGGGAGTATA 58.364 37.037 0.00 0.00 0.00 1.47
2205 2525 6.667558 AGAACGGAGGGAGTATATTTTAGG 57.332 41.667 0.00 0.00 0.00 2.69
2215 2535 9.322769 AGGGAGTATATTTTAGGGTATGTAGTG 57.677 37.037 0.00 0.00 0.00 2.74
2220 2540 9.866798 GTATATTTTAGGGTATGTAGTGTAGCC 57.133 37.037 0.00 0.00 39.44 3.93
2398 2719 4.351192 GCAACTGGCAATCTAAATTACCG 58.649 43.478 0.00 0.00 43.97 4.02
2819 3148 6.705302 TGTAGAGATTCTTTGTGCTGATCTT 58.295 36.000 0.00 0.00 0.00 2.40
3011 3343 0.740868 ACAATCCATCACGACTGCCG 60.741 55.000 0.00 0.00 45.44 5.69
3228 3565 0.737367 GCAAAAGGATTCTTGCGGGC 60.737 55.000 0.00 0.00 38.66 6.13
3451 3788 2.745968 ACTTTGCTTGTTTTCCTGGGA 58.254 42.857 0.00 0.00 0.00 4.37
3471 3808 3.549794 GATTCCAGGCTTACTGCTTCAT 58.450 45.455 0.00 0.00 46.14 2.57
3501 3840 5.778862 AGTTGTTTATTACGGCATTGCTTT 58.221 33.333 8.82 0.00 0.00 3.51
3508 3847 1.512734 CGGCATTGCTTTCGCTGAC 60.513 57.895 8.82 0.00 36.97 3.51
3704 4321 7.454380 TCATCAAATTTACCAGTCCATTTTCCT 59.546 33.333 0.00 0.00 0.00 3.36
3709 4647 8.664669 AATTTACCAGTCCATTTTCCTTACAT 57.335 30.769 0.00 0.00 0.00 2.29
3764 4702 0.529378 GCCCATTGCTCTGTTTCCTG 59.471 55.000 0.00 0.00 36.87 3.86
3767 4705 3.420893 CCCATTGCTCTGTTTCCTGTTA 58.579 45.455 0.00 0.00 0.00 2.41
3818 4756 8.253113 TCCGTCCTTTTAGTAAATTATCTCGTT 58.747 33.333 0.00 0.00 0.00 3.85
3950 4888 3.133183 GTCATAAGGTCCTCTTCTCCACC 59.867 52.174 0.00 0.00 36.93 4.61
3985 4923 5.863397 CGGTCTTGCATAAATTTGTTGACAT 59.137 36.000 0.00 0.00 0.00 3.06
4029 4967 1.523938 GTTGGATCTGTAGCCGGGC 60.524 63.158 12.11 12.11 32.07 6.13
4036 4974 1.524621 CTGTAGCCGGGCATGGAAG 60.525 63.158 23.09 7.27 0.00 3.46
4061 4999 1.604693 GGTCGTGGAATTGTCAGTCGT 60.605 52.381 0.00 0.00 0.00 4.34
4100 5038 4.889832 AGTTCAGAAACTTTGTGCTGAG 57.110 40.909 0.00 0.00 43.28 3.35
4116 5054 2.481854 CTGAGGCACTAGATGTCATGC 58.518 52.381 0.00 0.00 41.55 4.06
4202 5140 9.650539 CCTTCACATTAGATCTAACATATGGAG 57.349 37.037 17.35 15.02 0.00 3.86
4286 5224 9.740710 AGCTTCATAAAGTTTGAACCTATAACT 57.259 29.630 0.00 0.00 34.79 2.24
4769 5707 3.708403 TCAGACAAAGTGCCTCATCAT 57.292 42.857 0.00 0.00 0.00 2.45
5270 6208 0.762461 GGCTGGAGACTGAGGGCTAT 60.762 60.000 0.00 0.00 0.00 2.97
5500 6438 2.049063 GCGACGGAAGCTGTCACT 60.049 61.111 7.13 0.00 39.51 3.41
5511 6449 1.419387 AGCTGTCACTGCCTTCTCTTT 59.581 47.619 2.51 0.00 0.00 2.52
5532 6471 4.660938 GGGAGGGTGCGTGCCTTT 62.661 66.667 0.00 0.00 0.00 3.11
5647 6586 0.034337 TGTAACCTTGTCTGTCCGCC 59.966 55.000 0.00 0.00 0.00 6.13
5688 6627 4.929479 TGTTACCTGGCACCTTATTTCAT 58.071 39.130 0.00 0.00 0.00 2.57
5689 6628 4.947388 TGTTACCTGGCACCTTATTTCATC 59.053 41.667 0.00 0.00 0.00 2.92
5807 6748 0.543749 ACCTTGGTAGCATGAGGAGC 59.456 55.000 17.56 0.00 33.47 4.70
5810 6755 0.107508 TTGGTAGCATGAGGAGCTGC 60.108 55.000 0.00 0.00 43.33 5.25
5811 6756 1.593750 GGTAGCATGAGGAGCTGCG 60.594 63.158 0.00 0.00 44.29 5.18
5812 6757 2.107750 TAGCATGAGGAGCTGCGC 59.892 61.111 0.00 0.00 43.33 6.09
5813 6758 3.780064 TAGCATGAGGAGCTGCGCG 62.780 63.158 0.00 0.00 43.33 6.86
5874 6820 0.673437 AGTCGTCGGTCGGGTTAAAA 59.327 50.000 0.00 0.00 40.32 1.52
5956 6902 4.457257 GCTGAATCTGGCTGAGTTTTTACT 59.543 41.667 0.00 0.00 0.00 2.24
5998 6962 3.954200 TGAGTTTGCAGCTCCATTGATA 58.046 40.909 14.98 0.00 32.31 2.15
6012 6976 3.552273 CCATTGATATGCAGAGCTTTGCC 60.552 47.826 24.94 11.01 43.43 4.52
6150 7124 2.401766 GGCCATGACCAGCAGTTCG 61.402 63.158 0.00 0.00 0.00 3.95
6190 7179 2.408835 GATGGAACCATTGCCGCG 59.591 61.111 7.79 0.00 36.70 6.46
6206 7195 3.329231 CGCACTCAACGCCAAAGA 58.671 55.556 0.00 0.00 0.00 2.52
6221 7210 4.270245 CCAAAGAATGGCAGCCTAAAAA 57.730 40.909 14.15 0.00 43.80 1.94
6234 7223 5.338137 GCAGCCTAAAAACCCTAGACTCTTA 60.338 44.000 0.00 0.00 0.00 2.10
6237 7228 5.046087 GCCTAAAAACCCTAGACTCTTACCA 60.046 44.000 0.00 0.00 0.00 3.25
6242 7233 6.361768 AAACCCTAGACTCTTACCAAGAAG 57.638 41.667 0.00 0.00 37.02 2.85
6293 7314 6.304208 GCGAAAACATTCTTTCTCAAGATCAC 59.696 38.462 0.00 0.00 38.89 3.06
6297 7318 4.629200 ACATTCTTTCTCAAGATCACGAGC 59.371 41.667 6.54 0.00 38.89 5.03
6347 7368 3.135225 CAACCAGTCCAACACGTTCATA 58.865 45.455 0.00 0.00 0.00 2.15
6352 7373 4.330074 CCAGTCCAACACGTTCATATTCTC 59.670 45.833 0.00 0.00 0.00 2.87
6379 7400 1.478510 TCCATCTCGAAGTCCAAGAGC 59.521 52.381 0.00 0.00 32.42 4.09
6382 7403 3.529533 CATCTCGAAGTCCAAGAGCATT 58.470 45.455 0.00 0.00 32.42 3.56
6383 7404 3.685139 TCTCGAAGTCCAAGAGCATTT 57.315 42.857 0.00 0.00 32.42 2.32
6408 7433 4.471025 TGCATGAAGAAGAGGTAGGATTGA 59.529 41.667 0.00 0.00 0.00 2.57
6414 7439 2.674796 AGAGGTAGGATTGACGCAAC 57.325 50.000 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.687242 CGGCTAATAGATCTGAGTATATTTGGA 58.313 37.037 5.18 0.00 0.00 3.53
6 7 7.436673 GCGGCTAATAGATCTGAGTATATTTGG 59.563 40.741 5.18 0.00 0.00 3.28
7 8 7.166638 CGCGGCTAATAGATCTGAGTATATTTG 59.833 40.741 5.18 0.00 0.00 2.32
14 15 1.542030 CCGCGGCTAATAGATCTGAGT 59.458 52.381 14.67 0.00 0.00 3.41
42 43 4.600692 ATTTTTCAGGGTTGGCTTGTAC 57.399 40.909 0.00 0.00 0.00 2.90
66 67 6.509386 TCCCTAGGGACCTGTTATAATATCC 58.491 44.000 27.73 0.00 39.76 2.59
101 103 1.032114 GGCCCAACGAGAAGGATTGG 61.032 60.000 0.00 0.00 42.21 3.16
128 130 4.430765 AGAGTGGTTACGGCGGCG 62.431 66.667 31.06 31.06 0.00 6.46
136 138 1.073284 GGAAGGTTGCCAGAGTGGTTA 59.927 52.381 0.00 0.00 40.46 2.85
177 179 2.025898 TGACCGTGTCAGTGTACAAGA 58.974 47.619 0.00 0.00 37.67 3.02
197 199 0.400213 TTTGGCACCGATGACTTCCT 59.600 50.000 0.00 0.00 33.48 3.36
199 201 1.234821 TGTTTGGCACCGATGACTTC 58.765 50.000 0.00 0.00 33.48 3.01
208 210 3.359695 TCCTATAGGTTGTTTGGCACC 57.640 47.619 18.51 0.00 36.34 5.01
209 211 5.007332 CGTTATCCTATAGGTTGTTTGGCAC 59.993 44.000 18.51 3.62 36.34 5.01
210 212 5.104859 TCGTTATCCTATAGGTTGTTTGGCA 60.105 40.000 18.51 0.00 36.34 4.92
233 236 5.569059 TCGTTAGTTTCGGATAAACGACTTC 59.431 40.000 4.66 0.00 44.76 3.01
234 237 5.460646 TCGTTAGTTTCGGATAAACGACTT 58.539 37.500 4.66 0.00 44.76 3.01
238 241 5.551370 CGTCATCGTTAGTTTCGGATAAACG 60.551 44.000 0.00 0.00 43.07 3.60
239 242 5.512788 TCGTCATCGTTAGTTTCGGATAAAC 59.487 40.000 0.00 0.00 38.33 2.01
240 243 5.639757 TCGTCATCGTTAGTTTCGGATAAA 58.360 37.500 0.00 0.00 38.33 1.40
241 244 5.233957 TCGTCATCGTTAGTTTCGGATAA 57.766 39.130 0.00 0.00 38.33 1.75
242 245 4.880886 TCGTCATCGTTAGTTTCGGATA 57.119 40.909 0.00 0.00 38.33 2.59
359 370 2.496470 TGCCAATGATAGTTGCATTGCA 59.504 40.909 7.38 7.38 46.94 4.08
436 466 8.040716 TCGGTGTGTGTCTATACTATGATATG 57.959 38.462 0.00 0.00 0.00 1.78
437 467 7.337184 CCTCGGTGTGTGTCTATACTATGATAT 59.663 40.741 0.00 0.00 0.00 1.63
455 485 4.082354 GTGTTACTCATCTAACCTCGGTGT 60.082 45.833 0.00 0.00 0.00 4.16
458 488 4.082408 TGTGTGTTACTCATCTAACCTCGG 60.082 45.833 0.00 0.00 0.00 4.63
486 517 3.741249 AGGCATGAGAGATTGTGCATAG 58.259 45.455 0.00 0.00 39.27 2.23
487 518 3.851458 AGGCATGAGAGATTGTGCATA 57.149 42.857 0.00 0.00 39.27 3.14
490 521 3.057033 ACAAAAGGCATGAGAGATTGTGC 60.057 43.478 0.00 0.00 36.88 4.57
495 526 2.799017 TGCACAAAAGGCATGAGAGAT 58.201 42.857 0.00 0.00 36.11 2.75
526 557 9.528489 ACACCAAATAATAAGATTGTGTAACCT 57.472 29.630 0.00 0.00 34.36 3.50
527 558 9.567848 CACACCAAATAATAAGATTGTGTAACC 57.432 33.333 0.00 0.00 34.36 2.85
543 574 7.373617 TCTATGGCTATTCTCACACCAAATA 57.626 36.000 0.00 0.00 33.30 1.40
548 579 4.453819 GCAATCTATGGCTATTCTCACACC 59.546 45.833 0.00 0.00 0.00 4.16
561 592 5.776716 ACATGGAAAATAGGGCAATCTATGG 59.223 40.000 0.00 0.00 34.47 2.74
605 637 3.582120 CAACCGCGGCTTGTGTGT 61.582 61.111 28.58 0.00 0.00 3.72
625 667 1.075861 GGTTTTGGGTAGGCAGGGTTA 59.924 52.381 0.00 0.00 0.00 2.85
653 695 1.194772 GTCAACACGGAGCAGTTAAGC 59.805 52.381 0.00 0.00 0.00 3.09
655 697 1.541670 GGGTCAACACGGAGCAGTTAA 60.542 52.381 0.00 0.00 37.03 2.01
656 698 0.034337 GGGTCAACACGGAGCAGTTA 59.966 55.000 0.00 0.00 37.03 2.24
657 699 1.227853 GGGTCAACACGGAGCAGTT 60.228 57.895 0.00 0.00 37.03 3.16
658 700 2.426023 GGGTCAACACGGAGCAGT 59.574 61.111 0.00 0.00 37.03 4.40
659 701 2.358737 GGGGTCAACACGGAGCAG 60.359 66.667 0.00 0.00 37.03 4.24
859 932 1.436195 CTCTCCTCCTCTGCGTCTCG 61.436 65.000 0.00 0.00 0.00 4.04
889 962 2.365635 TCTGCTGCTACCCTCCCC 60.366 66.667 0.00 0.00 0.00 4.81
891 964 1.381872 TCCTCTGCTGCTACCCTCC 60.382 63.158 0.00 0.00 0.00 4.30
921 994 2.681778 CGTGGACTCAGCCCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
922 995 2.997897 ACGTGGACTCAGCCCTCC 60.998 66.667 0.00 0.00 0.00 4.30
923 996 1.816863 TTCACGTGGACTCAGCCCTC 61.817 60.000 17.00 0.00 0.00 4.30
924 997 1.821061 CTTCACGTGGACTCAGCCCT 61.821 60.000 17.00 0.00 0.00 5.19
925 998 1.374758 CTTCACGTGGACTCAGCCC 60.375 63.158 17.00 0.00 0.00 5.19
947 1020 3.024356 TCCTCCTCCTCCGCCTCT 61.024 66.667 0.00 0.00 0.00 3.69
948 1021 2.520741 CTCCTCCTCCTCCGCCTC 60.521 72.222 0.00 0.00 0.00 4.70
949 1022 4.851214 GCTCCTCCTCCTCCGCCT 62.851 72.222 0.00 0.00 0.00 5.52
952 1025 2.904866 CTCGCTCCTCCTCCTCCG 60.905 72.222 0.00 0.00 0.00 4.63
954 1027 0.110486 ATCTCTCGCTCCTCCTCCTC 59.890 60.000 0.00 0.00 0.00 3.71
955 1028 0.110486 GATCTCTCGCTCCTCCTCCT 59.890 60.000 0.00 0.00 0.00 3.69
1033 1114 1.755008 GGACAGGGAGAGGGAGACG 60.755 68.421 0.00 0.00 0.00 4.18
1035 1116 2.212794 GACGGACAGGGAGAGGGAGA 62.213 65.000 0.00 0.00 0.00 3.71
1041 1122 1.679305 GCAGAGACGGACAGGGAGA 60.679 63.158 0.00 0.00 0.00 3.71
1042 1123 2.716017 GGCAGAGACGGACAGGGAG 61.716 68.421 0.00 0.00 0.00 4.30
1044 1125 2.303549 GATGGCAGAGACGGACAGGG 62.304 65.000 0.00 0.00 0.00 4.45
1048 1129 1.142748 CCAGATGGCAGAGACGGAC 59.857 63.158 0.00 0.00 0.00 4.79
1049 1130 3.621225 CCAGATGGCAGAGACGGA 58.379 61.111 0.00 0.00 0.00 4.69
1213 1345 2.464459 CCAAATCTCGGGCGCAGAC 61.464 63.158 10.83 0.00 0.00 3.51
1214 1346 2.125147 CCAAATCTCGGGCGCAGA 60.125 61.111 10.83 7.25 0.00 4.26
1283 1415 3.667429 GAATTCACCGCGCTGCACC 62.667 63.158 5.56 0.00 0.00 5.01
1284 1416 2.202349 GAATTCACCGCGCTGCAC 60.202 61.111 5.56 0.00 0.00 4.57
1285 1417 3.787676 CGAATTCACCGCGCTGCA 61.788 61.111 5.56 0.00 0.00 4.41
1286 1418 2.686518 GATCGAATTCACCGCGCTGC 62.687 60.000 5.56 0.00 0.00 5.25
1287 1419 1.273887 GATCGAATTCACCGCGCTG 59.726 57.895 5.56 0.00 0.00 5.18
1288 1420 2.230940 CGATCGAATTCACCGCGCT 61.231 57.895 10.26 0.00 0.00 5.92
1289 1421 2.242670 CGATCGAATTCACCGCGC 59.757 61.111 10.26 0.00 0.00 6.86
1311 1443 2.029838 ACGACTAGTACTACCACCGG 57.970 55.000 0.00 0.00 0.00 5.28
1504 1659 1.603326 GGGAAAACGACGTAAAGCCAA 59.397 47.619 0.00 0.00 0.00 4.52
1524 1679 2.117137 CATCGACACGTAAATCCCTCG 58.883 52.381 0.00 0.00 0.00 4.63
1582 1737 2.513897 GCCCCAGGAACCGAATCG 60.514 66.667 0.00 0.00 0.00 3.34
1634 1789 1.066454 CATCCACATGCATGCGAACAT 59.934 47.619 26.53 8.77 36.79 2.71
1673 1828 1.615919 CCCCTGCCGTCCTTACAAAAT 60.616 52.381 0.00 0.00 0.00 1.82
1700 1860 7.815068 CCTGGATCCTAGTAACAGATTTAATCG 59.185 40.741 14.23 0.00 0.00 3.34
1715 1875 1.950909 GACACGACTCCTGGATCCTAG 59.049 57.143 14.23 10.26 0.00 3.02
1716 1876 1.283905 TGACACGACTCCTGGATCCTA 59.716 52.381 14.23 0.00 0.00 2.94
1718 1878 0.457851 CTGACACGACTCCTGGATCC 59.542 60.000 4.20 4.20 0.00 3.36
1719 1879 1.133407 GACTGACACGACTCCTGGATC 59.867 57.143 0.00 0.00 0.00 3.36
1720 1880 1.178276 GACTGACACGACTCCTGGAT 58.822 55.000 0.00 0.00 0.00 3.41
1721 1881 0.110678 AGACTGACACGACTCCTGGA 59.889 55.000 0.00 0.00 0.00 3.86
1722 1882 0.523966 GAGACTGACACGACTCCTGG 59.476 60.000 0.00 0.00 0.00 4.45
1727 1887 1.870383 GCGAGAGACTGACACGACT 59.130 57.895 0.00 0.00 0.00 4.18
1728 1888 1.510204 CGCGAGAGACTGACACGAC 60.510 63.158 0.00 0.00 0.00 4.34
1729 1889 1.504647 AACGCGAGAGACTGACACGA 61.505 55.000 15.93 0.00 0.00 4.35
1730 1890 1.060726 GAACGCGAGAGACTGACACG 61.061 60.000 15.93 0.00 0.00 4.49
1731 1891 0.729816 GGAACGCGAGAGACTGACAC 60.730 60.000 15.93 0.00 0.00 3.67
1732 1892 1.170290 TGGAACGCGAGAGACTGACA 61.170 55.000 15.93 0.00 0.00 3.58
1734 1894 0.171231 CATGGAACGCGAGAGACTGA 59.829 55.000 15.93 0.00 0.00 3.41
1861 2041 2.371841 ACCAGACACAGGCACATTAAGA 59.628 45.455 0.00 0.00 0.00 2.10
2022 2340 9.219497 CAGTGCTATACTACGTACTCTAAAAAC 57.781 37.037 0.00 0.00 37.60 2.43
2030 2348 5.678583 TCTTCCAGTGCTATACTACGTACT 58.321 41.667 0.00 0.00 37.60 2.73
2080 2400 8.718734 ACAAATCTAAGACAACTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
2081 2401 8.842358 ACAAATCTAAGACAACTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
2082 2402 8.311836 AGACAAATCTAAGACAACTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
2083 2403 8.480643 AGACAAATCTAAGACAACTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
2090 2410 8.407064 CCGTATCTAGACAAATCTAAGACAACT 58.593 37.037 0.00 0.00 36.98 3.16
2091 2411 8.404000 TCCGTATCTAGACAAATCTAAGACAAC 58.596 37.037 0.00 0.00 36.98 3.32
2092 2412 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2093 2413 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2094 2414 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2095 2415 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2111 2431 8.803235 TCATTTTAGTGCTAGATACATCCGTAT 58.197 33.333 0.00 0.00 41.16 3.06
2112 2432 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
2113 2433 7.050970 TCATTTTAGTGCTAGATACATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
2114 2434 7.148641 ACTCATTTTAGTGCTAGATACATCCG 58.851 38.462 0.00 0.00 0.00 4.18
2115 2435 8.364142 AGACTCATTTTAGTGCTAGATACATCC 58.636 37.037 0.00 0.00 0.00 3.51
2118 2438 9.185680 TGTAGACTCATTTTAGTGCTAGATACA 57.814 33.333 0.00 0.00 0.00 2.29
2122 2442 9.185680 TGTATGTAGACTCATTTTAGTGCTAGA 57.814 33.333 0.00 0.00 0.00 2.43
2123 2443 9.973450 ATGTATGTAGACTCATTTTAGTGCTAG 57.027 33.333 0.00 0.00 0.00 3.42
2124 2444 9.967346 GATGTATGTAGACTCATTTTAGTGCTA 57.033 33.333 0.00 0.00 0.00 3.49
2125 2445 7.928706 GGATGTATGTAGACTCATTTTAGTGCT 59.071 37.037 0.00 0.00 0.00 4.40
2126 2446 7.096023 CGGATGTATGTAGACTCATTTTAGTGC 60.096 40.741 0.00 0.00 0.00 4.40
2127 2447 7.921214 ACGGATGTATGTAGACTCATTTTAGTG 59.079 37.037 0.00 0.00 0.00 2.74
2128 2448 8.008513 ACGGATGTATGTAGACTCATTTTAGT 57.991 34.615 0.00 0.00 0.00 2.24
2131 2451 8.861086 AGATACGGATGTATGTAGACTCATTTT 58.139 33.333 0.00 0.00 41.37 1.82
2132 2452 8.410673 AGATACGGATGTATGTAGACTCATTT 57.589 34.615 0.00 0.00 41.37 2.32
2141 2461 8.737175 GGATTTGTCTAGATACGGATGTATGTA 58.263 37.037 0.00 0.00 41.37 2.29
2142 2462 7.232737 TGGATTTGTCTAGATACGGATGTATGT 59.767 37.037 0.00 0.00 41.37 2.29
2143 2463 7.602753 TGGATTTGTCTAGATACGGATGTATG 58.397 38.462 0.00 0.00 41.37 2.39
2144 2464 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
2145 2465 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
2146 2466 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
2147 2467 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
2148 2468 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
2149 2469 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
2150 2470 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
2151 2471 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
2152 2472 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2154 2474 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2155 2475 9.793259 AAATTACTTGTCTTGGATTTGTCTAGA 57.207 29.630 0.00 0.00 0.00 2.43
2158 2478 9.793259 TCTAAATTACTTGTCTTGGATTTGTCT 57.207 29.630 0.00 0.00 0.00 3.41
2161 2481 9.329913 CGTTCTAAATTACTTGTCTTGGATTTG 57.670 33.333 0.00 0.00 0.00 2.32
2162 2482 8.512138 CCGTTCTAAATTACTTGTCTTGGATTT 58.488 33.333 0.00 0.00 0.00 2.17
2163 2483 7.881232 TCCGTTCTAAATTACTTGTCTTGGATT 59.119 33.333 0.00 0.00 0.00 3.01
2164 2484 7.391620 TCCGTTCTAAATTACTTGTCTTGGAT 58.608 34.615 0.00 0.00 0.00 3.41
2165 2485 6.761312 TCCGTTCTAAATTACTTGTCTTGGA 58.239 36.000 0.00 0.00 0.00 3.53
2166 2486 6.092259 CCTCCGTTCTAAATTACTTGTCTTGG 59.908 42.308 0.00 0.00 0.00 3.61
2167 2487 6.092259 CCCTCCGTTCTAAATTACTTGTCTTG 59.908 42.308 0.00 0.00 0.00 3.02
2168 2488 6.013984 TCCCTCCGTTCTAAATTACTTGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2169 2489 5.482878 TCCCTCCGTTCTAAATTACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
2170 2490 5.727434 TCCCTCCGTTCTAAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
2171 2491 5.247792 ACTCCCTCCGTTCTAAATTACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
2172 2492 5.731591 ACTCCCTCCGTTCTAAATTACTTG 58.268 41.667 0.00 0.00 0.00 3.16
2173 2493 7.672122 ATACTCCCTCCGTTCTAAATTACTT 57.328 36.000 0.00 0.00 0.00 2.24
2174 2494 8.953223 ATATACTCCCTCCGTTCTAAATTACT 57.047 34.615 0.00 0.00 0.00 2.24
2175 2495 9.993454 AAATATACTCCCTCCGTTCTAAATTAC 57.007 33.333 0.00 0.00 0.00 1.89
2179 2499 8.645110 CCTAAAATATACTCCCTCCGTTCTAAA 58.355 37.037 0.00 0.00 0.00 1.85
2180 2500 7.234166 CCCTAAAATATACTCCCTCCGTTCTAA 59.766 40.741 0.00 0.00 0.00 2.10
2181 2501 6.723052 CCCTAAAATATACTCCCTCCGTTCTA 59.277 42.308 0.00 0.00 0.00 2.10
2182 2502 5.543020 CCCTAAAATATACTCCCTCCGTTCT 59.457 44.000 0.00 0.00 0.00 3.01
2183 2503 5.306419 ACCCTAAAATATACTCCCTCCGTTC 59.694 44.000 0.00 0.00 0.00 3.95
2184 2504 5.222086 ACCCTAAAATATACTCCCTCCGTT 58.778 41.667 0.00 0.00 0.00 4.44
2185 2505 4.824276 ACCCTAAAATATACTCCCTCCGT 58.176 43.478 0.00 0.00 0.00 4.69
2186 2506 6.439692 ACATACCCTAAAATATACTCCCTCCG 59.560 42.308 0.00 0.00 0.00 4.63
2187 2507 7.809880 ACATACCCTAAAATATACTCCCTCC 57.190 40.000 0.00 0.00 0.00 4.30
2188 2508 9.544579 ACTACATACCCTAAAATATACTCCCTC 57.455 37.037 0.00 0.00 0.00 4.30
2189 2509 9.322769 CACTACATACCCTAAAATATACTCCCT 57.677 37.037 0.00 0.00 0.00 4.20
2190 2510 9.097946 ACACTACATACCCTAAAATATACTCCC 57.902 37.037 0.00 0.00 0.00 4.30
2194 2514 9.866798 GGCTACACTACATACCCTAAAATATAC 57.133 37.037 0.00 0.00 0.00 1.47
2195 2515 9.833179 AGGCTACACTACATACCCTAAAATATA 57.167 33.333 0.00 0.00 0.00 0.86
2196 2516 8.737601 AGGCTACACTACATACCCTAAAATAT 57.262 34.615 0.00 0.00 0.00 1.28
2197 2517 8.426489 CAAGGCTACACTACATACCCTAAAATA 58.574 37.037 0.00 0.00 0.00 1.40
2198 2518 7.092578 ACAAGGCTACACTACATACCCTAAAAT 60.093 37.037 0.00 0.00 0.00 1.82
2205 2525 5.359009 TGACTACAAGGCTACACTACATACC 59.641 44.000 0.00 0.00 0.00 2.73
2215 2535 1.275291 TGGCACTGACTACAAGGCTAC 59.725 52.381 0.00 0.00 0.00 3.58
2220 2540 1.436600 CTGCTGGCACTGACTACAAG 58.563 55.000 0.00 0.00 0.00 3.16
2271 2591 4.024725 TGGTTTGTACACGACATAACAAGC 60.025 41.667 0.00 0.00 34.23 4.01
2398 2719 7.551035 AGAAATAGCATGACAAATGAGAGAC 57.449 36.000 0.00 0.00 0.00 3.36
2583 2906 5.769662 TCAATCTTGTGCACCAGTAGATTTT 59.230 36.000 21.21 8.56 34.31 1.82
2819 3148 5.734140 TCCAGTATATTTCCTTTCCCTTCCA 59.266 40.000 0.00 0.00 0.00 3.53
3011 3343 1.199789 TGCGGATTGTTGACAGCAATC 59.800 47.619 27.64 27.64 46.76 2.67
3228 3565 3.250280 GCACACTCAAGATGGCATGATAG 59.750 47.826 3.81 0.00 0.00 2.08
3421 3758 8.352942 AGGAAAACAAGCAAAGTAACAATCTAG 58.647 33.333 0.00 0.00 0.00 2.43
3471 3808 4.760715 TGCCGTAATAAACAACTAAGGCAA 59.239 37.500 2.62 0.00 43.97 4.52
3685 4302 8.664669 AATGTAAGGAAAATGGACTGGTAAAT 57.335 30.769 0.00 0.00 0.00 1.40
3709 4647 8.321353 TGGATCAGAAATCTTAAGAGTTGCTAA 58.679 33.333 21.90 6.65 32.01 3.09
3985 4923 2.554032 GCCTCAAGTTTCTGCTTTGCTA 59.446 45.455 0.00 0.00 0.00 3.49
4029 4967 1.484653 TCCACGACCCATACTTCCATG 59.515 52.381 0.00 0.00 0.00 3.66
4036 4974 2.936498 CTGACAATTCCACGACCCATAC 59.064 50.000 0.00 0.00 0.00 2.39
4061 4999 3.838244 ACTTCAGCACCACAAGTAAGA 57.162 42.857 0.00 0.00 0.00 2.10
4100 5038 2.158986 AGACTGCATGACATCTAGTGCC 60.159 50.000 0.00 0.00 36.79 5.01
4116 5054 5.799213 AGATTCAACAGGGAACTTAGACTG 58.201 41.667 0.00 0.00 40.21 3.51
4220 5158 6.436847 TGGATCCTGAAAATGCAAAGATACAA 59.563 34.615 14.23 0.00 0.00 2.41
4223 5161 7.664552 ATTGGATCCTGAAAATGCAAAGATA 57.335 32.000 14.23 0.00 37.87 1.98
4470 5408 4.437930 GCTGAATGCAGTTACCTTGATCAC 60.438 45.833 1.73 0.00 44.17 3.06
4832 5770 2.378445 GAGCTTCCTCCAGTTCAGTC 57.622 55.000 0.00 0.00 31.68 3.51
5270 6208 3.907474 TCACCCTGAAGTTGGTCTCAATA 59.093 43.478 0.00 0.00 35.10 1.90
5500 6438 1.537889 TCCCCGGAAAGAGAAGGCA 60.538 57.895 0.73 0.00 0.00 4.75
5688 6627 5.188948 ACAGACTAGAGAGTAGCAGAAGAGA 59.811 44.000 0.00 0.00 35.45 3.10
5689 6628 5.428253 ACAGACTAGAGAGTAGCAGAAGAG 58.572 45.833 0.00 0.00 35.45 2.85
5812 6757 1.911293 TTAACCCGACCGACGACTCG 61.911 60.000 0.00 1.93 45.77 4.18
5813 6758 0.240945 TTTAACCCGACCGACGACTC 59.759 55.000 0.00 0.00 45.77 3.36
5874 6820 5.014858 ACAGAAGATTTCATGTTCCATGCT 58.985 37.500 0.00 0.00 33.38 3.79
5956 6902 7.320399 ACTCAAACAGATATAATGACGACACA 58.680 34.615 0.00 0.00 0.00 3.72
5998 6962 0.321919 TCGAAGGCAAAGCTCTGCAT 60.322 50.000 15.17 3.10 44.52 3.96
6012 6976 3.927142 AGACGGAAGCAAAGTAATCGAAG 59.073 43.478 0.00 0.00 0.00 3.79
6048 7018 3.964688 TGGAAGAACAGACAGACTAACCA 59.035 43.478 0.00 0.00 0.00 3.67
6150 7124 0.321671 TGGTAACAGGAGAGCTGCAC 59.678 55.000 1.02 0.00 46.17 4.57
6190 7179 1.666888 CCATTCTTTGGCGTTGAGTGC 60.667 52.381 0.00 0.00 39.09 4.40
6206 7195 2.325661 AGGGTTTTTAGGCTGCCATT 57.674 45.000 22.65 3.15 0.00 3.16
6221 7210 5.013258 ACTTCTTGGTAAGAGTCTAGGGT 57.987 43.478 0.00 0.00 39.03 4.34
6234 7223 1.598130 GGTGCTGCGACTTCTTGGT 60.598 57.895 0.00 0.00 0.00 3.67
6237 7228 0.947244 CAAAGGTGCTGCGACTTCTT 59.053 50.000 8.72 0.00 0.00 2.52
6293 7314 2.436646 AAGAACGGCCATGGCTCG 60.437 61.111 34.70 33.49 41.60 5.03
6297 7318 2.620251 TATCTGAAGAACGGCCATGG 57.380 50.000 7.63 7.63 0.00 3.66
6347 7368 1.696336 CGAGATGGATGGGTGGAGAAT 59.304 52.381 0.00 0.00 0.00 2.40
6352 7373 0.833287 ACTTCGAGATGGATGGGTGG 59.167 55.000 0.00 0.00 0.00 4.61
6379 7400 5.296283 CCTACCTCTTCTTCATGCAGAAATG 59.704 44.000 9.13 4.99 35.40 2.32
6382 7403 4.096681 TCCTACCTCTTCTTCATGCAGAA 58.903 43.478 7.58 7.58 34.41 3.02
6383 7404 3.713003 TCCTACCTCTTCTTCATGCAGA 58.287 45.455 0.00 0.00 0.00 4.26
6408 7433 2.069273 CTTGAATCTTCTCCGTTGCGT 58.931 47.619 0.00 0.00 0.00 5.24
6414 7439 2.102252 CCCTCTCCTTGAATCTTCTCCG 59.898 54.545 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.