Multiple sequence alignment - TraesCS4B01G357500

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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 TraesCS4B01G357500 chr4B 100.000 4825 0 0 1 4825 648094560 648089736 0.000000e+00 8911.0
1 TraesCS4B01G357500 chr4B 91.905 1606 116 11 1889 3491 647728302 647729896 0.000000e+00 2233.0
2 TraesCS4B01G357500 chr4B 92.781 1219 64 6 57 1272 647711282 647712479 0.000000e+00 1742.0
3 TraesCS4B01G357500 chr4B 92.089 632 43 7 4194 4822 647731285 647731912 0.000000e+00 883.0
4 TraesCS4B01G357500 chr4B 82.448 433 49 19 1469 1887 647727803 647728222 2.140000e-93 353.0
5 TraesCS4B01G357500 chr4B 85.399 363 25 10 3452 3795 647729884 647730237 7.680000e-93 351.0
6 TraesCS4B01G357500 chr4B 83.913 230 25 7 3825 4051 647408937 647409157 4.890000e-50 209.0
7 TraesCS4B01G357500 chr4B 89.130 138 11 3 235 368 647709955 647709818 8.310000e-38 169.0
8 TraesCS4B01G357500 chr4B 84.615 117 8 6 3796 3906 646987037 646987149 1.840000e-19 108.0
9 TraesCS4B01G357500 chr4B 86.517 89 5 2 56 143 348951047 348950965 1.850000e-14 91.6
10 TraesCS4B01G357500 chr4D 88.064 1617 140 33 2307 3889 503153834 503152237 0.000000e+00 1868.0
11 TraesCS4B01G357500 chr4D 91.114 844 59 12 1465 2303 503154772 503153940 0.000000e+00 1129.0
12 TraesCS4B01G357500 chr4D 84.216 906 112 18 2155 3043 502875844 502874953 0.000000e+00 852.0
13 TraesCS4B01G357500 chr4D 87.736 530 43 13 3148 3673 502784792 502784281 2.490000e-167 599.0
14 TraesCS4B01G357500 chr4D 86.680 518 44 18 828 1339 503155266 503154768 7.060000e-153 551.0
15 TraesCS4B01G357500 chr4D 86.992 369 24 13 4473 4825 503151477 503151117 1.260000e-105 394.0
16 TraesCS4B01G357500 chr4D 87.106 349 24 9 4136 4475 503151974 503151638 4.560000e-100 375.0
17 TraesCS4B01G357500 chr4D 84.856 383 43 10 1458 1838 502884160 502883791 5.900000e-99 372.0
18 TraesCS4B01G357500 chr4D 81.519 395 39 17 3682 4049 502784127 502783740 1.310000e-75 294.0
19 TraesCS4B01G357500 chr4D 90.551 127 7 2 3755 3880 502594864 502594986 3.860000e-36 163.0
20 TraesCS4B01G357500 chr4D 80.176 227 27 10 4136 4346 502783554 502783330 2.330000e-33 154.0
21 TraesCS4B01G357500 chr5A 90.899 879 73 5 2687 3563 687347493 687348366 0.000000e+00 1173.0
22 TraesCS4B01G357500 chr5A 92.172 792 43 5 1889 2673 687346620 687347399 0.000000e+00 1101.0
23 TraesCS4B01G357500 chr5A 83.364 1082 109 40 828 1887 687345508 687346540 0.000000e+00 935.0
24 TraesCS4B01G357500 chr5A 86.358 799 54 22 4057 4822 687349300 687350076 0.000000e+00 821.0
25 TraesCS4B01G357500 chr5A 84.169 379 33 11 3686 4046 687084252 687084621 4.620000e-90 342.0
26 TraesCS4B01G357500 chr5A 80.741 270 21 10 3630 3889 687348863 687349111 1.070000e-41 182.0
27 TraesCS4B01G357500 chr5A 84.270 89 8 4 57 145 92220205 92220123 1.110000e-11 82.4
28 TraesCS4B01G357500 chr3A 85.385 130 15 3 243 368 123685341 123685470 1.090000e-26 132.0
29 TraesCS4B01G357500 chr5D 87.640 89 5 3 57 145 103246250 103246332 1.110000e-16 99.0
30 TraesCS4B01G357500 chr1D 87.640 89 5 3 57 145 72575048 72575130 1.110000e-16 99.0
31 TraesCS4B01G357500 chr7D 77.914 163 31 2 659 820 388699557 388699715 3.970000e-16 97.1
32 TraesCS4B01G357500 chr6D 94.828 58 3 0 57 114 327002354 327002297 1.850000e-14 91.6
33 TraesCS4B01G357500 chr2A 93.103 58 4 0 57 114 85293428 85293485 8.600000e-13 86.1
34 TraesCS4B01G357500 chr7B 94.444 54 3 0 57 110 104241630 104241577 3.090000e-12 84.2
35 TraesCS4B01G357500 chr7B 84.270 89 8 3 57 145 81344600 81344518 1.110000e-11 82.4


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 TraesCS4B01G357500 chr4B 648089736 648094560 4824 True 8911.0 8911 100.000000 1 4825 1 chr4B.!!$R3 4824
1 TraesCS4B01G357500 chr4B 647711282 647712479 1197 False 1742.0 1742 92.781000 57 1272 1 chr4B.!!$F3 1215
2 TraesCS4B01G357500 chr4B 647727803 647731912 4109 False 955.0 2233 87.960250 1469 4822 4 chr4B.!!$F4 3353
3 TraesCS4B01G357500 chr4D 503151117 503155266 4149 True 863.4 1868 87.991200 828 4825 5 chr4D.!!$R4 3997
4 TraesCS4B01G357500 chr4D 502874953 502875844 891 True 852.0 852 84.216000 2155 3043 1 chr4D.!!$R1 888
5 TraesCS4B01G357500 chr4D 502783330 502784792 1462 True 349.0 599 83.143667 3148 4346 3 chr4D.!!$R3 1198
6 TraesCS4B01G357500 chr5A 687345508 687350076 4568 False 842.4 1173 86.706800 828 4822 5 chr5A.!!$F2 3994

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
38 39 0.027194 CACGCGAGGCATCAATCAAG 59.973 55.0 15.93 0.0 0.0 3.02 F
1241 1269 0.109342 CCTCTGTTGGTGTGGCTTCT 59.891 55.0 0.00 0.0 0.0 2.85 F
2823 3161 0.317160 TAGGCGTCTGACACTGGTTG 59.683 55.0 0.00 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1299 1327 0.603975 GGAGCAACTGACTCACCACC 60.604 60.000 0.00 0.00 35.79 4.61 R
2853 3191 1.073763 CCACCCATCACTGAAACTGGA 59.926 52.381 0.00 0.00 0.00 3.86 R
4011 5682 0.034059 AGGCTGTCCAACAACTCGAG 59.966 55.000 11.84 11.84 33.74 4.04 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
22 23 4.662145 GTTAAATGAAGCCTTGATCCACG 58.338 43.478 0.00 0.00 0.00 4.94
23 24 1.098050 AATGAAGCCTTGATCCACGC 58.902 50.000 0.00 0.00 0.00 5.34
24 25 1.091771 ATGAAGCCTTGATCCACGCG 61.092 55.000 3.53 3.53 0.00 6.01
25 26 1.447838 GAAGCCTTGATCCACGCGA 60.448 57.895 15.93 0.00 0.00 5.87
26 27 1.424493 GAAGCCTTGATCCACGCGAG 61.424 60.000 15.93 4.16 0.00 5.03
27 28 2.859273 AAGCCTTGATCCACGCGAGG 62.859 60.000 17.19 17.19 0.00 4.63
28 29 2.892425 CCTTGATCCACGCGAGGC 60.892 66.667 18.51 5.45 0.00 4.70
29 30 2.125552 CTTGATCCACGCGAGGCA 60.126 61.111 18.51 8.27 0.00 4.75
30 31 1.522355 CTTGATCCACGCGAGGCAT 60.522 57.895 18.51 11.96 0.00 4.40
31 32 1.493950 CTTGATCCACGCGAGGCATC 61.494 60.000 18.51 19.41 0.00 3.91
32 33 2.106938 GATCCACGCGAGGCATCA 59.893 61.111 18.51 0.27 0.00 3.07
33 34 1.521457 GATCCACGCGAGGCATCAA 60.521 57.895 18.51 0.00 0.00 2.57
34 35 0.882042 GATCCACGCGAGGCATCAAT 60.882 55.000 18.51 5.52 0.00 2.57
35 36 0.882042 ATCCACGCGAGGCATCAATC 60.882 55.000 18.51 0.00 0.00 2.67
36 37 1.815003 CCACGCGAGGCATCAATCA 60.815 57.895 15.93 0.00 0.00 2.57
37 38 1.368345 CCACGCGAGGCATCAATCAA 61.368 55.000 15.93 0.00 0.00 2.57
38 39 0.027194 CACGCGAGGCATCAATCAAG 59.973 55.000 15.93 0.00 0.00 3.02
39 40 0.391661 ACGCGAGGCATCAATCAAGT 60.392 50.000 15.93 0.00 0.00 3.16
40 41 1.134818 ACGCGAGGCATCAATCAAGTA 60.135 47.619 15.93 0.00 0.00 2.24
41 42 1.258982 CGCGAGGCATCAATCAAGTAC 59.741 52.381 0.00 0.00 0.00 2.73
42 43 2.279741 GCGAGGCATCAATCAAGTACA 58.720 47.619 0.00 0.00 0.00 2.90
43 44 2.677836 GCGAGGCATCAATCAAGTACAA 59.322 45.455 0.00 0.00 0.00 2.41
44 45 3.485877 GCGAGGCATCAATCAAGTACAAC 60.486 47.826 0.00 0.00 0.00 3.32
45 46 3.935203 CGAGGCATCAATCAAGTACAACT 59.065 43.478 0.00 0.00 0.00 3.16
46 47 4.033358 CGAGGCATCAATCAAGTACAACTC 59.967 45.833 0.00 0.00 0.00 3.01
47 48 4.265073 AGGCATCAATCAAGTACAACTCC 58.735 43.478 0.00 0.00 0.00 3.85
48 49 4.009675 GGCATCAATCAAGTACAACTCCA 58.990 43.478 0.00 0.00 0.00 3.86
49 50 4.641989 GGCATCAATCAAGTACAACTCCAT 59.358 41.667 0.00 0.00 0.00 3.41
50 51 5.449588 GGCATCAATCAAGTACAACTCCATG 60.450 44.000 0.00 0.00 0.00 3.66
51 52 5.124457 GCATCAATCAAGTACAACTCCATGT 59.876 40.000 0.00 0.00 37.32 3.21
52 53 6.549061 CATCAATCAAGTACAACTCCATGTG 58.451 40.000 0.00 0.00 34.75 3.21
53 54 4.455533 TCAATCAAGTACAACTCCATGTGC 59.544 41.667 0.00 0.00 36.33 4.57
54 55 3.483808 TCAAGTACAACTCCATGTGCA 57.516 42.857 0.00 0.00 38.25 4.57
55 56 3.814625 TCAAGTACAACTCCATGTGCAA 58.185 40.909 0.00 0.00 38.25 4.08
98 99 4.473922 GGAGGGAAGTTAGGGAATTGTAGT 59.526 45.833 0.00 0.00 0.00 2.73
105 106 8.542926 GGAAGTTAGGGAATTGTAGTTTAGGTA 58.457 37.037 0.00 0.00 0.00 3.08
127 128 7.363431 GGTAACTTTCCTTGAGTTTCTTCATG 58.637 38.462 0.00 0.00 38.28 3.07
131 132 8.697507 ACTTTCCTTGAGTTTCTTCATGTTAT 57.302 30.769 0.00 0.00 0.00 1.89
149 150 4.412199 TGTTATAGGATCCACTTCCCAAGG 59.588 45.833 15.82 0.00 36.35 3.61
156 157 1.132527 TCCACTTCCCAAGGAGAAGGA 60.133 52.381 16.48 7.55 44.13 3.36
160 161 1.205893 CTTCCCAAGGAGAAGGAGACG 59.794 57.143 8.57 0.00 37.64 4.18
183 184 6.097356 CGACTCGGGCTGCTATATTATAAAA 58.903 40.000 0.00 0.00 0.00 1.52
184 185 6.034683 CGACTCGGGCTGCTATATTATAAAAC 59.965 42.308 0.00 0.00 0.00 2.43
186 187 7.450903 ACTCGGGCTGCTATATTATAAAACTT 58.549 34.615 0.00 0.00 0.00 2.66
250 252 5.743636 ACCAGCCAATACATGTCAAAAAT 57.256 34.783 0.00 0.00 0.00 1.82
256 258 5.111293 CCAATACATGTCAAAAATCAGCCC 58.889 41.667 0.00 0.00 0.00 5.19
360 362 9.567776 TTTGAAGGTAGTTTGAGATTGTAATGA 57.432 29.630 0.00 0.00 0.00 2.57
400 404 5.060427 TCCCAAAAAGAATCACAGAAGGA 57.940 39.130 0.00 0.00 0.00 3.36
402 406 6.789268 TCCCAAAAAGAATCACAGAAGGATA 58.211 36.000 0.00 0.00 0.00 2.59
403 407 6.886459 TCCCAAAAAGAATCACAGAAGGATAG 59.114 38.462 0.00 0.00 0.00 2.08
404 408 6.405176 CCCAAAAAGAATCACAGAAGGATAGC 60.405 42.308 0.00 0.00 0.00 2.97
405 409 6.151648 CCAAAAAGAATCACAGAAGGATAGCA 59.848 38.462 0.00 0.00 0.00 3.49
406 410 7.309377 CCAAAAAGAATCACAGAAGGATAGCAA 60.309 37.037 0.00 0.00 0.00 3.91
407 411 7.951347 AAAAGAATCACAGAAGGATAGCAAT 57.049 32.000 0.00 0.00 0.00 3.56
408 412 9.466497 AAAAAGAATCACAGAAGGATAGCAATA 57.534 29.630 0.00 0.00 0.00 1.90
409 413 8.443953 AAAGAATCACAGAAGGATAGCAATAC 57.556 34.615 0.00 0.00 0.00 1.89
410 414 6.529220 AGAATCACAGAAGGATAGCAATACC 58.471 40.000 0.00 0.00 0.00 2.73
411 415 6.328672 AGAATCACAGAAGGATAGCAATACCT 59.671 38.462 0.00 0.00 35.36 3.08
412 416 5.537300 TCACAGAAGGATAGCAATACCTC 57.463 43.478 0.00 0.00 33.16 3.85
413 417 4.962362 TCACAGAAGGATAGCAATACCTCA 59.038 41.667 0.00 0.00 33.16 3.86
414 418 5.604231 TCACAGAAGGATAGCAATACCTCAT 59.396 40.000 0.00 0.00 33.16 2.90
415 419 5.931146 CACAGAAGGATAGCAATACCTCATC 59.069 44.000 0.00 0.00 33.16 2.92
416 420 5.167121 CAGAAGGATAGCAATACCTCATCG 58.833 45.833 0.00 0.00 33.16 3.84
448 452 5.918011 CCTCTAGCAGAACGATTAGCTAAAG 59.082 44.000 10.85 10.24 38.92 1.85
474 478 4.707448 AGAGTGTACAGACTAGAACATGGG 59.293 45.833 0.00 0.00 0.00 4.00
479 483 4.323569 ACAGACTAGAACATGGGAGAGA 57.676 45.455 0.00 0.00 0.00 3.10
493 497 3.453717 TGGGAGAGAGATGGTTCATCAAG 59.546 47.826 10.08 0.00 42.72 3.02
503 507 5.488919 AGATGGTTCATCAAGGTTAGAAGGA 59.511 40.000 10.08 0.00 42.72 3.36
505 509 5.947663 TGGTTCATCAAGGTTAGAAGGAAA 58.052 37.500 0.00 0.00 0.00 3.13
538 542 8.745590 ACATGGAAACCAATATTTAGTGTAACC 58.254 33.333 0.00 0.00 36.95 2.85
542 546 6.990341 AACCAATATTTAGTGTAACCGGTC 57.010 37.500 8.04 0.00 37.80 4.79
620 624 8.017946 GGACATTAAGAGGATAATGCGAAATTC 58.982 37.037 6.89 0.00 43.80 2.17
624 628 6.773976 AAGAGGATAATGCGAAATTCCAAA 57.226 33.333 0.00 0.00 0.00 3.28
626 630 7.352079 AGAGGATAATGCGAAATTCCAAATT 57.648 32.000 0.00 0.00 0.00 1.82
639 643 8.365210 CGAAATTCCAAATTCAGAAACATTACG 58.635 33.333 0.00 0.00 0.00 3.18
652 656 3.454371 ACATTACGGGATGTGAGCTAC 57.546 47.619 5.28 0.00 38.75 3.58
653 657 2.764010 ACATTACGGGATGTGAGCTACA 59.236 45.455 5.28 0.00 44.87 2.74
660 664 4.082787 ACGGGATGTGAGCTACAAAAATTG 60.083 41.667 0.00 0.00 43.77 2.32
673 677 6.128580 GCTACAAAAATTGAATTGTGCCGAAT 60.129 34.615 12.35 0.00 39.89 3.34
759 763 5.066634 TGTTTTAACTTGAAGTTCCGCATGA 59.933 36.000 14.64 0.00 39.51 3.07
760 764 5.957842 TTTAACTTGAAGTTCCGCATGAT 57.042 34.783 14.64 0.00 39.51 2.45
897 902 1.522668 TCTTTCACATCCAACGGCTG 58.477 50.000 0.00 0.00 0.00 4.85
914 919 2.370189 GGCTGATAAGGAGTAGGTGCAT 59.630 50.000 0.00 0.00 0.00 3.96
932 937 2.411547 GCATCAGTTCTTCCGTTTCACG 60.412 50.000 0.00 0.00 42.11 4.35
1203 1229 0.615331 TTTGGCCTCACTGGAGCTAG 59.385 55.000 3.32 0.00 39.96 3.42
1241 1269 0.109342 CCTCTGTTGGTGTGGCTTCT 59.891 55.000 0.00 0.00 0.00 2.85
1242 1270 1.347707 CCTCTGTTGGTGTGGCTTCTA 59.652 52.381 0.00 0.00 0.00 2.10
1310 1338 2.916052 GCGTCTCGGTGGTGAGTCA 61.916 63.158 0.00 0.00 37.28 3.41
1324 1352 1.416813 GAGTCAGTTGCTCCGATGCG 61.417 60.000 0.00 0.00 35.36 4.73
1330 1358 1.447838 TTGCTCCGATGCGTTCTCC 60.448 57.895 0.00 0.00 35.36 3.71
1351 1379 1.077357 TTTGTTGGGTGCGTGGAGT 60.077 52.632 0.00 0.00 0.00 3.85
1362 1390 3.958860 GTGGAGTGGCAGGGTGCT 61.959 66.667 0.00 0.00 44.28 4.40
1363 1391 3.640407 TGGAGTGGCAGGGTGCTC 61.640 66.667 0.00 0.00 44.28 4.26
1364 1392 3.325753 GGAGTGGCAGGGTGCTCT 61.326 66.667 0.00 0.00 44.28 4.09
1365 1393 2.046507 GAGTGGCAGGGTGCTCTG 60.047 66.667 0.00 0.00 44.28 3.35
1393 1421 2.023673 TCTGGGTCTGTTGTTTGCTTG 58.976 47.619 0.00 0.00 0.00 4.01
1466 1494 7.085116 GGTACTGTACATGCTAGCTAGTATTG 58.915 42.308 20.35 17.08 0.00 1.90
1471 1499 8.196802 TGTACATGCTAGCTAGTATTGTTTTG 57.803 34.615 20.35 12.79 0.00 2.44
1475 1503 4.394920 TGCTAGCTAGTATTGTTTTGGTGC 59.605 41.667 21.62 3.92 0.00 5.01
1517 1545 4.744137 TGCTAACAAACATGTGCAATGTTC 59.256 37.500 20.22 11.64 40.94 3.18
1534 1562 6.525976 GCAATGTTCTTCAGCTAGAAATTGTC 59.474 38.462 20.55 14.87 36.44 3.18
1566 1594 1.617947 GGAGTGCTAGAGGTGGGTGG 61.618 65.000 0.00 0.00 0.00 4.61
1592 1621 4.216257 CCTTTCTCGCCATTCTTCTGAAAA 59.784 41.667 0.00 0.00 35.63 2.29
1627 1660 3.375299 ACCATTATCGTTGCTCTCTTTGC 59.625 43.478 0.00 0.00 0.00 3.68
1649 1682 6.798482 TGCTAGCATTTTGATTGATTGGTAG 58.202 36.000 14.93 0.00 39.92 3.18
1716 1750 3.304911 TGACATTTGGGGTGAGTTTCA 57.695 42.857 0.00 0.00 0.00 2.69
1804 1856 5.065914 ACTGCTTTTTAGCATCAAGTCTGA 58.934 37.500 0.00 0.00 44.47 3.27
1896 2027 3.213206 ACAATTGAACTGAGCTGTCCA 57.787 42.857 13.59 0.00 0.00 4.02
1922 2053 0.611714 CCCCAGGTACGCTAACTGTT 59.388 55.000 0.00 0.00 41.94 3.16
1957 2088 4.193826 AGTTGCTCATGATACGTTCTGT 57.806 40.909 0.00 0.00 0.00 3.41
2144 2277 2.035961 TCCCATAGTCTGCGATTACTGC 59.964 50.000 0.00 0.00 0.00 4.40
2193 2326 5.176407 TGTACAGTTTGGCAATGTAACAC 57.824 39.130 13.63 6.78 31.61 3.32
2277 2410 2.204463 TGGACATTCTATCCCTTGGCA 58.796 47.619 0.00 0.00 35.12 4.92
2600 2843 1.135286 GCAATGCTGGTGCTAAAGTCC 60.135 52.381 0.00 0.00 39.00 3.85
2621 2864 7.514721 AGTCCTTAAGGTTTCATGACTTGTAA 58.485 34.615 21.04 0.00 36.34 2.41
2639 2882 5.990120 TGTAACCCTCCTCTTGTAGTTAC 57.010 43.478 0.00 0.00 39.80 2.50
2646 2902 5.357596 CCCTCCTCTTGTAGTTACAGTAGAC 59.642 48.000 5.16 0.00 37.52 2.59
2648 2904 6.603997 CCTCCTCTTGTAGTTACAGTAGACAT 59.396 42.308 5.16 0.00 37.52 3.06
2663 2919 7.881142 ACAGTAGACATAGATCAGAGCATTAC 58.119 38.462 0.00 0.00 0.00 1.89
2675 2931 9.887629 AGATCAGAGCATTACCAATATATTCTG 57.112 33.333 0.00 0.00 0.00 3.02
2676 2932 9.881649 GATCAGAGCATTACCAATATATTCTGA 57.118 33.333 9.32 9.32 41.64 3.27
2678 2934 8.650490 TCAGAGCATTACCAATATATTCTGACA 58.350 33.333 0.00 0.00 35.08 3.58
2679 2935 9.276590 CAGAGCATTACCAATATATTCTGACAA 57.723 33.333 0.00 0.00 33.22 3.18
2724 3060 4.846779 AAACAATGTACGTTCCTGCAAT 57.153 36.364 0.00 0.00 0.00 3.56
2731 3067 5.446143 TGTACGTTCCTGCAATCATTTTT 57.554 34.783 0.00 0.00 0.00 1.94
2732 3068 6.561737 TGTACGTTCCTGCAATCATTTTTA 57.438 33.333 0.00 0.00 0.00 1.52
2737 3073 6.365789 ACGTTCCTGCAATCATTTTTATTGTG 59.634 34.615 0.00 0.00 36.82 3.33
2740 3076 9.369904 GTTCCTGCAATCATTTTTATTGTGTAT 57.630 29.630 0.00 0.00 36.82 2.29
2762 3098 8.296000 TGTATTAATCACCAAAATGTGTCACTG 58.704 33.333 4.27 0.00 37.51 3.66
2763 3099 3.648339 ATCACCAAAATGTGTCACTGC 57.352 42.857 4.27 0.00 37.51 4.40
2777 3113 6.567959 TGTGTCACTGCATTTTGTAATGAAA 58.432 32.000 4.27 0.00 43.12 2.69
2779 3115 7.009999 TGTGTCACTGCATTTTGTAATGAAAAC 59.990 33.333 4.27 0.00 43.12 2.43
2783 3120 7.763528 TCACTGCATTTTGTAATGAAAACTGTT 59.236 29.630 2.25 0.00 43.12 3.16
2786 3123 9.212687 CTGCATTTTGTAATGAAAACTGTTTTG 57.787 29.630 22.06 6.10 43.12 2.44
2809 3146 5.124776 TGGTTTTCCATTCTGTTTATAGGCG 59.875 40.000 0.00 0.00 46.22 5.52
2819 3157 3.845178 TGTTTATAGGCGTCTGACACTG 58.155 45.455 0.00 0.00 0.00 3.66
2821 3159 2.139323 TATAGGCGTCTGACACTGGT 57.861 50.000 0.00 2.48 0.00 4.00
2823 3161 0.317160 TAGGCGTCTGACACTGGTTG 59.683 55.000 0.00 0.00 0.00 3.77
2830 3168 2.354821 GTCTGACACTGGTTGGTTTGTC 59.645 50.000 2.24 0.00 39.09 3.18
2853 3191 9.263446 TGTCTGGTCTACTTTAATTAGGTGTAT 57.737 33.333 4.19 0.00 0.00 2.29
2956 3294 7.506971 GCAAGGAATTACTATAGGTAAGTGGT 58.493 38.462 4.43 0.00 42.74 4.16
2957 3295 7.441458 GCAAGGAATTACTATAGGTAAGTGGTG 59.559 40.741 4.43 0.00 42.74 4.17
2959 3297 9.719433 AAGGAATTACTATAGGTAAGTGGTGTA 57.281 33.333 4.43 0.00 42.74 2.90
2985 3323 7.039644 AGTCTAGTATCCATCGTCCCTATTTTG 60.040 40.741 0.00 0.00 0.00 2.44
3008 3347 8.954950 TTGTTTTCCTCTTTTTGCAAATATCA 57.045 26.923 13.65 0.00 0.00 2.15
3016 3355 8.783093 CCTCTTTTTGCAAATATCATCCGTATA 58.217 33.333 13.65 0.00 0.00 1.47
3044 3383 4.002906 TGGTGTCTAAGTAGCAACCTTG 57.997 45.455 9.39 0.00 0.00 3.61
3051 3390 5.758784 GTCTAAGTAGCAACCTTGAAGTGTT 59.241 40.000 0.00 0.00 0.00 3.32
3082 3421 7.653713 TCATAACACTGAGACTCTTTCAAAGAC 59.346 37.037 3.68 0.00 33.12 3.01
3135 3474 7.447545 AGTGTAGATATCGGTTAGCTGTATGAA 59.552 37.037 0.00 0.00 0.00 2.57
3143 3482 7.108841 TCGGTTAGCTGTATGAAACTATTCT 57.891 36.000 0.00 0.00 36.48 2.40
3355 3694 3.359654 CAAAAACCGAGTAGTGTGCAAC 58.640 45.455 0.00 0.00 37.35 4.17
3590 3958 3.710722 CTGAAGCCCTCACCGCCT 61.711 66.667 0.00 0.00 0.00 5.52
3601 3969 4.008933 ACCGCCTGGCACTGTCTC 62.009 66.667 20.29 0.00 39.70 3.36
3603 3971 2.345244 CGCCTGGCACTGTCTCTT 59.655 61.111 20.29 0.00 0.00 2.85
3680 4623 5.426689 AGTCCAATCTCATTCAACTGCTA 57.573 39.130 0.00 0.00 0.00 3.49
3712 4655 4.320714 CCACAAGTCCACATTCATTGACTG 60.321 45.833 2.71 2.71 38.07 3.51
3714 4660 4.889409 ACAAGTCCACATTCATTGACTGTT 59.111 37.500 6.90 0.00 38.07 3.16
3795 4755 0.597637 AACTCTGAACCTCACGCACG 60.598 55.000 0.00 0.00 0.00 5.34
3796 4756 2.355837 TCTGAACCTCACGCACGC 60.356 61.111 0.00 0.00 0.00 5.34
3797 4757 2.661537 CTGAACCTCACGCACGCA 60.662 61.111 0.00 0.00 0.00 5.24
3798 4758 2.943345 CTGAACCTCACGCACGCAC 61.943 63.158 0.00 0.00 0.00 5.34
3854 4818 0.890542 GCATCACCACCAGCACAAGA 60.891 55.000 0.00 0.00 0.00 3.02
3876 5456 1.300465 CTGCATAGCGTGATCGGCT 60.300 57.895 14.53 14.53 37.56 5.52
3892 5472 4.198625 CTACAGAGCAGCAGTGGC 57.801 61.111 0.00 0.00 41.61 5.01
3914 5494 4.541482 GCACGCATGCCATGTCCG 62.541 66.667 13.15 4.90 46.97 4.79
3915 5495 3.879682 CACGCATGCCATGTCCGG 61.880 66.667 13.15 0.00 0.00 5.14
3923 5503 4.033776 CCATGTCCGGCACCCACT 62.034 66.667 0.00 0.00 0.00 4.00
3924 5504 2.436646 CATGTCCGGCACCCACTC 60.437 66.667 0.00 0.00 0.00 3.51
3925 5505 2.607750 ATGTCCGGCACCCACTCT 60.608 61.111 0.00 0.00 0.00 3.24
3926 5506 2.959484 ATGTCCGGCACCCACTCTG 61.959 63.158 0.00 0.00 0.00 3.35
3927 5507 3.626924 GTCCGGCACCCACTCTGT 61.627 66.667 0.00 0.00 0.00 3.41
3928 5508 2.118732 TCCGGCACCCACTCTGTA 59.881 61.111 0.00 0.00 0.00 2.74
3929 5509 1.982395 TCCGGCACCCACTCTGTAG 60.982 63.158 0.00 0.00 0.00 2.74
3930 5510 1.982395 CCGGCACCCACTCTGTAGA 60.982 63.158 0.00 0.00 0.00 2.59
3931 5511 1.215647 CGGCACCCACTCTGTAGAC 59.784 63.158 0.00 0.00 0.00 2.59
3932 5512 1.532604 CGGCACCCACTCTGTAGACA 61.533 60.000 0.00 0.00 0.00 3.41
3933 5513 0.247736 GGCACCCACTCTGTAGACAG 59.752 60.000 3.12 3.12 45.08 3.51
3945 5525 4.044336 CTGTAGACAGAGATGCAGAAGG 57.956 50.000 3.45 0.00 46.59 3.46
3946 5526 3.698539 CTGTAGACAGAGATGCAGAAGGA 59.301 47.826 3.45 0.00 46.59 3.36
3947 5527 3.698539 TGTAGACAGAGATGCAGAAGGAG 59.301 47.826 0.00 0.00 0.00 3.69
3948 5528 1.481772 AGACAGAGATGCAGAAGGAGC 59.518 52.381 0.00 0.00 0.00 4.70
3950 5530 1.207570 ACAGAGATGCAGAAGGAGCAG 59.792 52.381 0.00 0.00 46.36 4.24
3952 5532 3.407657 GATGCAGAAGGAGCAGCG 58.592 61.111 0.00 0.00 46.36 5.18
3953 5533 2.124819 ATGCAGAAGGAGCAGCGG 60.125 61.111 0.00 0.00 46.36 5.52
3956 5536 2.818714 CAGAAGGAGCAGCGGCAG 60.819 66.667 12.44 0.00 44.61 4.85
3957 5537 4.774503 AGAAGGAGCAGCGGCAGC 62.775 66.667 12.44 9.56 44.61 5.25
3979 5639 0.320421 ACGTGGCAGCAGTCGTAATT 60.320 50.000 6.91 0.00 34.78 1.40
4077 5846 2.425668 TCGTACCTGAAGCGATTGATGA 59.574 45.455 0.00 0.00 0.00 2.92
4078 5847 2.535984 CGTACCTGAAGCGATTGATGAC 59.464 50.000 0.00 0.00 0.00 3.06
4079 5848 2.029838 ACCTGAAGCGATTGATGACC 57.970 50.000 0.00 0.00 0.00 4.02
4080 5849 1.278985 ACCTGAAGCGATTGATGACCA 59.721 47.619 0.00 0.00 0.00 4.02
4081 5850 1.938577 CCTGAAGCGATTGATGACCAG 59.061 52.381 0.00 0.00 0.00 4.00
4082 5851 1.938577 CTGAAGCGATTGATGACCAGG 59.061 52.381 0.00 0.00 0.00 4.45
4083 5852 1.554617 TGAAGCGATTGATGACCAGGA 59.445 47.619 0.00 0.00 0.00 3.86
4084 5853 2.171237 TGAAGCGATTGATGACCAGGAT 59.829 45.455 0.00 0.00 0.00 3.24
4085 5854 2.540265 AGCGATTGATGACCAGGATC 57.460 50.000 0.00 0.00 0.00 3.36
4086 5855 1.764723 AGCGATTGATGACCAGGATCA 59.235 47.619 0.00 0.00 0.00 2.92
4125 6032 2.849880 TTCATACGTACGTGGGTAGC 57.150 50.000 30.25 0.00 0.00 3.58
4164 6087 4.519213 GGGTTACATTGCACTACATACCA 58.481 43.478 0.00 0.00 0.00 3.25
4165 6088 4.944930 GGGTTACATTGCACTACATACCAA 59.055 41.667 0.00 0.00 0.00 3.67
4214 6160 0.745486 CTCAAGATGGTGATGGCGCA 60.745 55.000 10.83 0.00 0.00 6.09
4223 6170 1.815003 TGATGGCGCATCCTTGTCG 60.815 57.895 10.83 0.00 39.87 4.35
4225 6172 1.369091 GATGGCGCATCCTTGTCGTT 61.369 55.000 10.83 0.00 35.07 3.85
4226 6173 1.647545 ATGGCGCATCCTTGTCGTTG 61.648 55.000 10.83 0.00 35.26 4.10
4403 6357 8.630054 TTGCAGTTTCAGGTATAAACATAGTT 57.370 30.769 0.00 0.00 38.92 2.24
4446 6400 9.179552 TGTTCATCAAGTATTTCAAAATGTTCG 57.820 29.630 0.00 0.00 0.00 3.95
4659 6790 9.109393 GCTTTCCCTGTTTCTTTTTATTTCTTT 57.891 29.630 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.662145 CGTGGATCAAGGCTTCATTTAAC 58.338 43.478 0.00 0.00 0.00 2.01
3 4 1.474077 GCGTGGATCAAGGCTTCATTT 59.526 47.619 7.55 0.00 0.00 2.32
4 5 1.098050 GCGTGGATCAAGGCTTCATT 58.902 50.000 7.55 0.00 0.00 2.57
5 6 1.091771 CGCGTGGATCAAGGCTTCAT 61.092 55.000 12.73 0.00 0.00 2.57
6 7 1.741401 CGCGTGGATCAAGGCTTCA 60.741 57.895 12.73 0.00 0.00 3.02
7 8 1.424493 CTCGCGTGGATCAAGGCTTC 61.424 60.000 12.73 0.00 0.00 3.86
8 9 1.448540 CTCGCGTGGATCAAGGCTT 60.449 57.895 12.73 0.00 0.00 4.35
9 10 2.185350 CTCGCGTGGATCAAGGCT 59.815 61.111 12.73 0.00 0.00 4.58
10 11 2.892425 CCTCGCGTGGATCAAGGC 60.892 66.667 22.35 4.61 0.00 4.35
11 12 2.892425 GCCTCGCGTGGATCAAGG 60.892 66.667 30.07 16.88 0.00 3.61
12 13 1.493950 GATGCCTCGCGTGGATCAAG 61.494 60.000 30.07 6.57 0.00 3.02
15 16 0.882042 ATTGATGCCTCGCGTGGATC 60.882 55.000 30.07 25.09 0.00 3.36
16 17 0.882042 GATTGATGCCTCGCGTGGAT 60.882 55.000 30.07 19.13 0.00 3.41
18 19 1.368345 TTGATTGATGCCTCGCGTGG 61.368 55.000 22.48 22.48 0.00 4.94
19 20 0.027194 CTTGATTGATGCCTCGCGTG 59.973 55.000 5.77 2.75 0.00 5.34
20 21 0.391661 ACTTGATTGATGCCTCGCGT 60.392 50.000 5.77 0.00 0.00 6.01
21 22 1.258982 GTACTTGATTGATGCCTCGCG 59.741 52.381 0.00 0.00 0.00 5.87
22 23 2.279741 TGTACTTGATTGATGCCTCGC 58.720 47.619 0.00 0.00 0.00 5.03
23 24 3.935203 AGTTGTACTTGATTGATGCCTCG 59.065 43.478 0.00 0.00 0.00 4.63
24 25 4.333926 GGAGTTGTACTTGATTGATGCCTC 59.666 45.833 0.00 0.00 0.00 4.70
25 26 4.263462 TGGAGTTGTACTTGATTGATGCCT 60.263 41.667 0.00 0.00 0.00 4.75
26 27 4.009675 TGGAGTTGTACTTGATTGATGCC 58.990 43.478 0.00 0.00 0.00 4.40
27 28 5.124457 ACATGGAGTTGTACTTGATTGATGC 59.876 40.000 0.00 0.00 0.00 3.91
28 29 6.549061 CACATGGAGTTGTACTTGATTGATG 58.451 40.000 0.00 0.00 0.00 3.07
29 30 5.124457 GCACATGGAGTTGTACTTGATTGAT 59.876 40.000 0.00 0.00 0.00 2.57
30 31 4.455533 GCACATGGAGTTGTACTTGATTGA 59.544 41.667 0.00 0.00 0.00 2.57
31 32 4.216042 TGCACATGGAGTTGTACTTGATTG 59.784 41.667 0.00 0.00 0.00 2.67
32 33 4.397420 TGCACATGGAGTTGTACTTGATT 58.603 39.130 0.00 0.00 0.00 2.57
33 34 4.019792 TGCACATGGAGTTGTACTTGAT 57.980 40.909 0.00 0.00 0.00 2.57
34 35 3.483808 TGCACATGGAGTTGTACTTGA 57.516 42.857 0.00 0.00 0.00 3.02
35 36 4.771590 ATTGCACATGGAGTTGTACTTG 57.228 40.909 0.00 0.00 0.00 3.16
36 37 6.892658 TTAATTGCACATGGAGTTGTACTT 57.107 33.333 0.00 0.00 0.00 2.24
37 38 6.658816 TGATTAATTGCACATGGAGTTGTACT 59.341 34.615 0.00 0.00 0.00 2.73
38 39 6.851609 TGATTAATTGCACATGGAGTTGTAC 58.148 36.000 0.00 0.00 0.00 2.90
39 40 7.643569 ATGATTAATTGCACATGGAGTTGTA 57.356 32.000 0.00 0.00 0.00 2.41
40 41 5.981088 TGATTAATTGCACATGGAGTTGT 57.019 34.783 0.00 0.00 0.00 3.32
41 42 7.597369 CCATATGATTAATTGCACATGGAGTTG 59.403 37.037 8.18 0.00 34.84 3.16
42 43 7.506599 TCCATATGATTAATTGCACATGGAGTT 59.493 33.333 11.32 0.00 36.62 3.01
43 44 7.005902 TCCATATGATTAATTGCACATGGAGT 58.994 34.615 11.32 0.00 36.62 3.85
44 45 7.457024 TCCATATGATTAATTGCACATGGAG 57.543 36.000 11.32 0.00 36.62 3.86
45 46 7.506599 ACTTCCATATGATTAATTGCACATGGA 59.493 33.333 11.32 11.32 39.06 3.41
46 47 7.597369 CACTTCCATATGATTAATTGCACATGG 59.403 37.037 3.65 7.74 34.32 3.66
47 48 8.354426 TCACTTCCATATGATTAATTGCACATG 58.646 33.333 3.65 0.00 0.00 3.21
48 49 8.467963 TCACTTCCATATGATTAATTGCACAT 57.532 30.769 3.65 0.00 0.00 3.21
49 50 7.878547 TCACTTCCATATGATTAATTGCACA 57.121 32.000 3.65 0.00 0.00 4.57
50 51 7.864379 CCTTCACTTCCATATGATTAATTGCAC 59.136 37.037 3.65 0.00 0.00 4.57
51 52 7.779326 TCCTTCACTTCCATATGATTAATTGCA 59.221 33.333 3.65 0.00 0.00 4.08
52 53 8.169977 TCCTTCACTTCCATATGATTAATTGC 57.830 34.615 3.65 0.00 0.00 3.56
53 54 8.790718 CCTCCTTCACTTCCATATGATTAATTG 58.209 37.037 3.65 1.09 0.00 2.32
54 55 7.946776 CCCTCCTTCACTTCCATATGATTAATT 59.053 37.037 3.65 0.00 0.00 1.40
55 56 7.295672 TCCCTCCTTCACTTCCATATGATTAAT 59.704 37.037 3.65 0.00 0.00 1.40
98 99 9.117183 GAAGAAACTCAAGGAAAGTTACCTAAA 57.883 33.333 0.00 0.00 35.96 1.85
105 106 7.410120 AACATGAAGAAACTCAAGGAAAGTT 57.590 32.000 0.00 0.00 38.59 2.66
114 115 7.987458 GTGGATCCTATAACATGAAGAAACTCA 59.013 37.037 14.23 0.00 0.00 3.41
115 116 8.207545 AGTGGATCCTATAACATGAAGAAACTC 58.792 37.037 14.23 0.00 0.00 3.01
116 117 8.095452 AGTGGATCCTATAACATGAAGAAACT 57.905 34.615 14.23 0.00 0.00 2.66
117 118 8.738645 AAGTGGATCCTATAACATGAAGAAAC 57.261 34.615 14.23 0.00 0.00 2.78
118 119 7.993183 GGAAGTGGATCCTATAACATGAAGAAA 59.007 37.037 14.23 0.00 36.50 2.52
119 120 7.420214 GGGAAGTGGATCCTATAACATGAAGAA 60.420 40.741 14.23 0.00 39.57 2.52
127 128 4.658901 TCCTTGGGAAGTGGATCCTATAAC 59.341 45.833 14.23 2.19 39.57 1.89
131 132 2.317900 TCTCCTTGGGAAGTGGATCCTA 59.682 50.000 14.23 0.00 39.57 2.94
149 150 1.995646 GCCCGAGTCGTCTCCTTCTC 61.996 65.000 12.31 0.00 37.40 2.87
156 157 0.179026 TATAGCAGCCCGAGTCGTCT 60.179 55.000 12.31 5.26 0.00 4.18
160 161 7.097834 AGTTTTATAATATAGCAGCCCGAGTC 58.902 38.462 0.00 0.00 0.00 3.36
203 204 3.117701 TGACCAGTCAAAATCCCAGTCAA 60.118 43.478 0.00 0.00 36.53 3.18
232 233 4.567959 GGCTGATTTTTGACATGTATTGGC 59.432 41.667 0.00 0.00 0.00 4.52
250 252 2.990740 AAATAACAACCCTGGGCTGA 57.009 45.000 22.54 1.37 0.00 4.26
256 258 6.043411 TCAAAACCGAAAAATAACAACCCTG 58.957 36.000 0.00 0.00 0.00 4.45
359 361 7.923414 TTGGGAGCTTAAAAATAGAGAAGTC 57.077 36.000 0.00 0.00 0.00 3.01
360 362 8.706322 TTTTGGGAGCTTAAAAATAGAGAAGT 57.294 30.769 0.00 0.00 0.00 3.01
400 404 5.991933 ATCACTCGATGAGGTATTGCTAT 57.008 39.130 0.00 0.00 41.91 2.97
402 406 4.021894 GGTATCACTCGATGAGGTATTGCT 60.022 45.833 0.00 0.00 41.91 3.91
403 407 4.021894 AGGTATCACTCGATGAGGTATTGC 60.022 45.833 0.00 0.00 41.91 3.56
404 408 5.475220 AGAGGTATCACTCGATGAGGTATTG 59.525 44.000 0.00 0.00 41.91 1.90
405 409 5.636123 AGAGGTATCACTCGATGAGGTATT 58.364 41.667 0.00 0.00 41.91 1.89
406 410 5.249780 AGAGGTATCACTCGATGAGGTAT 57.750 43.478 0.00 0.00 41.91 2.73
407 411 4.708576 AGAGGTATCACTCGATGAGGTA 57.291 45.455 0.00 0.00 41.91 3.08
408 412 3.586470 AGAGGTATCACTCGATGAGGT 57.414 47.619 0.00 0.00 41.91 3.85
409 413 3.438781 GCTAGAGGTATCACTCGATGAGG 59.561 52.174 0.00 0.00 41.91 3.86
410 414 4.068599 TGCTAGAGGTATCACTCGATGAG 58.931 47.826 0.00 0.00 41.91 2.90
411 415 4.068599 CTGCTAGAGGTATCACTCGATGA 58.931 47.826 0.00 0.00 42.31 2.92
412 416 4.068599 TCTGCTAGAGGTATCACTCGATG 58.931 47.826 0.00 0.00 42.31 3.84
413 417 4.359434 TCTGCTAGAGGTATCACTCGAT 57.641 45.455 0.00 0.00 42.31 3.59
414 418 3.840124 TCTGCTAGAGGTATCACTCGA 57.160 47.619 0.00 0.00 42.31 4.04
415 419 3.303461 CGTTCTGCTAGAGGTATCACTCG 60.303 52.174 0.00 0.00 42.31 4.18
416 420 3.878103 TCGTTCTGCTAGAGGTATCACTC 59.122 47.826 0.00 0.00 37.77 3.51
448 452 5.961396 TGTTCTAGTCTGTACACTCTTCC 57.039 43.478 0.00 0.00 0.00 3.46
474 478 4.751767 ACCTTGATGAACCATCTCTCTC 57.248 45.455 8.22 0.00 41.06 3.20
479 483 5.488919 TCCTTCTAACCTTGATGAACCATCT 59.511 40.000 8.22 0.00 41.06 2.90
493 497 8.519799 TCCATGTGATATTTTTCCTTCTAACC 57.480 34.615 0.00 0.00 0.00 2.85
538 542 0.248134 TTTTCGCGTGGTTTTGACCG 60.248 50.000 5.77 0.00 0.00 4.79
542 546 1.749153 ATCGTTTTCGCGTGGTTTTG 58.251 45.000 5.77 0.00 43.73 2.44
567 571 9.331282 CTATTTTTCAGATTCTCCCGAAACTAT 57.669 33.333 0.00 0.17 31.87 2.12
568 572 7.769044 CCTATTTTTCAGATTCTCCCGAAACTA 59.231 37.037 0.00 0.00 31.87 2.24
575 579 5.755849 TGTCCCTATTTTTCAGATTCTCCC 58.244 41.667 0.00 0.00 0.00 4.30
582 586 8.158025 TCCTCTTAATGTCCCTATTTTTCAGA 57.842 34.615 0.00 0.00 0.00 3.27
591 595 5.778241 TCGCATTATCCTCTTAATGTCCCTA 59.222 40.000 6.18 0.00 40.27 3.53
592 596 4.593206 TCGCATTATCCTCTTAATGTCCCT 59.407 41.667 6.18 0.00 40.27 4.20
609 613 6.705381 TGTTTCTGAATTTGGAATTTCGCATT 59.295 30.769 0.00 0.00 0.00 3.56
620 624 5.637006 TCCCGTAATGTTTCTGAATTTGG 57.363 39.130 0.00 0.00 0.00 3.28
624 628 5.496556 TCACATCCCGTAATGTTTCTGAAT 58.503 37.500 0.00 0.00 37.78 2.57
626 630 4.503910 CTCACATCCCGTAATGTTTCTGA 58.496 43.478 0.00 0.00 37.78 3.27
639 643 5.643379 TCAATTTTTGTAGCTCACATCCC 57.357 39.130 0.00 0.00 36.90 3.85
652 656 7.350110 ACTATTCGGCACAATTCAATTTTTG 57.650 32.000 0.00 0.00 0.00 2.44
653 657 9.651913 ATTACTATTCGGCACAATTCAATTTTT 57.348 25.926 0.00 0.00 0.00 1.94
660 664 6.037172 AGTGTCATTACTATTCGGCACAATTC 59.963 38.462 0.00 0.00 0.00 2.17
760 764 9.213777 AGATGTTAAGAGGGTGATGTTCTATTA 57.786 33.333 0.00 0.00 0.00 0.98
785 789 9.640974 TTTCAAAAAGTACGAGAAAAATACGAG 57.359 29.630 0.00 0.00 0.00 4.18
897 902 4.946478 ACTGATGCACCTACTCCTTATC 57.054 45.455 0.00 0.00 0.00 1.75
932 937 0.831307 AGGAAAGCGTATCCTGTCCC 59.169 55.000 7.12 0.00 45.60 4.46
1184 1210 0.615331 CTAGCTCCAGTGAGGCCAAA 59.385 55.000 5.01 0.00 39.14 3.28
1203 1229 2.155279 GGAAAGAACAGAAGGGTCAGC 58.845 52.381 0.00 0.00 0.00 4.26
1241 1269 2.494445 CCGTCTCGCCACTGCATA 59.506 61.111 0.00 0.00 37.32 3.14
1299 1327 0.603975 GGAGCAACTGACTCACCACC 60.604 60.000 0.00 0.00 35.79 4.61
1310 1338 0.737715 GAGAACGCATCGGAGCAACT 60.738 55.000 1.23 0.00 0.00 3.16
1324 1352 0.666374 CACCCAACAAACCGGAGAAC 59.334 55.000 9.46 0.00 0.00 3.01
1330 1358 2.025441 CACGCACCCAACAAACCG 59.975 61.111 0.00 0.00 0.00 4.44
1367 1395 2.665185 AACAGACCCAGAACGCGC 60.665 61.111 5.73 0.00 0.00 6.86
1368 1396 1.157870 AACAACAGACCCAGAACGCG 61.158 55.000 3.53 3.53 0.00 6.01
1369 1397 1.021968 AAACAACAGACCCAGAACGC 58.978 50.000 0.00 0.00 0.00 4.84
1370 1398 1.268539 GCAAACAACAGACCCAGAACG 60.269 52.381 0.00 0.00 0.00 3.95
1371 1399 2.024414 AGCAAACAACAGACCCAGAAC 58.976 47.619 0.00 0.00 0.00 3.01
1378 1406 8.129211 AGAATTAAGTACAAGCAAACAACAGAC 58.871 33.333 0.00 0.00 0.00 3.51
1393 1421 9.032420 CCGTCCAGAAAAGATAGAATTAAGTAC 57.968 37.037 0.00 0.00 0.00 2.73
1412 1440 2.241435 TTCCTCCAAGGATCCGTCCAG 61.241 57.143 5.98 0.75 45.34 3.86
1442 1470 7.649973 ACAATACTAGCTAGCATGTACAGTAC 58.350 38.462 20.91 3.49 0.00 2.73
1466 1494 4.507756 GGACAAGAAATGAAGCACCAAAAC 59.492 41.667 0.00 0.00 0.00 2.43
1471 1499 2.229784 CAGGGACAAGAAATGAAGCACC 59.770 50.000 0.00 0.00 0.00 5.01
1475 1503 2.229784 GCACCAGGGACAAGAAATGAAG 59.770 50.000 0.00 0.00 0.00 3.02
1517 1545 5.645067 TGGACATGACAATTTCTAGCTGAAG 59.355 40.000 0.00 0.00 35.89 3.02
1592 1621 5.445964 ACGATAATGGTAGAAGGGCAAAAT 58.554 37.500 0.00 0.00 0.00 1.82
1627 1660 9.064706 AGATCTACCAATCAATCAAAATGCTAG 57.935 33.333 0.00 0.00 0.00 3.42
1649 1682 4.081420 TCCTCAACAACCTGCTAGAAGATC 60.081 45.833 0.00 0.00 0.00 2.75
1896 2027 2.031465 CGTACCTGGGGTTGCGTT 59.969 61.111 0.00 0.00 37.09 4.84
1973 2104 1.897802 AGGACCGTACCAACCTAAGTG 59.102 52.381 0.00 0.00 0.00 3.16
2114 2247 3.347216 GCAGACTATGGGAAACATGTGT 58.653 45.455 0.00 0.00 40.82 3.72
2144 2277 7.155328 GGAATGTCCCTAGTGATGTGTATAAG 58.845 42.308 0.00 0.00 0.00 1.73
2600 2843 6.715264 AGGGTTACAAGTCATGAAACCTTAAG 59.285 38.462 20.41 0.00 34.54 1.85
2621 2864 4.129317 ACTGTAACTACAAGAGGAGGGT 57.871 45.455 0.00 0.00 35.50 4.34
2639 2882 7.040132 TGGTAATGCTCTGATCTATGTCTACTG 60.040 40.741 0.00 0.00 0.00 2.74
2714 3050 7.656707 ACACAATAAAAATGATTGCAGGAAC 57.343 32.000 0.00 0.00 37.74 3.62
2732 3068 9.638239 GACACATTTTGGTGATTAATACACAAT 57.362 29.630 15.37 6.60 41.32 2.71
2737 3073 7.273381 GCAGTGACACATTTTGGTGATTAATAC 59.727 37.037 8.59 0.00 41.32 1.89
2740 3076 5.068329 TGCAGTGACACATTTTGGTGATTAA 59.932 36.000 8.59 0.00 41.32 1.40
2744 3080 2.373224 TGCAGTGACACATTTTGGTGA 58.627 42.857 8.59 0.00 41.32 4.02
2745 3081 2.867287 TGCAGTGACACATTTTGGTG 57.133 45.000 8.59 0.00 44.35 4.17
2762 3098 8.180920 ACCAAAACAGTTTTCATTACAAAATGC 58.819 29.630 8.40 0.00 41.96 3.56
2777 3113 6.048732 ACAGAATGGAAAACCAAAACAGTT 57.951 33.333 0.00 0.00 43.62 3.16
2779 3115 6.983474 AAACAGAATGGAAAACCAAAACAG 57.017 33.333 0.00 0.00 43.62 3.16
2783 3120 7.382898 GCCTATAAACAGAATGGAAAACCAAA 58.617 34.615 0.00 0.00 43.62 3.28
2786 3123 5.124936 ACGCCTATAAACAGAATGGAAAACC 59.875 40.000 0.00 0.00 43.62 3.27
2794 3131 5.105310 AGTGTCAGACGCCTATAAACAGAAT 60.105 40.000 10.65 0.00 0.00 2.40
2800 3137 2.829720 ACCAGTGTCAGACGCCTATAAA 59.170 45.455 10.65 0.00 0.00 1.40
2809 3146 2.354821 GACAAACCAACCAGTGTCAGAC 59.645 50.000 0.00 0.00 40.10 3.51
2819 3157 3.487120 AGTAGACCAGACAAACCAACC 57.513 47.619 0.00 0.00 0.00 3.77
2821 3159 9.280174 CTAATTAAAGTAGACCAGACAAACCAA 57.720 33.333 0.00 0.00 0.00 3.67
2823 3161 7.881751 ACCTAATTAAAGTAGACCAGACAAACC 59.118 37.037 0.00 0.00 0.00 3.27
2830 3168 8.701895 TGGATACACCTAATTAAAGTAGACCAG 58.298 37.037 0.00 0.00 46.17 4.00
2853 3191 1.073763 CCACCCATCACTGAAACTGGA 59.926 52.381 0.00 0.00 0.00 3.86
2956 3294 4.350225 AGGGACGATGGATACTAGACTACA 59.650 45.833 0.00 0.00 37.61 2.74
2957 3295 4.909001 AGGGACGATGGATACTAGACTAC 58.091 47.826 0.00 0.00 37.61 2.73
2959 3297 5.782677 ATAGGGACGATGGATACTAGACT 57.217 43.478 0.00 0.00 37.61 3.24
2985 3323 8.659491 GGATGATATTTGCAAAAAGAGGAAAAC 58.341 33.333 17.19 1.69 30.18 2.43
3008 3347 5.871396 AGACACCAACAGAATATACGGAT 57.129 39.130 0.00 0.00 0.00 4.18
3016 3355 5.483685 TGCTACTTAGACACCAACAGAAT 57.516 39.130 0.00 0.00 0.00 2.40
3051 3390 7.768582 TGAAAGAGTCTCAGTGTTATGAAACAA 59.231 33.333 1.94 0.00 46.84 2.83
3082 3421 7.959733 TGAATAACTTGCGTAATTACTCTGTG 58.040 34.615 13.56 0.00 0.00 3.66
3115 3454 9.640963 AATAGTTTCATACAGCTAACCGATATC 57.359 33.333 0.00 0.00 0.00 1.63
3135 3474 5.279910 GGCCATAGCATCAGAGAGAATAGTT 60.280 44.000 0.00 0.00 42.56 2.24
3143 3482 1.415289 CAGTGGCCATAGCATCAGAGA 59.585 52.381 9.72 0.00 42.56 3.10
3355 3694 2.607771 CCCGTTTTCTGAACTGCAATGG 60.608 50.000 4.51 4.51 0.00 3.16
3595 3963 0.179176 CGAGCCGACTGAAGAGACAG 60.179 60.000 0.00 0.00 42.78 3.51
3596 3964 1.876664 CGAGCCGACTGAAGAGACA 59.123 57.895 0.00 0.00 0.00 3.41
3601 3969 2.811317 GTGGCGAGCCGACTGAAG 60.811 66.667 9.78 0.00 39.42 3.02
3625 3993 1.264749 AACTAGCCATCTGTCGCCCA 61.265 55.000 0.00 0.00 0.00 5.36
3627 3995 2.202566 GTTAACTAGCCATCTGTCGCC 58.797 52.381 0.00 0.00 0.00 5.54
3628 3996 2.888594 TGTTAACTAGCCATCTGTCGC 58.111 47.619 7.22 0.00 0.00 5.19
3659 4457 5.181748 AGTAGCAGTTGAATGAGATTGGAC 58.818 41.667 0.00 0.00 0.00 4.02
3680 4623 1.692519 GTGGACTTGTGGAGTGGTAGT 59.307 52.381 0.00 0.00 39.19 2.73
3725 4671 4.966805 AGCTGGGTACTTACTAGGCATAAA 59.033 41.667 0.00 0.00 0.00 1.40
3731 4677 3.028094 TGGAGCTGGGTACTTACTAGG 57.972 52.381 0.00 0.00 0.00 3.02
3735 4681 2.302157 AGTGTTGGAGCTGGGTACTTAC 59.698 50.000 0.00 0.00 0.00 2.34
3737 4683 1.435256 AGTGTTGGAGCTGGGTACTT 58.565 50.000 0.00 0.00 0.00 2.24
3741 4691 1.900486 GTAGTAGTGTTGGAGCTGGGT 59.100 52.381 0.00 0.00 0.00 4.51
3795 4755 3.777925 CGTAGCCGTGCACTGTGC 61.778 66.667 25.15 25.15 45.29 4.57
3796 4756 3.112075 CCGTAGCCGTGCACTGTG 61.112 66.667 16.19 2.76 0.00 3.66
3797 4757 4.373116 CCCGTAGCCGTGCACTGT 62.373 66.667 16.19 1.28 0.00 3.55
3854 4818 0.877649 CGATCACGCTATGCAGCCTT 60.878 55.000 0.00 0.00 45.64 4.35
3876 5456 2.262603 CGCCACTGCTGCTCTGTA 59.737 61.111 0.00 0.00 34.43 2.74
3898 5478 3.879682 CCGGACATGGCATGCGTG 61.880 66.667 26.70 15.28 0.00 5.34
3906 5486 3.976701 GAGTGGGTGCCGGACATGG 62.977 68.421 5.05 0.00 0.00 3.66
3907 5487 2.436646 GAGTGGGTGCCGGACATG 60.437 66.667 5.05 0.00 0.00 3.21
3908 5488 2.607750 AGAGTGGGTGCCGGACAT 60.608 61.111 5.05 0.00 0.00 3.06
3909 5489 3.625897 CAGAGTGGGTGCCGGACA 61.626 66.667 5.05 0.00 0.00 4.02
3910 5490 2.227089 CTACAGAGTGGGTGCCGGAC 62.227 65.000 5.05 0.00 0.00 4.79
3911 5491 1.982395 CTACAGAGTGGGTGCCGGA 60.982 63.158 5.05 0.00 0.00 5.14
3912 5492 1.982395 TCTACAGAGTGGGTGCCGG 60.982 63.158 0.00 0.00 0.00 6.13
3913 5493 1.215647 GTCTACAGAGTGGGTGCCG 59.784 63.158 0.00 0.00 0.00 5.69
3914 5494 0.247736 CTGTCTACAGAGTGGGTGCC 59.752 60.000 3.99 0.00 46.59 5.01
3915 5495 3.822607 CTGTCTACAGAGTGGGTGC 57.177 57.895 3.99 0.00 46.59 5.01
3924 5504 3.698539 TCCTTCTGCATCTCTGTCTACAG 59.301 47.826 3.64 3.64 45.08 2.74
3925 5505 3.698539 CTCCTTCTGCATCTCTGTCTACA 59.301 47.826 0.00 0.00 0.00 2.74
3926 5506 3.490761 GCTCCTTCTGCATCTCTGTCTAC 60.491 52.174 0.00 0.00 0.00 2.59
3927 5507 2.692557 GCTCCTTCTGCATCTCTGTCTA 59.307 50.000 0.00 0.00 0.00 2.59
3928 5508 1.481772 GCTCCTTCTGCATCTCTGTCT 59.518 52.381 0.00 0.00 0.00 3.41
3929 5509 1.206610 TGCTCCTTCTGCATCTCTGTC 59.793 52.381 0.00 0.00 35.31 3.51
3930 5510 1.207570 CTGCTCCTTCTGCATCTCTGT 59.792 52.381 0.00 0.00 39.86 3.41
3931 5511 1.942677 CTGCTCCTTCTGCATCTCTG 58.057 55.000 0.00 0.00 39.86 3.35
3932 5512 0.178533 GCTGCTCCTTCTGCATCTCT 59.821 55.000 0.00 0.00 39.86 3.10
3933 5513 1.152989 CGCTGCTCCTTCTGCATCTC 61.153 60.000 0.00 0.00 39.86 2.75
3934 5514 1.153409 CGCTGCTCCTTCTGCATCT 60.153 57.895 0.00 0.00 39.86 2.90
3935 5515 2.178890 CCGCTGCTCCTTCTGCATC 61.179 63.158 0.00 0.00 39.86 3.91
3936 5516 2.124819 CCGCTGCTCCTTCTGCAT 60.125 61.111 0.00 0.00 39.86 3.96
3939 5519 2.818714 CTGCCGCTGCTCCTTCTG 60.819 66.667 0.70 0.00 38.71 3.02
3940 5520 4.774503 GCTGCCGCTGCTCCTTCT 62.775 66.667 14.47 0.00 38.71 2.85
3958 5538 3.567478 TACGACTGCTGCCACGTGG 62.567 63.158 30.66 30.66 39.28 4.94
3959 5539 1.014044 ATTACGACTGCTGCCACGTG 61.014 55.000 19.78 9.08 39.28 4.49
3960 5540 0.320421 AATTACGACTGCTGCCACGT 60.320 50.000 16.60 16.60 41.66 4.49
3961 5541 0.095245 CAATTACGACTGCTGCCACG 59.905 55.000 0.00 2.92 0.00 4.94
3962 5542 0.179189 GCAATTACGACTGCTGCCAC 60.179 55.000 0.00 0.00 35.62 5.01
3963 5543 2.170738 GCAATTACGACTGCTGCCA 58.829 52.632 0.00 0.00 35.62 4.92
3964 5544 1.429423 GGCAATTACGACTGCTGCC 59.571 57.895 0.00 0.00 45.27 4.85
4011 5682 0.034059 AGGCTGTCCAACAACTCGAG 59.966 55.000 11.84 11.84 33.74 4.04
4077 5846 5.044624 TCTGAATTTCCTGATTGATCCTGGT 60.045 40.000 0.00 0.00 0.00 4.00
4078 5847 5.443283 TCTGAATTTCCTGATTGATCCTGG 58.557 41.667 0.00 0.00 0.00 4.45
4079 5848 7.068348 ACAATCTGAATTTCCTGATTGATCCTG 59.932 37.037 28.89 15.28 46.42 3.86
4080 5849 7.124052 ACAATCTGAATTTCCTGATTGATCCT 58.876 34.615 28.89 15.79 46.42 3.24
4081 5850 7.344095 ACAATCTGAATTTCCTGATTGATCC 57.656 36.000 28.89 0.00 46.42 3.36
4082 5851 9.298774 GAAACAATCTGAATTTCCTGATTGATC 57.701 33.333 28.89 24.00 46.42 2.92
4083 5852 8.809066 TGAAACAATCTGAATTTCCTGATTGAT 58.191 29.630 28.89 21.67 46.42 2.57
4084 5853 8.180706 TGAAACAATCTGAATTTCCTGATTGA 57.819 30.769 28.89 15.79 46.42 2.57
4164 6087 3.039988 CTGCTGCTGCTGCACTTT 58.960 55.556 27.01 0.00 45.31 2.66
4186 6121 1.000521 CCATCTTGAGCCTTGCCCA 60.001 57.895 0.00 0.00 0.00 5.36
4214 6160 3.654414 GAACAGAGACAACGACAAGGAT 58.346 45.455 0.00 0.00 0.00 3.24
4223 6170 1.261619 CTTGTGCCGAACAGAGACAAC 59.738 52.381 0.00 0.00 40.74 3.32
4225 6172 0.464036 ACTTGTGCCGAACAGAGACA 59.536 50.000 0.00 0.00 40.74 3.41
4226 6173 1.527311 GAACTTGTGCCGAACAGAGAC 59.473 52.381 0.00 0.00 40.74 3.36
4375 6328 5.753744 TGTTTATACCTGAAACTGCAAACG 58.246 37.500 0.00 0.00 37.62 3.60
4428 6382 8.126700 AGAAACGACGAACATTTTGAAATACTT 58.873 29.630 0.00 0.00 0.00 2.24
4467 6421 7.425606 ACACAAGGTCTTTTGAAATACATGAC 58.574 34.615 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.