Multiple sequence alignment - TraesCS3A01G059300

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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 TraesCS3A01G059300 chr3A 100.000 3407 0 0 1 3407 35767589 35770995 0.000000e+00 6292.0
1 TraesCS3A01G059300 chr3A 89.677 1608 120 20 857 2437 35755170 35753582 0.000000e+00 2008.0
2 TraesCS3A01G059300 chr3A 92.259 633 40 5 2782 3407 35753214 35752584 0.000000e+00 889.0
3 TraesCS3A01G059300 chr3A 95.833 96 4 0 674 769 35755534 35755439 4.550000e-34 156.0
4 TraesCS3A01G059300 chr3A 95.455 88 4 0 449 536 303756792 303756879 1.270000e-29 141.0
5 TraesCS3A01G059300 chr3B 94.624 1953 74 11 853 2779 43192913 43190966 0.000000e+00 2996.0
6 TraesCS3A01G059300 chr3B 88.150 1941 159 32 853 2775 43312802 43314689 0.000000e+00 2244.0
7 TraesCS3A01G059300 chr3B 88.833 1791 162 24 981 2740 74176679 74178462 0.000000e+00 2165.0
8 TraesCS3A01G059300 chr3B 92.857 602 41 2 2784 3385 74178526 74179125 0.000000e+00 872.0
9 TraesCS3A01G059300 chr3B 91.601 631 45 6 970 1596 74173598 74174224 0.000000e+00 865.0
10 TraesCS3A01G059300 chr3B 83.099 568 79 11 2779 3333 43314752 43315315 5.080000e-138 501.0
11 TraesCS3A01G059300 chr3B 78.814 590 83 25 2782 3336 43190804 43190222 3.230000e-95 359.0
12 TraesCS3A01G059300 chr3B 94.853 136 7 0 853 988 74176470 74176605 2.660000e-51 213.0
13 TraesCS3A01G059300 chr3B 89.231 130 6 1 677 798 43193247 43193118 4.550000e-34 156.0
14 TraesCS3A01G059300 chr3B 95.833 96 4 0 674 769 43312416 43312511 4.550000e-34 156.0
15 TraesCS3A01G059300 chr3B 88.732 71 8 0 824 894 74173448 74173518 1.680000e-13 87.9
16 TraesCS3A01G059300 chr3D 88.745 1928 173 19 827 2719 26019831 26017913 0.000000e+00 2318.0
17 TraesCS3A01G059300 chr3D 87.081 1997 160 35 824 2775 26073171 26075114 0.000000e+00 2169.0
18 TraesCS3A01G059300 chr3D 90.613 1566 139 6 1161 2719 25987839 25986275 0.000000e+00 2071.0
19 TraesCS3A01G059300 chr3D 87.513 929 97 12 1855 2779 25984954 25984041 0.000000e+00 1055.0
20 TraesCS3A01G059300 chr3D 91.499 647 37 7 2779 3407 25983980 25983334 0.000000e+00 874.0
21 TraesCS3A01G059300 chr3D 90.253 554 48 5 2782 3334 26017811 26017263 0.000000e+00 719.0
22 TraesCS3A01G059300 chr3D 89.892 554 50 5 2782 3334 25986173 25985625 0.000000e+00 708.0
23 TraesCS3A01G059300 chr3D 84.228 596 71 13 2779 3358 26075177 26075765 2.970000e-155 558.0
24 TraesCS3A01G059300 chr3D 83.444 302 12 6 535 798 26020300 26019999 2.630000e-61 246.0
25 TraesCS3A01G059300 chr3D 87.838 148 10 5 970 1113 25987991 25987848 2.100000e-37 167.0
26 TraesCS3A01G059300 chr3D 88.636 132 5 3 857 988 25988131 25988010 5.890000e-33 152.0
27 TraesCS3A01G059300 chrUn 90.253 554 48 5 2782 3334 321664859 321664311 0.000000e+00 719.0
28 TraesCS3A01G059300 chrUn 90.664 482 42 2 2241 2719 321665442 321664961 3.710000e-179 638.0
29 TraesCS3A01G059300 chr4A 94.101 356 18 2 1 354 23992165 23991811 3.870000e-149 538.0
30 TraesCS3A01G059300 chr4A 95.294 85 4 0 449 533 82849186 82849270 5.930000e-28 135.0
31 TraesCS3A01G059300 chr6A 93.220 354 23 1 1 354 536569700 536569348 1.400000e-143 520.0
32 TraesCS3A01G059300 chr4D 89.577 355 29 4 1 354 168077989 168078336 8.680000e-121 444.0
33 TraesCS3A01G059300 chr1B 96.386 83 3 0 452 534 662158860 662158778 1.650000e-28 137.0
34 TraesCS3A01G059300 chr1B 96.386 83 3 0 452 534 662161413 662161331 1.650000e-28 137.0
35 TraesCS3A01G059300 chr2A 91.753 97 7 1 446 541 690329424 690329328 2.130000e-27 134.0
36 TraesCS3A01G059300 chr2A 95.122 82 4 0 452 533 636911536 636911455 2.760000e-26 130.0
37 TraesCS3A01G059300 chr2A 91.304 92 8 0 448 539 31043404 31043313 3.570000e-25 126.0
38 TraesCS3A01G059300 chr1A 94.186 86 5 0 448 533 511001509 511001594 7.670000e-27 132.0
39 TraesCS3A01G059300 chr5D 95.122 82 4 0 452 533 231356358 231356277 2.760000e-26 130.0
40 TraesCS3A01G059300 chr5B 92.593 81 6 0 717 797 479722007 479721927 2.150000e-22 117.0


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 TraesCS3A01G059300 chr3A 35767589 35770995 3406 False 6292.000000 6292 100.000000 1 3407 1 chr3A.!!$F1 3406
1 TraesCS3A01G059300 chr3A 35752584 35755534 2950 True 1017.666667 2008 92.589667 674 3407 3 chr3A.!!$R1 2733
2 TraesCS3A01G059300 chr3B 43190222 43193247 3025 True 1170.333333 2996 87.556333 677 3336 3 chr3B.!!$R1 2659
3 TraesCS3A01G059300 chr3B 43312416 43315315 2899 False 967.000000 2244 89.027333 674 3333 3 chr3B.!!$F1 2659
4 TraesCS3A01G059300 chr3B 74173448 74179125 5677 False 840.580000 2165 91.375200 824 3385 5 chr3B.!!$F2 2561
5 TraesCS3A01G059300 chr3D 26073171 26075765 2594 False 1363.500000 2169 85.654500 824 3358 2 chr3D.!!$F1 2534
6 TraesCS3A01G059300 chr3D 26017263 26020300 3037 True 1094.333333 2318 87.480667 535 3334 3 chr3D.!!$R2 2799
7 TraesCS3A01G059300 chr3D 25983334 25988131 4797 True 837.833333 2071 89.331833 857 3407 6 chr3D.!!$R1 2550
8 TraesCS3A01G059300 chrUn 321664311 321665442 1131 True 678.500000 719 90.458500 2241 3334 2 chrUn.!!$R1 1093

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
820 867 0.042731 ATTCTCTCCTTGGGTCCGGA 59.957 55.0 0.00 0.0 0.0 5.14 F
821 868 0.042731 TTCTCTCCTTGGGTCCGGAT 59.957 55.0 7.81 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 4732 1.337703 TCACAGTTGTTGGCTCATTGC 59.662 47.619 0.0 0.0 41.94 3.56 R
2520 4866 5.049167 GCACAAAAGGATGTTGATGTTCAA 58.951 37.500 0.0 0.0 34.38 2.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.344763 AGGACATGTATAAGGAGGCGC 59.655 52.381 0.00 0.00 0.00 6.53
21 22 1.344763 GGACATGTATAAGGAGGCGCT 59.655 52.381 7.64 0.00 0.00 5.92
22 23 2.408050 GACATGTATAAGGAGGCGCTG 58.592 52.381 7.64 0.00 0.00 5.18
25 26 1.717032 TGTATAAGGAGGCGCTGGAT 58.283 50.000 7.64 0.00 0.00 3.41
26 27 1.344438 TGTATAAGGAGGCGCTGGATG 59.656 52.381 7.64 0.00 0.00 3.51
27 28 1.344763 GTATAAGGAGGCGCTGGATGT 59.655 52.381 7.64 0.00 0.00 3.06
28 29 0.107456 ATAAGGAGGCGCTGGATGTG 59.893 55.000 7.64 0.00 0.00 3.21
31 32 2.401766 GGAGGCGCTGGATGTGTTG 61.402 63.158 7.64 0.00 0.00 3.33
32 33 1.375908 GAGGCGCTGGATGTGTTGA 60.376 57.895 7.64 0.00 0.00 3.18
34 35 1.028330 AGGCGCTGGATGTGTTGATG 61.028 55.000 7.64 0.00 0.00 3.07
35 36 1.430632 GCGCTGGATGTGTTGATGG 59.569 57.895 0.00 0.00 0.00 3.51
36 37 1.308069 GCGCTGGATGTGTTGATGGT 61.308 55.000 0.00 0.00 0.00 3.55
37 38 0.448990 CGCTGGATGTGTTGATGGTG 59.551 55.000 0.00 0.00 0.00 4.17
38 39 0.813184 GCTGGATGTGTTGATGGTGG 59.187 55.000 0.00 0.00 0.00 4.61
39 40 0.813184 CTGGATGTGTTGATGGTGGC 59.187 55.000 0.00 0.00 0.00 5.01
40 41 0.405198 TGGATGTGTTGATGGTGGCT 59.595 50.000 0.00 0.00 0.00 4.75
41 42 0.813184 GGATGTGTTGATGGTGGCTG 59.187 55.000 0.00 0.00 0.00 4.85
42 43 1.614051 GGATGTGTTGATGGTGGCTGA 60.614 52.381 0.00 0.00 0.00 4.26
43 44 1.741706 GATGTGTTGATGGTGGCTGAG 59.258 52.381 0.00 0.00 0.00 3.35
45 46 0.250901 GTGTTGATGGTGGCTGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
48 49 2.292267 GTTGATGGTGGCTGAGGTATG 58.708 52.381 0.00 0.00 0.00 2.39
50 51 0.181114 GATGGTGGCTGAGGTATGCA 59.819 55.000 0.00 0.00 0.00 3.96
51 52 0.625316 ATGGTGGCTGAGGTATGCAA 59.375 50.000 0.00 0.00 0.00 4.08
52 53 0.322456 TGGTGGCTGAGGTATGCAAC 60.322 55.000 0.00 0.00 32.67 4.17
64 65 3.609853 GGTATGCAACCTTCTGTGATCA 58.390 45.455 9.89 0.00 45.75 2.92
65 66 4.202441 GGTATGCAACCTTCTGTGATCAT 58.798 43.478 0.00 0.00 45.75 2.45
66 67 4.641989 GGTATGCAACCTTCTGTGATCATT 59.358 41.667 0.00 0.00 45.75 2.57
67 68 4.713824 ATGCAACCTTCTGTGATCATTG 57.286 40.909 0.00 0.00 0.00 2.82
68 69 3.489355 TGCAACCTTCTGTGATCATTGT 58.511 40.909 0.00 0.00 0.00 2.71
69 70 3.890756 TGCAACCTTCTGTGATCATTGTT 59.109 39.130 0.00 0.00 0.00 2.83
71 72 4.261741 GCAACCTTCTGTGATCATTGTTGT 60.262 41.667 0.00 0.00 35.49 3.32
73 74 4.717877 ACCTTCTGTGATCATTGTTGTCA 58.282 39.130 0.00 0.00 0.00 3.58
74 75 5.319453 ACCTTCTGTGATCATTGTTGTCAT 58.681 37.500 0.00 0.00 0.00 3.06
76 77 6.372659 ACCTTCTGTGATCATTGTTGTCATAC 59.627 38.462 0.00 0.00 0.00 2.39
77 78 6.596888 CCTTCTGTGATCATTGTTGTCATACT 59.403 38.462 0.00 0.00 0.00 2.12
78 79 6.973229 TCTGTGATCATTGTTGTCATACTG 57.027 37.500 0.00 0.00 0.00 2.74
79 80 6.466812 TCTGTGATCATTGTTGTCATACTGT 58.533 36.000 0.00 0.00 0.00 3.55
80 81 7.610865 TCTGTGATCATTGTTGTCATACTGTA 58.389 34.615 0.00 0.00 0.00 2.74
81 82 8.093927 TCTGTGATCATTGTTGTCATACTGTAA 58.906 33.333 0.00 0.00 0.00 2.41
82 83 8.614469 TGTGATCATTGTTGTCATACTGTAAA 57.386 30.769 0.00 0.00 0.00 2.01
86 87 8.970691 ATCATTGTTGTCATACTGTAAAAAGC 57.029 30.769 0.00 0.00 0.00 3.51
89 90 9.838975 CATTGTTGTCATACTGTAAAAAGCATA 57.161 29.630 0.00 0.00 0.00 3.14
136 137 7.775397 AGTGATGAAAAACAAAAATGTGAGG 57.225 32.000 0.00 0.00 0.00 3.86
138 139 7.823799 AGTGATGAAAAACAAAAATGTGAGGTT 59.176 29.630 0.00 0.00 0.00 3.50
139 140 8.450180 GTGATGAAAAACAAAAATGTGAGGTTT 58.550 29.630 0.00 0.00 33.45 3.27
140 141 8.449397 TGATGAAAAACAAAAATGTGAGGTTTG 58.551 29.630 0.00 0.00 38.06 2.93
142 143 8.833231 TGAAAAACAAAAATGTGAGGTTTGTA 57.167 26.923 1.78 0.00 42.96 2.41
143 144 9.273016 TGAAAAACAAAAATGTGAGGTTTGTAA 57.727 25.926 1.78 0.00 42.96 2.41
144 145 9.753669 GAAAAACAAAAATGTGAGGTTTGTAAG 57.246 29.630 1.78 0.00 42.96 2.34
147 148 8.840833 AACAAAAATGTGAGGTTTGTAAGTTT 57.159 26.923 1.78 0.00 42.96 2.66
148 149 9.930693 AACAAAAATGTGAGGTTTGTAAGTTTA 57.069 25.926 1.78 0.00 42.96 2.01
149 150 9.581099 ACAAAAATGTGAGGTTTGTAAGTTTAG 57.419 29.630 0.00 0.00 42.20 1.85
150 151 9.796120 CAAAAATGTGAGGTTTGTAAGTTTAGA 57.204 29.630 0.00 0.00 0.00 2.10
264 265 8.674263 TTATTTGATTTTGGATGCACTTGTTT 57.326 26.923 0.00 0.00 0.00 2.83
265 266 6.998968 TTTGATTTTGGATGCACTTGTTTT 57.001 29.167 0.00 0.00 0.00 2.43
266 267 8.674263 ATTTGATTTTGGATGCACTTGTTTTA 57.326 26.923 0.00 0.00 0.00 1.52
267 268 7.475771 TTGATTTTGGATGCACTTGTTTTAC 57.524 32.000 0.00 0.00 0.00 2.01
268 269 6.815089 TGATTTTGGATGCACTTGTTTTACT 58.185 32.000 0.00 0.00 0.00 2.24
269 270 7.946207 TGATTTTGGATGCACTTGTTTTACTA 58.054 30.769 0.00 0.00 0.00 1.82
270 271 8.417106 TGATTTTGGATGCACTTGTTTTACTAA 58.583 29.630 0.00 0.00 0.00 2.24
271 272 9.255304 GATTTTGGATGCACTTGTTTTACTAAA 57.745 29.630 0.00 0.00 0.00 1.85
273 274 9.606631 TTTTGGATGCACTTGTTTTACTAAATT 57.393 25.926 0.00 0.00 0.00 1.82
274 275 9.606631 TTTGGATGCACTTGTTTTACTAAATTT 57.393 25.926 0.00 0.00 0.00 1.82
275 276 9.606631 TTGGATGCACTTGTTTTACTAAATTTT 57.393 25.926 0.00 0.00 0.00 1.82
328 329 1.341187 TGTTTATAACAAGGGGCCCCG 60.341 52.381 35.78 24.53 38.72 5.73
329 330 0.259356 TTTATAACAAGGGGCCCCGG 59.741 55.000 35.78 31.53 41.95 5.73
331 332 0.920271 TATAACAAGGGGCCCCGGTT 60.920 55.000 39.03 39.03 41.95 4.44
332 333 2.219449 ATAACAAGGGGCCCCGGTTC 62.219 60.000 40.46 19.98 41.95 3.62
334 335 3.012722 CAAGGGGCCCCGGTTCTA 61.013 66.667 35.78 0.00 41.95 2.10
335 336 2.691252 AAGGGGCCCCGGTTCTAG 60.691 66.667 35.78 0.00 41.95 2.43
336 337 3.574395 AAGGGGCCCCGGTTCTAGT 62.574 63.158 35.78 12.83 41.95 2.57
339 340 2.433146 GGGCCCCGGTTCTAGTCTC 61.433 68.421 12.23 0.00 0.00 3.36
340 341 2.783288 GGCCCCGGTTCTAGTCTCG 61.783 68.421 0.00 0.00 0.00 4.04
342 343 2.783288 CCCCGGTTCTAGTCTCGCC 61.783 68.421 0.00 0.00 0.00 5.54
343 344 1.753463 CCCGGTTCTAGTCTCGCCT 60.753 63.158 0.00 0.00 0.00 5.52
344 345 1.726533 CCCGGTTCTAGTCTCGCCTC 61.727 65.000 0.00 0.00 0.00 4.70
346 347 1.728672 GGTTCTAGTCTCGCCTCGG 59.271 63.158 0.00 0.00 0.00 4.63
347 348 1.726533 GGTTCTAGTCTCGCCTCGGG 61.727 65.000 0.00 0.00 0.00 5.14
366 367 1.019805 GCCTCAGGCTAACCGTGTTC 61.020 60.000 9.09 0.00 46.69 3.18
367 368 0.608640 CCTCAGGCTAACCGTGTTCT 59.391 55.000 0.00 0.00 42.76 3.01
368 369 1.002087 CCTCAGGCTAACCGTGTTCTT 59.998 52.381 0.00 0.00 42.76 2.52
371 372 0.763035 AGGCTAACCGTGTTCTTGGT 59.237 50.000 0.00 0.00 42.76 3.67
374 375 1.534163 GCTAACCGTGTTCTTGGTTCC 59.466 52.381 0.00 0.00 45.10 3.62
375 376 2.809299 GCTAACCGTGTTCTTGGTTCCT 60.809 50.000 0.00 0.00 45.10 3.36
378 379 0.396811 CCGTGTTCTTGGTTCCTCCT 59.603 55.000 0.00 0.00 37.07 3.69
382 383 0.673956 GTTCTTGGTTCCTCCTCGGC 60.674 60.000 0.00 0.00 37.07 5.54
383 384 0.836400 TTCTTGGTTCCTCCTCGGCT 60.836 55.000 0.00 0.00 37.07 5.52
384 385 1.078848 CTTGGTTCCTCCTCGGCTG 60.079 63.158 0.00 0.00 37.07 4.85
388 389 1.066587 GTTCCTCCTCGGCTGATCG 59.933 63.158 0.00 0.00 0.00 3.69
389 390 1.076995 TTCCTCCTCGGCTGATCGA 60.077 57.895 0.00 0.00 37.60 3.59
390 391 0.683179 TTCCTCCTCGGCTGATCGAA 60.683 55.000 0.00 0.00 38.77 3.71
391 392 1.103987 TCCTCCTCGGCTGATCGAAG 61.104 60.000 0.00 0.00 38.77 3.79
394 395 0.679960 TCCTCGGCTGATCGAAGTGA 60.680 55.000 0.00 0.00 38.77 3.41
395 396 0.526524 CCTCGGCTGATCGAAGTGAC 60.527 60.000 0.00 0.00 38.77 3.67
396 397 0.863538 CTCGGCTGATCGAAGTGACG 60.864 60.000 0.00 4.16 38.77 4.35
397 398 2.508891 CGGCTGATCGAAGTGACGC 61.509 63.158 0.00 0.00 0.00 5.19
398 399 2.508891 GGCTGATCGAAGTGACGCG 61.509 63.158 3.53 3.53 0.00 6.01
399 400 1.801913 GCTGATCGAAGTGACGCGT 60.802 57.895 13.85 13.85 0.00 6.01
400 401 0.522705 GCTGATCGAAGTGACGCGTA 60.523 55.000 13.97 0.00 0.00 4.42
401 402 1.457738 CTGATCGAAGTGACGCGTAG 58.542 55.000 13.97 0.00 0.00 3.51
414 415 3.246064 CGTAGCGTCGGCCAAAAA 58.754 55.556 2.24 0.00 41.24 1.94
415 416 1.791662 CGTAGCGTCGGCCAAAAAT 59.208 52.632 2.24 0.00 41.24 1.82
416 417 1.000884 CGTAGCGTCGGCCAAAAATA 58.999 50.000 2.24 0.00 41.24 1.40
417 418 1.595794 CGTAGCGTCGGCCAAAAATAT 59.404 47.619 2.24 0.00 41.24 1.28
418 419 2.031191 CGTAGCGTCGGCCAAAAATATT 59.969 45.455 2.24 0.00 41.24 1.28
419 420 2.559998 AGCGTCGGCCAAAAATATTG 57.440 45.000 2.24 0.00 41.24 1.90
420 421 2.088423 AGCGTCGGCCAAAAATATTGA 58.912 42.857 2.24 0.00 41.24 2.57
421 422 2.687935 AGCGTCGGCCAAAAATATTGAT 59.312 40.909 2.24 0.00 41.24 2.57
422 423 3.042887 GCGTCGGCCAAAAATATTGATC 58.957 45.455 2.24 0.00 0.00 2.92
423 424 3.488384 GCGTCGGCCAAAAATATTGATCA 60.488 43.478 2.24 0.00 0.00 2.92
424 425 4.792704 GCGTCGGCCAAAAATATTGATCAT 60.793 41.667 2.24 0.00 0.00 2.45
426 427 5.748152 CGTCGGCCAAAAATATTGATCATTT 59.252 36.000 2.24 0.00 0.00 2.32
427 428 6.291743 CGTCGGCCAAAAATATTGATCATTTG 60.292 38.462 2.24 10.47 0.00 2.32
434 435 9.991906 CCAAAAATATTGATCATTTGGCTATCT 57.008 29.630 19.64 0.00 42.31 1.98
444 445 7.498900 TGATCATTTGGCTATCTATTTCGTGTT 59.501 33.333 0.00 0.00 0.00 3.32
446 447 8.050778 TCATTTGGCTATCTATTTCGTGTTTT 57.949 30.769 0.00 0.00 0.00 2.43
447 448 9.168451 TCATTTGGCTATCTATTTCGTGTTTTA 57.832 29.630 0.00 0.00 0.00 1.52
464 465 9.715121 TCGTGTTTTATATTCCTTCTGTAAACT 57.285 29.630 0.00 0.00 0.00 2.66
476 477 8.475331 TCCTTCTGTAAACTTTTATAAGAGCG 57.525 34.615 3.00 0.00 35.30 5.03
477 478 8.092687 TCCTTCTGTAAACTTTTATAAGAGCGT 58.907 33.333 3.00 0.00 35.30 5.07
478 479 8.718734 CCTTCTGTAAACTTTTATAAGAGCGTT 58.281 33.333 3.00 1.38 35.30 4.84
487 488 9.654663 AACTTTTATAAGAGCGTTTAGATCACT 57.345 29.630 3.00 0.00 37.82 3.41
494 495 9.733219 ATAAGAGCGTTTAGATCACTAAAGTAC 57.267 33.333 0.00 0.00 45.42 2.73
495 496 7.393841 AGAGCGTTTAGATCACTAAAGTACT 57.606 36.000 0.00 0.00 45.42 2.73
496 497 7.828712 AGAGCGTTTAGATCACTAAAGTACTT 58.171 34.615 1.12 1.12 45.42 2.24
498 499 9.733219 GAGCGTTTAGATCACTAAAGTACTTAT 57.267 33.333 8.92 0.00 45.42 1.73
500 501 9.733219 GCGTTTAGATCACTAAAGTACTTATCT 57.267 33.333 17.66 17.66 45.42 1.98
506 507 9.733219 AGATCACTAAAGTACTTATCTAAACGC 57.267 33.333 8.92 0.00 0.00 4.84
507 508 9.733219 GATCACTAAAGTACTTATCTAAACGCT 57.267 33.333 8.92 0.00 0.00 5.07
508 509 9.733219 ATCACTAAAGTACTTATCTAAACGCTC 57.267 33.333 8.92 0.00 0.00 5.03
509 510 8.954350 TCACTAAAGTACTTATCTAAACGCTCT 58.046 33.333 8.92 0.00 0.00 4.09
510 511 9.570488 CACTAAAGTACTTATCTAAACGCTCTT 57.430 33.333 8.92 0.00 0.00 2.85
527 528 7.772332 ACGCTCTTATATTTGTTTACAGAGG 57.228 36.000 0.00 0.00 0.00 3.69
528 529 6.761714 ACGCTCTTATATTTGTTTACAGAGGG 59.238 38.462 8.36 8.36 38.95 4.30
529 530 6.984474 CGCTCTTATATTTGTTTACAGAGGGA 59.016 38.462 4.76 0.00 36.40 4.20
530 531 7.169982 CGCTCTTATATTTGTTTACAGAGGGAG 59.830 40.741 4.76 0.00 36.40 4.30
542 543 6.758806 TTACAGAGGGAGTAGGAACTTTTT 57.241 37.500 0.00 0.00 41.75 1.94
544 545 3.753797 CAGAGGGAGTAGGAACTTTTTGC 59.246 47.826 0.00 0.00 41.75 3.68
547 548 1.199327 GGAGTAGGAACTTTTTGCGCC 59.801 52.381 4.18 0.00 41.75 6.53
549 550 0.869730 GTAGGAACTTTTTGCGCCGA 59.130 50.000 4.18 0.00 41.75 5.54
570 571 6.462347 GCCGAAAATATGGTGAAATTACCCAT 60.462 38.462 8.13 8.13 41.70 4.00
608 609 4.640771 TTGGCAATTTCTCTCTACCTGT 57.359 40.909 0.00 0.00 0.00 4.00
615 628 2.461300 TCTCTCTACCTGTCCATGGG 57.539 55.000 13.02 0.00 0.00 4.00
623 636 0.541392 CCTGTCCATGGGTCGATTGA 59.459 55.000 13.02 0.00 0.00 2.57
634 647 5.818136 TGGGTCGATTGAAGATCAAAATC 57.182 39.130 0.00 0.45 40.12 2.17
798 845 1.604023 GGCGCCTAGGCTCTAGCTA 60.604 63.158 30.55 0.00 42.90 3.32
800 847 1.868987 GCGCCTAGGCTCTAGCTACC 61.869 65.000 30.55 4.63 41.70 3.18
803 850 2.252714 GCCTAGGCTCTAGCTACCATT 58.747 52.381 27.17 0.00 41.70 3.16
805 852 3.773560 CCTAGGCTCTAGCTACCATTCT 58.226 50.000 0.00 0.00 41.70 2.40
806 853 3.761752 CCTAGGCTCTAGCTACCATTCTC 59.238 52.174 0.00 0.00 41.70 2.87
809 856 2.560981 GGCTCTAGCTACCATTCTCTCC 59.439 54.545 1.39 0.00 41.70 3.71
810 857 3.496331 GCTCTAGCTACCATTCTCTCCT 58.504 50.000 0.00 0.00 38.21 3.69
811 858 3.895041 GCTCTAGCTACCATTCTCTCCTT 59.105 47.826 0.00 0.00 38.21 3.36
812 859 4.261994 GCTCTAGCTACCATTCTCTCCTTG 60.262 50.000 0.00 0.00 38.21 3.61
814 861 2.122768 AGCTACCATTCTCTCCTTGGG 58.877 52.381 0.00 0.00 34.72 4.12
815 862 1.840635 GCTACCATTCTCTCCTTGGGT 59.159 52.381 0.00 0.00 34.72 4.51
817 864 1.290134 ACCATTCTCTCCTTGGGTCC 58.710 55.000 0.00 0.00 34.72 4.46
818 865 0.179000 CCATTCTCTCCTTGGGTCCG 59.821 60.000 0.00 0.00 0.00 4.79
819 866 0.179000 CATTCTCTCCTTGGGTCCGG 59.821 60.000 0.00 0.00 0.00 5.14
820 867 0.042731 ATTCTCTCCTTGGGTCCGGA 59.957 55.000 0.00 0.00 0.00 5.14
821 868 0.042731 TTCTCTCCTTGGGTCCGGAT 59.957 55.000 7.81 0.00 0.00 4.18
825 872 2.762459 CCTTGGGTCCGGATCCGA 60.762 66.667 35.42 25.84 42.83 4.55
846 3029 4.917415 CGAAATTCCTTCACCAATCAACAC 59.083 41.667 0.00 0.00 33.17 3.32
849 3032 2.229792 TCCTTCACCAATCAACACAGC 58.770 47.619 0.00 0.00 0.00 4.40
926 3125 1.384989 CCTCGGCCGGCGATCTATAT 61.385 60.000 27.83 0.00 0.00 0.86
942 3141 5.745312 TCTATATGTATTGGCAGGACCTG 57.255 43.478 17.83 17.83 40.22 4.00
1226 3569 3.950397 TCTTGATGGTTATCTTTGCCGT 58.050 40.909 0.00 0.00 34.31 5.68
1302 3645 2.478890 ATACGCCGAGCTACGCACT 61.479 57.895 0.00 0.00 41.07 4.40
1363 3706 5.362430 GTCTACACCTCTGAATCTGATCCTT 59.638 44.000 0.00 0.00 0.00 3.36
1414 3757 4.645588 CCGAGAAGAGGTCCTACAAGTTAT 59.354 45.833 0.00 0.00 0.00 1.89
1544 3887 3.817084 TGTGAACAGATTGCTCTTCCTTG 59.183 43.478 0.00 0.00 0.00 3.61
1694 4040 1.404843 GATAGACTCCAGCGGAAGGT 58.595 55.000 0.00 0.00 46.81 3.50
1806 4152 2.116238 GATAAGTGGACCTGGCTACCA 58.884 52.381 0.00 0.00 0.00 3.25
1842 4188 2.092211 CGACGACTGCATTTACAAGGAC 59.908 50.000 0.00 0.00 0.00 3.85
1876 4222 3.572255 TGCAGTGAATGTAAAAGGGGAAC 59.428 43.478 0.00 0.00 0.00 3.62
2065 4411 5.105716 GCATCTGAGTACTGGAAGACTACAA 60.106 44.000 0.00 0.00 37.43 2.41
2133 4479 0.310543 TCAATTGCTTGCGTGACCAC 59.689 50.000 0.00 0.00 32.11 4.16
2576 4923 0.875059 GACACTGCTGGTTTGGTAGC 59.125 55.000 0.00 0.00 40.29 3.58
2701 5050 8.773404 ATAGTTTCCTCAAATACTGTACACAC 57.227 34.615 0.00 0.00 0.00 3.82
2779 5129 8.205512 TGTTACTGGAATCTAACAGTGTTGTTA 58.794 33.333 18.90 4.13 46.58 2.41
2805 5314 7.025365 GTGTTCCCGTTTAATATTTTCCACTC 58.975 38.462 0.00 0.00 0.00 3.51
2844 5353 3.004734 CACAAGGATCTGGTTGTGGTTTC 59.995 47.826 19.82 0.00 46.49 2.78
2948 7685 5.193124 TCCTAGTACAACCAGGTCTCTATGA 59.807 44.000 0.00 0.00 0.00 2.15
3052 7792 4.555709 ACCTGCCGCACCGAACAA 62.556 61.111 0.00 0.00 0.00 2.83
3057 7797 2.674084 GCCGCACCGAACAACTACC 61.674 63.158 0.00 0.00 0.00 3.18
3086 7826 2.697363 CTTGTTGTAATGCGCGATCAG 58.303 47.619 12.10 0.00 0.00 2.90
3163 7927 5.743872 GGGTAAAATGATGCTCGTTTCAATC 59.256 40.000 4.52 0.00 34.75 2.67
3245 8009 1.006832 GACACACTGTTGTTGTCGCT 58.993 50.000 0.00 0.00 31.66 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.344763 GCGCCTCCTTATACATGTCCT 59.655 52.381 0.00 0.00 0.00 3.85
4 5 1.344438 TCCAGCGCCTCCTTATACATG 59.656 52.381 2.29 0.00 0.00 3.21
5 6 1.717032 TCCAGCGCCTCCTTATACAT 58.283 50.000 2.29 0.00 0.00 2.29
7 8 1.344763 ACATCCAGCGCCTCCTTATAC 59.655 52.381 2.29 0.00 0.00 1.47
9 10 0.107456 CACATCCAGCGCCTCCTTAT 59.893 55.000 2.29 0.00 0.00 1.73
10 11 1.264749 ACACATCCAGCGCCTCCTTA 61.265 55.000 2.29 0.00 0.00 2.69
11 12 2.129555 AACACATCCAGCGCCTCCTT 62.130 55.000 2.29 0.00 0.00 3.36
13 14 2.045926 AACACATCCAGCGCCTCC 60.046 61.111 2.29 0.00 0.00 4.30
14 15 0.745845 ATCAACACATCCAGCGCCTC 60.746 55.000 2.29 0.00 0.00 4.70
16 17 1.430632 CATCAACACATCCAGCGCC 59.569 57.895 2.29 0.00 0.00 6.53
17 18 1.308069 ACCATCAACACATCCAGCGC 61.308 55.000 0.00 0.00 0.00 5.92
19 20 0.813184 CCACCATCAACACATCCAGC 59.187 55.000 0.00 0.00 0.00 4.85
20 21 0.813184 GCCACCATCAACACATCCAG 59.187 55.000 0.00 0.00 0.00 3.86
21 22 0.405198 AGCCACCATCAACACATCCA 59.595 50.000 0.00 0.00 0.00 3.41
22 23 0.813184 CAGCCACCATCAACACATCC 59.187 55.000 0.00 0.00 0.00 3.51
25 26 0.250858 CCTCAGCCACCATCAACACA 60.251 55.000 0.00 0.00 0.00 3.72
26 27 0.250901 ACCTCAGCCACCATCAACAC 60.251 55.000 0.00 0.00 0.00 3.32
27 28 1.357137 TACCTCAGCCACCATCAACA 58.643 50.000 0.00 0.00 0.00 3.33
28 29 2.292267 CATACCTCAGCCACCATCAAC 58.708 52.381 0.00 0.00 0.00 3.18
31 32 0.181114 TGCATACCTCAGCCACCATC 59.819 55.000 0.00 0.00 0.00 3.51
32 33 0.625316 TTGCATACCTCAGCCACCAT 59.375 50.000 0.00 0.00 0.00 3.55
34 35 1.032114 GGTTGCATACCTCAGCCACC 61.032 60.000 9.89 0.00 44.10 4.61
35 36 2.482326 GGTTGCATACCTCAGCCAC 58.518 57.895 9.89 0.00 44.10 5.01
45 46 5.255687 ACAATGATCACAGAAGGTTGCATA 58.744 37.500 0.00 0.00 0.00 3.14
48 49 4.232221 CAACAATGATCACAGAAGGTTGC 58.768 43.478 0.00 0.00 0.00 4.17
50 51 5.132502 TGACAACAATGATCACAGAAGGTT 58.867 37.500 0.00 0.00 0.00 3.50
51 52 4.717877 TGACAACAATGATCACAGAAGGT 58.282 39.130 0.00 0.00 0.00 3.50
52 53 5.892160 ATGACAACAATGATCACAGAAGG 57.108 39.130 0.00 0.00 0.00 3.46
53 54 7.118825 ACAGTATGACAACAATGATCACAGAAG 59.881 37.037 0.00 0.00 39.69 2.85
56 57 6.732531 ACAGTATGACAACAATGATCACAG 57.267 37.500 0.00 0.00 39.69 3.66
57 58 8.614469 TTTACAGTATGACAACAATGATCACA 57.386 30.769 0.00 0.00 39.69 3.58
58 59 9.891828 TTTTTACAGTATGACAACAATGATCAC 57.108 29.630 0.00 0.00 39.69 3.06
60 61 9.065871 GCTTTTTACAGTATGACAACAATGATC 57.934 33.333 0.00 0.00 39.69 2.92
62 63 7.935520 TGCTTTTTACAGTATGACAACAATGA 58.064 30.769 0.00 0.00 39.69 2.57
111 112 8.474025 ACCTCACATTTTTGTTTTTCATCACTA 58.526 29.630 0.00 0.00 0.00 2.74
112 113 7.330262 ACCTCACATTTTTGTTTTTCATCACT 58.670 30.769 0.00 0.00 0.00 3.41
114 115 8.449397 CAAACCTCACATTTTTGTTTTTCATCA 58.551 29.630 0.00 0.00 0.00 3.07
115 116 8.450180 ACAAACCTCACATTTTTGTTTTTCATC 58.550 29.630 0.00 0.00 39.82 2.92
116 117 8.334263 ACAAACCTCACATTTTTGTTTTTCAT 57.666 26.923 0.00 0.00 39.82 2.57
118 119 9.753669 CTTACAAACCTCACATTTTTGTTTTTC 57.246 29.630 4.42 0.00 39.82 2.29
119 120 9.278978 ACTTACAAACCTCACATTTTTGTTTTT 57.721 25.926 4.42 0.00 39.82 1.94
120 121 8.840833 ACTTACAAACCTCACATTTTTGTTTT 57.159 26.923 4.42 0.00 39.82 2.43
123 124 9.581099 CTAAACTTACAAACCTCACATTTTTGT 57.419 29.630 4.51 4.51 43.91 2.83
124 125 9.796120 TCTAAACTTACAAACCTCACATTTTTG 57.204 29.630 0.00 0.00 36.49 2.44
155 156 8.677871 AGGTATGGTATCAATCCCATTCAATAA 58.322 33.333 0.00 0.00 41.61 1.40
156 157 8.230848 AGGTATGGTATCAATCCCATTCAATA 57.769 34.615 0.00 0.00 41.61 1.90
158 159 6.529084 AGGTATGGTATCAATCCCATTCAA 57.471 37.500 0.00 0.00 41.61 2.69
159 160 6.529084 AAGGTATGGTATCAATCCCATTCA 57.471 37.500 0.00 0.00 41.61 2.57
236 237 9.941325 ACAAGTGCATCCAAAATCAAATAATTA 57.059 25.926 0.00 0.00 0.00 1.40
237 238 8.851541 ACAAGTGCATCCAAAATCAAATAATT 57.148 26.923 0.00 0.00 0.00 1.40
238 239 8.851541 AACAAGTGCATCCAAAATCAAATAAT 57.148 26.923 0.00 0.00 0.00 1.28
239 240 8.674263 AAACAAGTGCATCCAAAATCAAATAA 57.326 26.923 0.00 0.00 0.00 1.40
240 241 8.674263 AAAACAAGTGCATCCAAAATCAAATA 57.326 26.923 0.00 0.00 0.00 1.40
241 242 7.571080 AAAACAAGTGCATCCAAAATCAAAT 57.429 28.000 0.00 0.00 0.00 2.32
242 243 6.998968 AAAACAAGTGCATCCAAAATCAAA 57.001 29.167 0.00 0.00 0.00 2.69
243 244 7.271511 AGTAAAACAAGTGCATCCAAAATCAA 58.728 30.769 0.00 0.00 0.00 2.57
244 245 6.815089 AGTAAAACAAGTGCATCCAAAATCA 58.185 32.000 0.00 0.00 0.00 2.57
245 246 8.810652 TTAGTAAAACAAGTGCATCCAAAATC 57.189 30.769 0.00 0.00 0.00 2.17
246 247 9.777297 ATTTAGTAAAACAAGTGCATCCAAAAT 57.223 25.926 0.00 0.00 0.00 1.82
249 250 9.606631 AAAATTTAGTAAAACAAGTGCATCCAA 57.393 25.926 0.00 0.00 0.00 3.53
298 299 8.038351 GCCCCTTGTTATAAACAACAACATAAT 58.962 33.333 1.21 0.00 45.79 1.28
300 301 6.071278 GGCCCCTTGTTATAAACAACAACATA 60.071 38.462 0.00 0.00 45.79 2.29
302 303 4.039366 GGCCCCTTGTTATAAACAACAACA 59.961 41.667 0.00 0.00 45.79 3.33
304 305 3.579151 GGGCCCCTTGTTATAAACAACAA 59.421 43.478 12.23 1.87 45.79 2.83
305 306 3.166679 GGGCCCCTTGTTATAAACAACA 58.833 45.455 12.23 0.00 45.79 3.33
306 307 2.498481 GGGGCCCCTTGTTATAAACAAC 59.502 50.000 35.49 0.00 45.79 3.32
309 310 1.395635 CGGGGCCCCTTGTTATAAAC 58.604 55.000 38.17 7.78 0.00 2.01
311 312 0.920271 ACCGGGGCCCCTTGTTATAA 60.920 55.000 38.17 0.00 0.00 0.98
312 313 0.920271 AACCGGGGCCCCTTGTTATA 60.920 55.000 38.17 0.00 30.50 0.98
314 315 2.859971 AACCGGGGCCCCTTGTTA 60.860 61.111 38.17 0.00 30.50 2.41
315 316 4.295199 GAACCGGGGCCCCTTGTT 62.295 66.667 38.17 35.80 33.46 2.83
316 317 3.876255 TAGAACCGGGGCCCCTTGT 62.876 63.158 38.17 30.34 0.00 3.16
317 318 3.012722 TAGAACCGGGGCCCCTTG 61.013 66.667 38.17 29.65 0.00 3.61
318 319 2.691252 CTAGAACCGGGGCCCCTT 60.691 66.667 38.17 26.97 0.00 3.95
319 320 3.997756 GACTAGAACCGGGGCCCCT 62.998 68.421 38.17 21.27 0.00 4.79
320 321 3.477346 GACTAGAACCGGGGCCCC 61.477 72.222 33.22 33.22 0.00 5.80
321 322 2.365237 AGACTAGAACCGGGGCCC 60.365 66.667 15.76 15.76 0.00 5.80
322 323 2.783288 CGAGACTAGAACCGGGGCC 61.783 68.421 6.32 0.00 0.00 5.80
323 324 2.806237 CGAGACTAGAACCGGGGC 59.194 66.667 6.32 0.00 0.00 5.80
324 325 2.783288 GGCGAGACTAGAACCGGGG 61.783 68.421 6.32 0.00 0.00 5.73
325 326 1.726533 GAGGCGAGACTAGAACCGGG 61.727 65.000 6.32 0.00 0.00 5.73
326 327 1.728672 GAGGCGAGACTAGAACCGG 59.271 63.158 0.00 0.00 0.00 5.28
328 329 1.726533 CCCGAGGCGAGACTAGAACC 61.727 65.000 0.00 0.00 0.00 3.62
329 330 1.728672 CCCGAGGCGAGACTAGAAC 59.271 63.158 0.00 0.00 0.00 3.01
331 332 2.516460 GCCCGAGGCGAGACTAGA 60.516 66.667 0.00 0.00 39.62 2.43
349 350 2.069273 CAAGAACACGGTTAGCCTGAG 58.931 52.381 0.00 0.00 0.00 3.35
350 351 1.270625 CCAAGAACACGGTTAGCCTGA 60.271 52.381 0.00 0.00 0.00 3.86
351 352 1.156736 CCAAGAACACGGTTAGCCTG 58.843 55.000 0.00 0.00 0.00 4.85
353 354 1.534163 GAACCAAGAACACGGTTAGCC 59.466 52.381 0.00 0.00 45.54 3.93
355 356 3.064931 GAGGAACCAAGAACACGGTTAG 58.935 50.000 0.00 0.00 45.54 2.34
358 359 0.108019 GGAGGAACCAAGAACACGGT 59.892 55.000 0.00 0.00 38.79 4.83
359 360 0.396811 AGGAGGAACCAAGAACACGG 59.603 55.000 0.00 0.00 42.04 4.94
361 362 1.608283 CCGAGGAGGAACCAAGAACAC 60.608 57.143 0.00 0.00 45.00 3.32
362 363 0.685097 CCGAGGAGGAACCAAGAACA 59.315 55.000 0.00 0.00 45.00 3.18
363 364 0.673956 GCCGAGGAGGAACCAAGAAC 60.674 60.000 0.00 0.00 45.00 3.01
366 367 1.078848 CAGCCGAGGAGGAACCAAG 60.079 63.158 0.00 0.00 45.00 3.61
367 368 0.909610 ATCAGCCGAGGAGGAACCAA 60.910 55.000 0.00 0.00 45.00 3.67
368 369 1.306141 ATCAGCCGAGGAGGAACCA 60.306 57.895 0.00 0.00 45.00 3.67
371 372 0.683179 TTCGATCAGCCGAGGAGGAA 60.683 55.000 0.00 0.00 45.00 3.36
372 373 1.076995 TTCGATCAGCCGAGGAGGA 60.077 57.895 0.00 0.00 45.00 3.71
374 375 0.248825 CACTTCGATCAGCCGAGGAG 60.249 60.000 0.00 0.00 39.90 3.69
375 376 0.679960 TCACTTCGATCAGCCGAGGA 60.680 55.000 0.00 0.00 39.90 3.71
378 379 1.136774 CGTCACTTCGATCAGCCGA 59.863 57.895 0.00 0.00 36.70 5.54
382 383 1.457738 CTACGCGTCACTTCGATCAG 58.542 55.000 18.63 0.00 0.00 2.90
383 384 0.522705 GCTACGCGTCACTTCGATCA 60.523 55.000 18.63 0.00 0.00 2.92
384 385 2.196497 GCTACGCGTCACTTCGATC 58.804 57.895 18.63 0.00 0.00 3.69
396 397 2.248274 ATTTTTGGCCGACGCTACGC 62.248 55.000 0.00 0.00 34.44 4.42
397 398 1.000884 TATTTTTGGCCGACGCTACG 58.999 50.000 0.00 0.00 34.44 3.51
398 399 3.064271 TCAATATTTTTGGCCGACGCTAC 59.936 43.478 0.00 0.00 34.44 3.58
399 400 3.271729 TCAATATTTTTGGCCGACGCTA 58.728 40.909 0.00 0.00 34.44 4.26
400 401 2.088423 TCAATATTTTTGGCCGACGCT 58.912 42.857 0.00 0.00 34.44 5.07
401 402 2.553079 TCAATATTTTTGGCCGACGC 57.447 45.000 0.00 0.00 0.00 5.19
402 403 4.285807 TGATCAATATTTTTGGCCGACG 57.714 40.909 0.00 0.00 0.00 5.12
404 405 6.047870 CCAAATGATCAATATTTTTGGCCGA 58.952 36.000 19.64 0.00 39.71 5.54
408 409 9.991906 AGATAGCCAAATGATCAATATTTTTGG 57.008 29.630 24.28 24.28 45.79 3.28
415 416 9.725019 ACGAAATAGATAGCCAAATGATCAATA 57.275 29.630 0.00 0.00 0.00 1.90
416 417 8.509690 CACGAAATAGATAGCCAAATGATCAAT 58.490 33.333 0.00 0.00 0.00 2.57
417 418 7.498900 ACACGAAATAGATAGCCAAATGATCAA 59.501 33.333 0.00 0.00 0.00 2.57
418 419 6.992123 ACACGAAATAGATAGCCAAATGATCA 59.008 34.615 0.00 0.00 0.00 2.92
419 420 7.426929 ACACGAAATAGATAGCCAAATGATC 57.573 36.000 0.00 0.00 0.00 2.92
420 421 7.807977 AACACGAAATAGATAGCCAAATGAT 57.192 32.000 0.00 0.00 0.00 2.45
421 422 7.624360 AAACACGAAATAGATAGCCAAATGA 57.376 32.000 0.00 0.00 0.00 2.57
422 423 9.950680 ATAAAACACGAAATAGATAGCCAAATG 57.049 29.630 0.00 0.00 0.00 2.32
438 439 9.715121 AGTTTACAGAAGGAATATAAAACACGA 57.285 29.630 0.00 0.00 0.00 4.35
450 451 8.932791 CGCTCTTATAAAAGTTTACAGAAGGAA 58.067 33.333 0.00 0.00 34.13 3.36
461 462 9.654663 AGTGATCTAAACGCTCTTATAAAAGTT 57.345 29.630 0.00 0.00 34.13 2.66
468 469 9.733219 GTACTTTAGTGATCTAAACGCTCTTAT 57.267 33.333 0.00 0.00 40.05 1.73
469 470 8.954350 AGTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
470 471 7.828712 AGTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
471 472 7.393841 AGTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
480 481 9.733219 GCGTTTAGATAAGTACTTTAGTGATCT 57.267 33.333 14.49 16.50 0.00 2.75
481 482 9.733219 AGCGTTTAGATAAGTACTTTAGTGATC 57.267 33.333 14.49 10.07 0.00 2.92
482 483 9.733219 GAGCGTTTAGATAAGTACTTTAGTGAT 57.267 33.333 14.49 0.00 0.00 3.06
483 484 8.954350 AGAGCGTTTAGATAAGTACTTTAGTGA 58.046 33.333 14.49 0.00 0.00 3.41
501 502 8.665685 CCTCTGTAAACAAATATAAGAGCGTTT 58.334 33.333 0.00 0.00 0.00 3.60
502 503 7.280205 CCCTCTGTAAACAAATATAAGAGCGTT 59.720 37.037 0.00 0.00 0.00 4.84
503 504 6.761714 CCCTCTGTAAACAAATATAAGAGCGT 59.238 38.462 0.00 0.00 0.00 5.07
505 506 7.988028 ACTCCCTCTGTAAACAAATATAAGAGC 59.012 37.037 0.00 0.00 0.00 4.09
508 509 9.765795 CCTACTCCCTCTGTAAACAAATATAAG 57.234 37.037 0.00 0.00 0.00 1.73
509 510 9.496710 TCCTACTCCCTCTGTAAACAAATATAA 57.503 33.333 0.00 0.00 0.00 0.98
510 511 9.496710 TTCCTACTCCCTCTGTAAACAAATATA 57.503 33.333 0.00 0.00 0.00 0.86
511 512 7.989947 TCCTACTCCCTCTGTAAACAAATAT 57.010 36.000 0.00 0.00 0.00 1.28
512 513 7.456902 AGTTCCTACTCCCTCTGTAAACAAATA 59.543 37.037 0.00 0.00 0.00 1.40
513 514 6.272558 AGTTCCTACTCCCTCTGTAAACAAAT 59.727 38.462 0.00 0.00 0.00 2.32
515 516 5.152934 AGTTCCTACTCCCTCTGTAAACAA 58.847 41.667 0.00 0.00 0.00 2.83
516 517 4.748701 AGTTCCTACTCCCTCTGTAAACA 58.251 43.478 0.00 0.00 0.00 2.83
517 518 5.741962 AAGTTCCTACTCCCTCTGTAAAC 57.258 43.478 0.00 0.00 31.99 2.01
519 520 6.531021 CAAAAAGTTCCTACTCCCTCTGTAA 58.469 40.000 0.00 0.00 31.99 2.41
520 521 5.512576 GCAAAAAGTTCCTACTCCCTCTGTA 60.513 44.000 0.00 0.00 31.99 2.74
521 522 4.747009 GCAAAAAGTTCCTACTCCCTCTGT 60.747 45.833 0.00 0.00 31.99 3.41
523 524 3.557264 CGCAAAAAGTTCCTACTCCCTCT 60.557 47.826 0.00 0.00 31.99 3.69
524 525 2.742589 CGCAAAAAGTTCCTACTCCCTC 59.257 50.000 0.00 0.00 31.99 4.30
525 526 2.779506 CGCAAAAAGTTCCTACTCCCT 58.220 47.619 0.00 0.00 31.99 4.20
526 527 1.199327 GCGCAAAAAGTTCCTACTCCC 59.801 52.381 0.30 0.00 31.99 4.30
527 528 1.199327 GGCGCAAAAAGTTCCTACTCC 59.801 52.381 10.83 0.00 31.99 3.85
528 529 1.136057 CGGCGCAAAAAGTTCCTACTC 60.136 52.381 10.83 0.00 31.99 2.59
529 530 0.872388 CGGCGCAAAAAGTTCCTACT 59.128 50.000 10.83 0.00 35.68 2.57
530 531 0.869730 TCGGCGCAAAAAGTTCCTAC 59.130 50.000 10.83 0.00 0.00 3.18
532 533 0.741915 TTTCGGCGCAAAAAGTTCCT 59.258 45.000 10.83 0.00 0.00 3.36
533 534 1.562017 TTTTCGGCGCAAAAAGTTCC 58.438 45.000 10.83 0.00 0.00 3.62
542 543 1.454201 TTCACCATATTTTCGGCGCA 58.546 45.000 10.83 0.00 0.00 6.09
544 545 4.973663 GGTAATTTCACCATATTTTCGGCG 59.026 41.667 0.00 0.00 38.55 6.46
547 548 8.940768 AAATGGGTAATTTCACCATATTTTCG 57.059 30.769 8.19 0.00 43.88 3.46
570 571 2.952702 GCCAATATGCCACAGGGGTAAA 60.953 50.000 0.00 0.00 39.65 2.01
608 609 2.771372 TGATCTTCAATCGACCCATGGA 59.229 45.455 15.22 0.00 0.00 3.41
615 628 4.884164 AGGGGATTTTGATCTTCAATCGAC 59.116 41.667 0.00 0.00 36.11 4.20
623 636 2.025887 ACGAGCAGGGGATTTTGATCTT 60.026 45.455 0.00 0.00 0.00 2.40
634 647 0.036010 ATGAACTGAACGAGCAGGGG 60.036 55.000 12.45 0.00 40.20 4.79
724 763 2.653702 GTGCTCGCTGGAGTCACT 59.346 61.111 0.00 0.00 42.53 3.41
786 833 4.507691 GGAGAGAATGGTAGCTAGAGCCTA 60.508 50.000 0.00 0.00 43.38 3.93
798 845 1.290134 GGACCCAAGGAGAGAATGGT 58.710 55.000 0.00 0.00 32.13 3.55
800 847 0.179000 CCGGACCCAAGGAGAGAATG 59.821 60.000 0.00 0.00 0.00 2.67
803 850 0.397254 GATCCGGACCCAAGGAGAGA 60.397 60.000 6.12 0.00 40.26 3.10
805 852 1.382695 GGATCCGGACCCAAGGAGA 60.383 63.158 11.17 0.00 40.26 3.71
806 853 2.797278 CGGATCCGGACCCAAGGAG 61.797 68.421 26.95 0.00 40.26 3.69
809 856 0.180406 ATTTCGGATCCGGACCCAAG 59.820 55.000 32.79 0.00 40.25 3.61
810 857 0.621609 AATTTCGGATCCGGACCCAA 59.378 50.000 32.79 17.18 40.25 4.12
811 858 0.179468 GAATTTCGGATCCGGACCCA 59.821 55.000 32.79 11.34 40.25 4.51
812 859 0.534427 GGAATTTCGGATCCGGACCC 60.534 60.000 32.79 20.87 40.25 4.46
814 861 2.210961 GAAGGAATTTCGGATCCGGAC 58.789 52.381 32.79 13.59 40.78 4.79
815 862 1.834896 TGAAGGAATTTCGGATCCGGA 59.165 47.619 32.79 24.14 40.78 5.14
817 864 1.940613 GGTGAAGGAATTTCGGATCCG 59.059 52.381 28.62 28.62 40.78 4.18
818 865 2.999331 TGGTGAAGGAATTTCGGATCC 58.001 47.619 0.00 0.00 38.71 3.36
819 866 4.640201 TGATTGGTGAAGGAATTTCGGATC 59.360 41.667 0.00 0.00 38.71 3.36
820 867 4.599041 TGATTGGTGAAGGAATTTCGGAT 58.401 39.130 0.00 0.00 38.71 4.18
821 868 4.027674 TGATTGGTGAAGGAATTTCGGA 57.972 40.909 0.00 0.00 38.71 4.55
825 872 5.739935 GCTGTGTTGATTGGTGAAGGAATTT 60.740 40.000 0.00 0.00 0.00 1.82
942 3141 3.260740 CAGTCTTGATGAGAGAACAGGC 58.739 50.000 0.00 0.00 34.31 4.85
1226 3569 2.060050 GAGGTCAGGGATCTCGAGAA 57.940 55.000 20.91 2.87 29.79 2.87
1302 3645 3.323775 ACCCTTCTTGTACTTCCCAAGA 58.676 45.455 0.00 0.00 44.83 3.02
1363 3706 5.428253 GCTGTAGAGGGACAAAACATCATA 58.572 41.667 0.00 0.00 0.00 2.15
1544 3887 1.741706 CATGCTCAATGGTGGTCACTC 59.258 52.381 0.93 0.00 32.10 3.51
1641 3984 4.491676 CAAGAGCAAAGATGGTTGGATTG 58.508 43.478 0.00 0.00 37.41 2.67
1694 4040 4.950475 TGGTTGTGTCAGGAAATACAAACA 59.050 37.500 0.00 0.00 45.38 2.83
1806 4152 3.695060 AGTCGTCGTGAAGATAATGAGGT 59.305 43.478 0.00 0.00 0.00 3.85
1842 4188 4.023792 ACATTCACTGCATACAATATGCCG 60.024 41.667 16.18 12.90 43.94 5.69
1876 4222 2.791560 CACTAAGATCGAATGCGTGGAG 59.208 50.000 0.00 0.00 38.98 3.86
2089 4435 4.041567 TGCCTCAGTTTTATTCCACAGAGA 59.958 41.667 0.00 0.00 30.13 3.10
2386 4732 1.337703 TCACAGTTGTTGGCTCATTGC 59.662 47.619 0.00 0.00 41.94 3.56
2520 4866 5.049167 GCACAAAAGGATGTTGATGTTCAA 58.951 37.500 0.00 0.00 34.38 2.69
2576 4923 5.417754 ACACCTGCATATATCATCTCTGG 57.582 43.478 0.00 0.00 0.00 3.86
2747 5097 5.310451 TGTTAGATTCCAGTAACAACACCC 58.690 41.667 0.00 0.00 36.45 4.61
2779 5129 6.717997 AGTGGAAAATATTAAACGGGAACACT 59.282 34.615 0.00 0.00 0.00 3.55
2780 5130 6.916440 AGTGGAAAATATTAAACGGGAACAC 58.084 36.000 0.00 0.00 0.00 3.32
2844 5353 6.545666 TGTGGGTTTATATGCTTATGGTTCTG 59.454 38.462 2.46 0.00 0.00 3.02
2908 5431 8.156994 TGTACTAGGAAACAAAATGTTGGTAC 57.843 34.615 0.00 2.00 40.14 3.34
2948 7685 0.466922 GCCTGCTGATTGGTGGCTAT 60.467 55.000 0.00 0.00 40.36 2.97
3006 7746 0.543749 CTGCTAAGGTTCCTCCAGGG 59.456 60.000 0.00 0.00 39.02 4.45
3052 7792 2.066262 CAACAAGCATCGTTCGGTAGT 58.934 47.619 0.00 0.00 0.00 2.73
3057 7797 2.840176 GCATTACAACAAGCATCGTTCG 59.160 45.455 0.00 0.00 0.00 3.95
3086 7826 3.249013 ACTTTCGTTCGCTTTTGTAGC 57.751 42.857 0.00 0.00 46.83 3.58
3163 7927 0.805322 GCGCACCTCTGATGTGAGAG 60.805 60.000 17.90 9.19 39.48 3.20
3245 8009 3.576118 GCAGAATAGCTACATCCTCTCCA 59.424 47.826 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.