Multiple sequence alignment - TraesCS4B01G186500

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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 TraesCS4B01G186500 chr4B 100.000 6435 0 0 1 6435 406462720 406456286 0.000000e+00 11884.0
1 TraesCS4B01G186500 chr4B 85.758 330 35 7 2387 2707 406460244 406459918 7.990000e-89 339.0
2 TraesCS4B01G186500 chr4B 85.671 328 39 4 2477 2803 406460334 406460014 7.990000e-89 339.0
3 TraesCS4B01G186500 chr4B 90.196 102 9 1 254 355 575761691 575761591 1.460000e-26 132.0
4 TraesCS4B01G186500 chr4B 97.368 38 1 0 2388 2425 406459955 406459918 1.500000e-06 65.8
5 TraesCS4B01G186500 chr4B 97.368 38 1 0 2766 2803 406460333 406460296 1.500000e-06 65.8
6 TraesCS4B01G186500 chr4D 92.990 5307 191 56 414 5656 326978428 326973239 0.000000e+00 7572.0
7 TraesCS4B01G186500 chr4D 97.967 246 4 1 1 246 326978786 326978542 5.960000e-115 425.0
8 TraesCS4B01G186500 chr4D 86.585 328 42 2 2477 2803 326976483 326976157 1.710000e-95 361.0
9 TraesCS4B01G186500 chr4D 84.848 330 38 7 2387 2707 326976387 326976061 8.050000e-84 322.0
10 TraesCS4B01G186500 chr4D 78.072 415 61 19 5871 6281 87943676 87944064 1.080000e-57 235.0
11 TraesCS4B01G186500 chr4D 83.824 136 20 2 2669 2803 326976483 326976349 1.880000e-25 128.0
12 TraesCS4B01G186500 chr4D 79.874 159 24 8 5687 5841 28887725 28887879 6.820000e-20 110.0
13 TraesCS4B01G186500 chr4D 84.906 106 13 3 5757 5860 131276092 131275988 3.170000e-18 104.0
14 TraesCS4B01G186500 chr4D 94.030 67 4 0 349 415 326978553 326978487 1.140000e-17 102.0
15 TraesCS4B01G186500 chr4D 97.368 38 1 0 2388 2425 326976098 326976061 1.500000e-06 65.8
16 TraesCS4B01G186500 chr4D 97.368 38 1 0 2766 2803 326976482 326976445 1.500000e-06 65.8
17 TraesCS4B01G186500 chr4A 93.300 5134 167 58 513 5549 144359850 144364903 0.000000e+00 7411.0
18 TraesCS4B01G186500 chr4A 88.110 328 37 2 2477 2803 144361709 144362035 7.820000e-104 388.0
19 TraesCS4B01G186500 chr4A 86.970 330 31 8 2387 2707 144361805 144362131 1.710000e-95 361.0
20 TraesCS4B01G186500 chr4A 96.020 201 5 3 1 200 144359075 144359273 2.240000e-84 324.0
21 TraesCS4B01G186500 chr4A 75.269 558 107 15 5742 6273 665712039 665712591 3.000000e-58 237.0
22 TraesCS4B01G186500 chr4A 93.069 101 4 2 415 515 144359479 144359576 1.870000e-30 145.0
23 TraesCS4B01G186500 chr4A 81.818 165 28 2 2640 2803 144361680 144361843 3.130000e-28 137.0
24 TraesCS4B01G186500 chr4A 91.935 62 2 1 188 246 144359296 144359357 4.130000e-12 84.2
25 TraesCS4B01G186500 chr4A 97.368 38 1 0 2388 2425 144362094 144362131 1.500000e-06 65.8
26 TraesCS4B01G186500 chr2A 79.814 753 127 18 5687 6420 207480173 207480919 5.720000e-145 525.0
27 TraesCS4B01G186500 chr2A 91.818 110 7 1 1 108 582966546 582966437 1.120000e-32 152.0
28 TraesCS4B01G186500 chr2A 91.667 96 7 1 258 353 36121103 36121009 1.460000e-26 132.0
29 TraesCS4B01G186500 chr5D 79.970 664 100 18 5793 6435 373956769 373956118 5.880000e-125 459.0
30 TraesCS4B01G186500 chr5D 76.720 567 107 19 5688 6234 551614713 551615274 6.310000e-75 292.0
31 TraesCS4B01G186500 chr3D 79.969 644 108 18 5792 6422 156640867 156640232 7.610000e-124 455.0
32 TraesCS4B01G186500 chr5A 79.363 659 118 16 5775 6418 676740896 676740241 1.270000e-121 448.0
33 TraesCS4B01G186500 chr5B 75.448 725 143 26 5726 6435 445599472 445598768 2.890000e-83 320.0
34 TraesCS4B01G186500 chr5B 95.370 108 5 0 1 108 700921631 700921524 8.580000e-39 172.0
35 TraesCS4B01G186500 chr5B 100.000 28 0 0 813 840 654954694 654954667 1.200000e-02 52.8
36 TraesCS4B01G186500 chr1D 76.461 616 114 25 5687 6279 36528151 36528758 8.110000e-79 305.0
37 TraesCS4B01G186500 chr1D 90.909 110 8 2 245 353 295841830 295841938 5.200000e-31 147.0
38 TraesCS4B01G186500 chr1D 78.607 201 33 10 5687 5880 60314307 60314110 2.440000e-24 124.0
39 TraesCS4B01G186500 chr7D 76.838 544 100 14 5761 6282 19589215 19588676 3.800000e-72 283.0
40 TraesCS4B01G186500 chr7D 79.602 201 36 3 6174 6370 588259168 588259367 8.700000e-29 139.0
41 TraesCS4B01G186500 chr7D 80.000 175 32 3 5688 5860 117268268 117268441 6.770000e-25 126.0
42 TraesCS4B01G186500 chr7D 88.462 104 7 5 252 353 101796066 101795966 3.150000e-23 121.0
43 TraesCS4B01G186500 chr7B 74.583 539 113 18 5743 6266 158433909 158434438 1.410000e-51 215.0
44 TraesCS4B01G186500 chr7B 86.290 124 16 1 6175 6298 550982058 550981936 4.050000e-27 134.0
45 TraesCS4B01G186500 chr7B 84.800 125 18 1 6175 6299 236685176 236685053 2.440000e-24 124.0
46 TraesCS4B01G186500 chr6D 79.386 228 41 4 6193 6420 306201552 306201773 8.640000e-34 156.0
47 TraesCS4B01G186500 chr6D 92.784 97 6 1 257 353 466894874 466894779 8.700000e-29 139.0
48 TraesCS4B01G186500 chr6D 78.363 171 28 9 5690 5855 456515392 456515226 1.140000e-17 102.0
49 TraesCS4B01G186500 chrUn 90.909 99 8 1 255 353 280376498 280376595 1.460000e-26 132.0
50 TraesCS4B01G186500 chr3A 80.226 177 30 4 5688 5860 474069341 474069516 1.880000e-25 128.0
51 TraesCS4B01G186500 chr3A 89.216 102 10 1 252 353 746096232 746096332 6.770000e-25 126.0
52 TraesCS4B01G186500 chr1B 80.233 172 28 6 5687 5855 598846447 598846279 2.440000e-24 124.0
53 TraesCS4B01G186500 chr3B 88.235 102 8 2 255 353 817516917 817516817 1.130000e-22 119.0
54 TraesCS4B01G186500 chr2D 87.500 104 11 2 250 353 602714913 602715014 1.130000e-22 119.0
55 TraesCS4B01G186500 chr2D 86.598 97 13 0 5687 5783 485597496 485597400 2.450000e-19 108.0
56 TraesCS4B01G186500 chr2D 86.598 97 13 0 5687 5783 485604382 485604286 2.450000e-19 108.0
57 TraesCS4B01G186500 chr2D 78.481 158 29 5 5687 5841 89391063 89390908 1.480000e-16 99.0


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 TraesCS4B01G186500 chr4B 406456286 406462720 6434 True 2538.72 11884 93.23300 1 6435 5 chr4B.!!$R2 6434
1 TraesCS4B01G186500 chr4D 326973239 326978786 5547 True 1130.20 7572 91.87250 1 5656 8 chr4D.!!$R2 5655
2 TraesCS4B01G186500 chr4A 144359075 144364903 5828 False 1114.50 7411 91.07375 1 5549 8 chr4A.!!$F2 5548
3 TraesCS4B01G186500 chr4A 665712039 665712591 552 False 237.00 237 75.26900 5742 6273 1 chr4A.!!$F1 531
4 TraesCS4B01G186500 chr2A 207480173 207480919 746 False 525.00 525 79.81400 5687 6420 1 chr2A.!!$F1 733
5 TraesCS4B01G186500 chr5D 373956118 373956769 651 True 459.00 459 79.97000 5793 6435 1 chr5D.!!$R1 642
6 TraesCS4B01G186500 chr5D 551614713 551615274 561 False 292.00 292 76.72000 5688 6234 1 chr5D.!!$F1 546
7 TraesCS4B01G186500 chr3D 156640232 156640867 635 True 455.00 455 79.96900 5792 6422 1 chr3D.!!$R1 630
8 TraesCS4B01G186500 chr5A 676740241 676740896 655 True 448.00 448 79.36300 5775 6418 1 chr5A.!!$R1 643
9 TraesCS4B01G186500 chr5B 445598768 445599472 704 True 320.00 320 75.44800 5726 6435 1 chr5B.!!$R1 709
10 TraesCS4B01G186500 chr1D 36528151 36528758 607 False 305.00 305 76.46100 5687 6279 1 chr1D.!!$F1 592
11 TraesCS4B01G186500 chr7D 19588676 19589215 539 True 283.00 283 76.83800 5761 6282 1 chr7D.!!$R1 521
12 TraesCS4B01G186500 chr7B 158433909 158434438 529 False 215.00 215 74.58300 5743 6266 1 chr7B.!!$F1 523

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
578 955 0.595053 ACGACGACGATGATGATGCC 60.595 55.000 15.32 0.0 42.66 4.40 F
1258 1687 0.322975 TCTGCTTCACTGCTCTTCCC 59.677 55.000 0.00 0.0 0.00 3.97 F
2483 2957 0.037326 GGTCGTCTTGCAGTCATCCA 60.037 55.000 0.00 0.0 0.00 3.41 F
3924 4405 1.421646 ACTGCTGCTGAAACCTAAGGT 59.578 47.619 13.69 0.0 37.65 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 2167 0.665835 CCTCGTCGAGATCTTCCTGG 59.334 60.000 23.74 0.14 0.00 4.45 R
3019 3493 1.746239 CCACTCCATGATGCACGCA 60.746 57.895 0.00 0.00 0.00 5.24 R
4120 4619 0.175989 GTACTTCTCTTCCCAGGCCG 59.824 60.000 0.00 0.00 0.00 6.13 R
5746 6283 0.163788 GCATCCGTGTTCACGAACTG 59.836 55.000 23.84 17.61 41.67 3.16 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
129 131 1.493022 AGGCAGGTTACAAGTGGACAA 59.507 47.619 0.00 0.00 0.00 3.18
235 272 8.915871 ATTGAATCAATGAAAGAACATTACCG 57.084 30.769 7.79 0.00 38.25 4.02
237 274 6.150976 TGAATCAATGAAAGAACATTACCGCT 59.849 34.615 0.00 0.00 38.25 5.52
238 275 5.957842 TCAATGAAAGAACATTACCGCTT 57.042 34.783 0.00 0.00 38.25 4.68
239 276 6.325919 TCAATGAAAGAACATTACCGCTTT 57.674 33.333 0.00 0.00 38.25 3.51
240 277 6.378582 TCAATGAAAGAACATTACCGCTTTC 58.621 36.000 0.00 0.00 43.88 2.62
241 278 4.759516 TGAAAGAACATTACCGCTTTCC 57.240 40.909 0.00 0.00 43.29 3.13
242 279 4.394729 TGAAAGAACATTACCGCTTTCCT 58.605 39.130 0.00 0.00 43.29 3.36
243 280 4.215399 TGAAAGAACATTACCGCTTTCCTG 59.785 41.667 0.00 0.00 43.29 3.86
244 281 3.418684 AGAACATTACCGCTTTCCTGT 57.581 42.857 0.00 0.00 0.00 4.00
245 282 3.335579 AGAACATTACCGCTTTCCTGTC 58.664 45.455 0.00 0.00 0.00 3.51
246 283 3.008049 AGAACATTACCGCTTTCCTGTCT 59.992 43.478 0.00 0.00 0.00 3.41
247 284 3.418684 ACATTACCGCTTTCCTGTCTT 57.581 42.857 0.00 0.00 0.00 3.01
248 285 3.751518 ACATTACCGCTTTCCTGTCTTT 58.248 40.909 0.00 0.00 0.00 2.52
249 286 4.142038 ACATTACCGCTTTCCTGTCTTTT 58.858 39.130 0.00 0.00 0.00 2.27
250 287 4.583073 ACATTACCGCTTTCCTGTCTTTTT 59.417 37.500 0.00 0.00 0.00 1.94
286 323 7.014092 CAACATTTTTGGTGTTGCTAAATGT 57.986 32.000 6.12 0.00 46.64 2.71
287 324 6.601741 ACATTTTTGGTGTTGCTAAATGTG 57.398 33.333 9.83 0.00 43.73 3.21
288 325 5.007528 ACATTTTTGGTGTTGCTAAATGTGC 59.992 36.000 9.83 0.00 43.73 4.57
289 326 3.808466 TTTGGTGTTGCTAAATGTGCA 57.192 38.095 0.00 0.00 38.80 4.57
290 327 4.333913 TTTGGTGTTGCTAAATGTGCAT 57.666 36.364 0.00 0.00 40.34 3.96
291 328 5.459536 TTTGGTGTTGCTAAATGTGCATA 57.540 34.783 0.00 0.00 40.34 3.14
292 329 4.433186 TGGTGTTGCTAAATGTGCATAC 57.567 40.909 0.00 0.00 40.34 2.39
293 330 3.192422 TGGTGTTGCTAAATGTGCATACC 59.808 43.478 12.53 12.53 42.81 2.73
294 331 3.425404 GTGTTGCTAAATGTGCATACCG 58.575 45.455 0.00 0.00 40.34 4.02
295 332 2.159448 TGTTGCTAAATGTGCATACCGC 60.159 45.455 0.00 0.00 40.34 5.68
304 341 3.513225 GCATACCGCAACATGGCT 58.487 55.556 0.00 0.00 41.79 4.75
305 342 1.356624 GCATACCGCAACATGGCTC 59.643 57.895 0.00 0.00 41.79 4.70
306 343 2.024918 CATACCGCAACATGGCTCC 58.975 57.895 0.00 0.00 0.00 4.70
307 344 1.523711 ATACCGCAACATGGCTCCG 60.524 57.895 0.00 0.00 0.00 4.63
310 347 4.170062 CGCAACATGGCTCCGCTG 62.170 66.667 0.00 0.00 0.00 5.18
311 348 4.487412 GCAACATGGCTCCGCTGC 62.487 66.667 0.00 0.00 0.00 5.25
312 349 4.170062 CAACATGGCTCCGCTGCG 62.170 66.667 16.34 16.34 0.00 5.18
313 350 4.393155 AACATGGCTCCGCTGCGA 62.393 61.111 25.45 8.79 0.00 5.10
323 360 4.126390 CGCTGCGACACGAGCTTG 62.126 66.667 18.66 0.00 35.28 4.01
324 361 2.734723 GCTGCGACACGAGCTTGA 60.735 61.111 8.31 0.00 35.28 3.02
325 362 2.097038 GCTGCGACACGAGCTTGAT 61.097 57.895 8.31 0.00 35.28 2.57
326 363 1.994467 CTGCGACACGAGCTTGATC 59.006 57.895 8.31 3.98 35.28 2.92
327 364 1.416813 CTGCGACACGAGCTTGATCC 61.417 60.000 8.31 0.71 35.28 3.36
328 365 1.446099 GCGACACGAGCTTGATCCA 60.446 57.895 8.31 0.00 0.00 3.41
329 366 1.416813 GCGACACGAGCTTGATCCAG 61.417 60.000 8.31 0.00 0.00 3.86
330 367 1.416813 CGACACGAGCTTGATCCAGC 61.417 60.000 10.77 10.77 40.44 4.85
338 375 1.599047 CTTGATCCAGCTCGTGGGT 59.401 57.895 0.00 0.00 45.49 4.51
340 377 2.105128 GATCCAGCTCGTGGGTCG 59.895 66.667 0.00 0.00 46.94 4.79
341 378 2.711922 GATCCAGCTCGTGGGTCGT 61.712 63.158 0.00 0.00 46.94 4.34
342 379 2.615262 GATCCAGCTCGTGGGTCGTC 62.615 65.000 0.00 0.00 46.94 4.20
343 380 4.778415 CCAGCTCGTGGGTCGTCG 62.778 72.222 0.00 0.00 43.63 5.12
344 381 4.778415 CAGCTCGTGGGTCGTCGG 62.778 72.222 0.00 0.00 40.80 4.79
347 384 4.415332 CTCGTGGGTCGTCGGGTG 62.415 72.222 0.00 0.00 40.80 4.61
356 393 3.411351 CGTCGGGTGTGCTTTCCG 61.411 66.667 0.00 0.00 44.59 4.30
360 397 2.430367 GGGTGTGCTTTCCGGTCT 59.570 61.111 0.00 0.00 0.00 3.85
381 418 7.758613 GTCTAGTAGACCTTGCAGTTATTTC 57.241 40.000 18.10 0.00 39.28 2.17
382 419 7.321153 GTCTAGTAGACCTTGCAGTTATTTCA 58.679 38.462 18.10 0.00 39.28 2.69
464 568 3.194542 AGTCTGGTTGCATCAGAGAGTAC 59.805 47.826 17.25 8.60 41.32 2.73
505 609 4.063529 TGTGCAACACAGCCTAGC 57.936 55.556 0.00 0.00 45.67 3.42
506 610 1.960763 TGTGCAACACAGCCTAGCG 60.961 57.895 0.00 0.00 45.67 4.26
507 611 1.961277 GTGCAACACAGCCTAGCGT 60.961 57.895 0.00 0.00 36.32 5.07
509 613 1.667830 GCAACACAGCCTAGCGTGA 60.668 57.895 15.02 0.00 36.88 4.35
511 615 0.792640 CAACACAGCCTAGCGTGAAG 59.207 55.000 15.02 6.27 36.88 3.02
557 934 4.394712 CCCAGGCCACCACGAGAC 62.395 72.222 5.01 0.00 0.00 3.36
559 936 3.680786 CAGGCCACCACGAGACGA 61.681 66.667 5.01 0.00 0.00 4.20
560 937 3.681835 AGGCCACCACGAGACGAC 61.682 66.667 5.01 0.00 0.00 4.34
563 940 2.126965 CCACCACGAGACGACGAC 60.127 66.667 0.00 0.00 37.03 4.34
566 943 2.202146 CCACGAGACGACGACGAC 60.202 66.667 15.32 8.08 42.66 4.34
577 954 0.772926 GACGACGACGATGATGATGC 59.227 55.000 15.32 0.00 42.66 3.91
578 955 0.595053 ACGACGACGATGATGATGCC 60.595 55.000 15.32 0.00 42.66 4.40
690 1075 1.300465 CGATGCGCTGCCTGATACT 60.300 57.895 9.73 0.00 0.00 2.12
691 1076 1.280886 CGATGCGCTGCCTGATACTC 61.281 60.000 9.73 0.00 0.00 2.59
692 1077 0.948141 GATGCGCTGCCTGATACTCC 60.948 60.000 9.73 0.00 0.00 3.85
693 1078 2.659897 GCGCTGCCTGATACTCCG 60.660 66.667 0.00 0.00 0.00 4.63
701 1098 2.007608 GCCTGATACTCCGAACCAAAC 58.992 52.381 0.00 0.00 0.00 2.93
810 1208 0.874390 TAGTCCAAGCAAAAGCAGCG 59.126 50.000 0.00 0.00 37.01 5.18
814 1212 2.353839 AAGCAAAAGCAGCGCACG 60.354 55.556 11.47 0.01 37.01 5.34
818 1216 3.898509 AAAAGCAGCGCACGCCAA 61.899 55.556 17.06 0.00 43.17 4.52
819 1217 4.629115 AAAGCAGCGCACGCCAAC 62.629 61.111 17.06 1.27 43.17 3.77
1093 1520 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1216 1645 0.850784 AAATCCATCCGGGGTTAGGG 59.149 55.000 0.00 0.00 39.84 3.53
1217 1646 0.328158 AATCCATCCGGGGTTAGGGT 60.328 55.000 0.00 0.00 38.59 4.34
1218 1647 1.060163 ATCCATCCGGGGTTAGGGTG 61.060 60.000 0.00 0.00 39.53 4.61
1219 1648 2.192175 CATCCGGGGTTAGGGTGC 59.808 66.667 0.00 0.00 32.56 5.01
1220 1649 2.042261 ATCCGGGGTTAGGGTGCT 59.958 61.111 0.00 0.00 0.00 4.40
1221 1650 2.375345 ATCCGGGGTTAGGGTGCTG 61.375 63.158 0.00 0.00 0.00 4.41
1222 1651 4.796495 CCGGGGTTAGGGTGCTGC 62.796 72.222 0.00 0.00 0.00 5.25
1223 1652 4.796495 CGGGGTTAGGGTGCTGCC 62.796 72.222 0.00 0.00 0.00 4.85
1224 1653 3.657350 GGGGTTAGGGTGCTGCCA 61.657 66.667 0.00 0.00 39.65 4.92
1225 1654 2.044946 GGGTTAGGGTGCTGCCAG 60.045 66.667 0.00 0.00 39.65 4.85
1226 1655 2.751837 GGTTAGGGTGCTGCCAGC 60.752 66.667 10.45 10.45 42.82 4.85
1227 1656 2.352805 GTTAGGGTGCTGCCAGCT 59.647 61.111 18.96 0.00 42.97 4.24
1228 1657 2.042831 GTTAGGGTGCTGCCAGCTG 61.043 63.158 18.96 6.78 42.97 4.24
1229 1658 2.223443 TTAGGGTGCTGCCAGCTGA 61.223 57.895 18.96 0.00 42.97 4.26
1230 1659 2.189191 TTAGGGTGCTGCCAGCTGAG 62.189 60.000 18.96 6.68 42.97 3.35
1255 1684 0.395686 TGCTCTGCTTCACTGCTCTT 59.604 50.000 0.00 0.00 0.00 2.85
1258 1687 0.322975 TCTGCTTCACTGCTCTTCCC 59.677 55.000 0.00 0.00 0.00 3.97
1272 1701 2.804828 CTTCCCTGGTGACTTCCGGC 62.805 65.000 0.00 0.00 32.85 6.13
1294 1723 1.082117 CGGCTCTCGCGTGGTAATTT 61.082 55.000 5.77 0.00 36.88 1.82
1300 1729 2.202557 GCGTGGTAATTTGGCGGC 60.203 61.111 0.00 0.00 0.00 6.53
1384 1813 1.415289 GGTGTGTAGGTAGGTATGGGC 59.585 57.143 0.00 0.00 0.00 5.36
1385 1814 2.112998 GTGTGTAGGTAGGTATGGGCA 58.887 52.381 0.00 0.00 0.00 5.36
1450 1894 0.452184 ACAGCGACGAGGAGTATGTG 59.548 55.000 0.00 0.00 0.00 3.21
1459 1903 2.496070 CGAGGAGTATGTGTTGGAGGAA 59.504 50.000 0.00 0.00 0.00 3.36
1468 1912 1.552792 GTGTTGGAGGAAGAGGAGGAG 59.447 57.143 0.00 0.00 0.00 3.69
1507 1951 3.834799 GAGTACGGCCACGGAGGG 61.835 72.222 2.24 0.00 46.48 4.30
1534 1978 4.208686 GCGTCCTCTAGTGCCGGG 62.209 72.222 2.18 0.00 0.00 5.73
1702 2146 1.452289 CTCGGAGGAGCTCGAGGAA 60.452 63.158 15.58 0.00 46.20 3.36
1717 2161 2.547642 CGAGGAAGATGAGGAGATTGGC 60.548 54.545 0.00 0.00 0.00 4.52
1718 2162 1.415659 AGGAAGATGAGGAGATTGGCG 59.584 52.381 0.00 0.00 0.00 5.69
1719 2163 1.414181 GGAAGATGAGGAGATTGGCGA 59.586 52.381 0.00 0.00 0.00 5.54
1720 2164 2.478831 GAAGATGAGGAGATTGGCGAC 58.521 52.381 0.00 0.00 0.00 5.19
1721 2165 1.786937 AGATGAGGAGATTGGCGACT 58.213 50.000 0.00 0.00 0.00 4.18
1722 2166 2.950781 AGATGAGGAGATTGGCGACTA 58.049 47.619 0.00 0.00 0.00 2.59
1723 2167 2.625790 AGATGAGGAGATTGGCGACTAC 59.374 50.000 0.00 0.00 0.00 2.73
1724 2168 1.112113 TGAGGAGATTGGCGACTACC 58.888 55.000 0.00 0.00 0.00 3.18
1725 2169 1.112113 GAGGAGATTGGCGACTACCA 58.888 55.000 0.00 0.00 38.16 3.25
1726 2170 1.067821 GAGGAGATTGGCGACTACCAG 59.932 57.143 0.00 0.00 41.82 4.00
1813 2266 0.804989 AGAAAGCGAAAATGCCTCCG 59.195 50.000 0.00 0.00 34.65 4.63
1890 2343 3.316573 CTGACTTGGACGAGGGGGC 62.317 68.421 0.00 0.00 0.00 5.80
1906 2359 3.311110 GCAGGGGACGAGGACACA 61.311 66.667 0.00 0.00 0.00 3.72
1942 2395 1.793414 TGGAGGGTGACGATGATGAT 58.207 50.000 0.00 0.00 0.00 2.45
1963 2416 0.879765 TTGAGGACGACGAAGAGGAC 59.120 55.000 0.00 0.00 0.00 3.85
1965 2418 1.979831 GAGGACGACGAAGAGGACGG 61.980 65.000 0.00 0.00 34.93 4.79
2043 2511 0.179150 CAGCGACGAGGGAAGAAGAG 60.179 60.000 0.00 0.00 0.00 2.85
2046 2514 0.736053 CGACGAGGGAAGAAGAGGAG 59.264 60.000 0.00 0.00 0.00 3.69
2119 2587 0.241749 TAAGGCGACGAAGAAAGCGA 59.758 50.000 0.00 0.00 0.00 4.93
2229 2697 2.991540 GTTTGGGAGGCAGGTGGC 60.992 66.667 0.00 0.00 43.74 5.01
2296 2764 6.985059 CAGCTATTGATTCAGACTCATCAGAA 59.015 38.462 0.00 0.00 35.12 3.02
2353 2821 1.302351 GCCAGTGAGAGCTGCAGTT 60.302 57.895 16.64 9.79 35.28 3.16
2483 2957 0.037326 GGTCGTCTTGCAGTCATCCA 60.037 55.000 0.00 0.00 0.00 3.41
3019 3493 4.157656 TGTTGCTCACACTACTTTTGCTTT 59.842 37.500 0.00 0.00 0.00 3.51
3247 3722 6.001460 TCATTTCGTTTTCTTATGGGTGAGT 58.999 36.000 0.00 0.00 0.00 3.41
3290 3765 5.970317 AACATCTTCATTGTCATTCTGCA 57.030 34.783 0.00 0.00 0.00 4.41
3362 3837 8.673711 TGGTAATTAACTTCTCCATTTCATTCG 58.326 33.333 1.50 0.00 0.00 3.34
3556 4031 4.524802 ACCTCAATCCTTAATCATGGCA 57.475 40.909 0.00 0.00 0.00 4.92
3683 4158 5.242393 AGCATTTCCACCTGCATATTATGTC 59.758 40.000 5.60 0.00 40.88 3.06
3746 4221 9.579768 TTTGAATTTTGGTTGATAATATGACCG 57.420 29.630 0.00 0.00 34.90 4.79
3922 4403 3.931578 AGTACTGCTGCTGAAACCTAAG 58.068 45.455 13.69 0.00 0.00 2.18
3923 4404 2.191128 ACTGCTGCTGAAACCTAAGG 57.809 50.000 13.69 0.00 0.00 2.69
3924 4405 1.421646 ACTGCTGCTGAAACCTAAGGT 59.578 47.619 13.69 0.00 37.65 3.50
3925 4406 2.637872 ACTGCTGCTGAAACCTAAGGTA 59.362 45.455 13.69 0.00 33.12 3.08
3926 4407 3.264450 ACTGCTGCTGAAACCTAAGGTAT 59.736 43.478 13.69 0.00 33.12 2.73
3927 4408 4.469945 ACTGCTGCTGAAACCTAAGGTATA 59.530 41.667 13.69 0.00 33.12 1.47
3928 4409 5.045869 ACTGCTGCTGAAACCTAAGGTATAA 60.046 40.000 13.69 0.00 33.12 0.98
3929 4410 5.183228 TGCTGCTGAAACCTAAGGTATAAC 58.817 41.667 0.00 0.00 33.12 1.89
3930 4411 5.183228 GCTGCTGAAACCTAAGGTATAACA 58.817 41.667 0.00 0.00 33.12 2.41
3931 4412 5.064834 GCTGCTGAAACCTAAGGTATAACAC 59.935 44.000 0.00 0.00 33.12 3.32
3958 4457 6.579666 AGTATGTTTGGGCATATGCTTATG 57.420 37.500 26.12 13.83 41.70 1.90
4120 4619 3.555956 CCTCGGCACATACTTATTGTGTC 59.444 47.826 5.78 2.33 44.96 3.67
4180 4679 2.043115 TGGAGGATGTAGACTCAGTGGT 59.957 50.000 0.00 0.00 35.45 4.16
4258 4757 2.094675 ACTGCACCCATTAGCACATTC 58.905 47.619 0.00 0.00 36.62 2.67
4429 4928 4.920640 TTCTAGAAGACGTGGATGGATC 57.079 45.455 0.00 0.00 0.00 3.36
4578 5077 5.463286 CAACTCTTTGCAGCACAATGATTA 58.537 37.500 0.00 0.00 40.50 1.75
4643 5142 3.030291 TGGGAAGCAAACAGTTCACAAT 58.970 40.909 0.00 0.00 33.09 2.71
4672 5171 0.548031 ATGACATTCGGGACCAGCAT 59.452 50.000 0.00 0.00 0.00 3.79
4726 5225 3.084039 CTCTACTCCATGCCTTTTTGCA 58.916 45.455 0.00 0.00 46.94 4.08
4769 5268 4.136796 AGCAGAAAGTGTCAACAGCAATA 58.863 39.130 0.00 0.00 0.00 1.90
4797 5296 3.798878 CACATGTGCAGTATAAGTCCTCG 59.201 47.826 13.94 0.00 0.00 4.63
4882 5410 4.961438 ATCACCCAAGTCAAATTTTGCT 57.039 36.364 4.19 2.78 0.00 3.91
5067 5599 7.254455 CGCTTCTTACCACACTTTAATATCCTG 60.254 40.741 0.00 0.00 0.00 3.86
5165 5697 4.832248 TCCTATGTGGTCAATGACAGAAC 58.168 43.478 15.86 10.37 37.07 3.01
5328 5861 7.382898 ACGGCATCATATGTGTATACATTGTA 58.617 34.615 10.60 0.00 45.01 2.41
5393 5926 5.450550 GACATCCTGTCGTCTCATGTAATGA 60.451 44.000 0.00 0.00 43.92 2.57
5394 5927 6.737070 GACATCCTGTCGTCTCATGTAATGAT 60.737 42.308 0.00 0.00 44.55 2.45
5395 5928 8.467771 GACATCCTGTCGTCTCATGTAATGATC 61.468 44.444 0.00 0.00 44.55 2.92
5438 5973 0.744414 ATCCATGCTTTCGTCCACGG 60.744 55.000 0.00 0.00 40.29 4.94
5439 5974 2.398554 CCATGCTTTCGTCCACGGG 61.399 63.158 0.00 0.00 40.29 5.28
5475 6010 4.365514 TTTAACTTCCCAGCATGTCTCA 57.634 40.909 0.00 0.00 0.00 3.27
5511 6046 0.181114 TTGCACAGTGGCTCTGAGTT 59.819 50.000 22.25 0.00 46.27 3.01
5527 6062 3.149196 TGAGTTGGAAAATGCTCCAGAC 58.851 45.455 0.00 0.00 46.20 3.51
5554 6089 4.424711 TGGCGAATCCACAGGCCC 62.425 66.667 0.00 0.00 44.96 5.80
5555 6090 4.115199 GGCGAATCCACAGGCCCT 62.115 66.667 0.00 0.00 39.67 5.19
5556 6091 2.514824 GCGAATCCACAGGCCCTC 60.515 66.667 0.00 0.00 0.00 4.30
5557 6092 2.989639 CGAATCCACAGGCCCTCA 59.010 61.111 0.00 0.00 0.00 3.86
5558 6093 1.450312 CGAATCCACAGGCCCTCAC 60.450 63.158 0.00 0.00 0.00 3.51
5559 6094 1.077429 GAATCCACAGGCCCTCACC 60.077 63.158 0.00 0.00 0.00 4.02
5560 6095 1.852157 AATCCACAGGCCCTCACCA 60.852 57.895 0.00 0.00 0.00 4.17
5561 6096 2.142292 AATCCACAGGCCCTCACCAC 62.142 60.000 0.00 0.00 0.00 4.16
5562 6097 4.704833 CCACAGGCCCTCACCACG 62.705 72.222 0.00 0.00 0.00 4.94
5573 6108 3.041940 CACCACGGGCTTGTCGAC 61.042 66.667 9.11 9.11 0.00 4.20
5582 6117 1.372997 GCTTGTCGACGAAGCCTGA 60.373 57.895 27.81 3.21 40.03 3.86
5584 6119 1.063806 CTTGTCGACGAAGCCTGAAG 58.936 55.000 11.62 2.35 0.00 3.02
5587 6122 1.605451 TCGACGAAGCCTGAAGGGA 60.605 57.895 0.00 0.00 37.23 4.20
5597 6132 2.175715 AGCCTGAAGGGAAGAGTTTGTT 59.824 45.455 0.00 0.00 37.23 2.83
5598 6133 2.554462 GCCTGAAGGGAAGAGTTTGTTC 59.446 50.000 0.00 0.00 37.23 3.18
5599 6134 3.748989 GCCTGAAGGGAAGAGTTTGTTCT 60.749 47.826 0.00 0.00 37.23 3.01
5600 6135 4.505039 GCCTGAAGGGAAGAGTTTGTTCTA 60.505 45.833 0.00 0.00 37.23 2.10
5601 6136 5.241662 CCTGAAGGGAAGAGTTTGTTCTAG 58.758 45.833 0.00 0.00 37.23 2.43
5615 6150 0.172803 TTCTAGCCGCCGAGAGAAAC 59.827 55.000 0.00 0.00 0.00 2.78
5616 6151 1.227002 CTAGCCGCCGAGAGAAACC 60.227 63.158 0.00 0.00 0.00 3.27
5631 6167 2.558359 AGAAACCGGAGAAAATGCTTGG 59.442 45.455 9.46 0.00 0.00 3.61
5633 6169 2.514458 ACCGGAGAAAATGCTTGGAT 57.486 45.000 9.46 0.00 0.00 3.41
5641 6177 6.528072 CGGAGAAAATGCTTGGATAAAAAGTC 59.472 38.462 0.00 0.00 0.00 3.01
5721 6258 2.443416 GGCAACCCGTAAATTTCCTCT 58.557 47.619 0.00 0.00 0.00 3.69
5732 6269 6.040878 CGTAAATTTCCTCTTGTATCCGTCT 58.959 40.000 0.00 0.00 0.00 4.18
5745 6282 4.082523 CGTCTGCGGACATGGGGT 62.083 66.667 24.91 0.00 42.21 4.95
5746 6283 2.125106 GTCTGCGGACATGGGGTC 60.125 66.667 21.02 0.00 46.20 4.46
5755 6295 0.320374 GACATGGGGTCAGTTCGTGA 59.680 55.000 0.00 0.00 46.19 4.35
5790 6330 1.140161 CAGCCATCCAATGTTGCCG 59.860 57.895 0.00 0.00 0.00 5.69
5836 6377 7.053316 TCAACAAAATGGATGAAACTCATGT 57.947 32.000 0.00 0.00 37.20 3.21
5841 6382 7.594758 ACAAAATGGATGAAACTCATGTAAACG 59.405 33.333 0.00 0.00 37.20 3.60
5916 6473 2.851263 AAACTATGTGCAAGTCCGGA 57.149 45.000 0.00 0.00 0.00 5.14
5950 6508 0.460311 CTCCCACGACAGGATACACC 59.540 60.000 0.00 0.00 41.41 4.16
5952 6510 0.175760 CCCACGACAGGATACACCAG 59.824 60.000 0.00 0.00 42.04 4.00
5959 6517 3.065510 CGACAGGATACACCAGACTAGTG 59.934 52.174 0.00 0.00 42.04 2.74
6000 6558 1.352352 CCCACTGTCTTTCCCATGTCT 59.648 52.381 0.00 0.00 0.00 3.41
6028 6586 1.795768 GCTCGTTGGACTGTCATGAA 58.204 50.000 10.38 0.00 0.00 2.57
6036 6594 1.351017 GGACTGTCATGAACCCTGGAA 59.649 52.381 10.38 0.00 0.00 3.53
6037 6595 2.224769 GGACTGTCATGAACCCTGGAAA 60.225 50.000 10.38 0.00 0.00 3.13
6049 6607 7.801716 TGAACCCTGGAAATATATTCTTTCG 57.198 36.000 0.00 0.00 34.19 3.46
6050 6608 6.770785 TGAACCCTGGAAATATATTCTTTCGG 59.229 38.462 0.00 0.00 34.19 4.30
6071 6629 3.640029 GGTGTATCTTCCCTATGTTCGGA 59.360 47.826 0.00 0.00 0.00 4.55
6103 6661 2.520968 GAGTGGCAAAGGGGGTGT 59.479 61.111 0.00 0.00 0.00 4.16
6120 6679 1.065709 GTGTTTCAGCCGAGGGGATTA 60.066 52.381 0.00 0.00 34.06 1.75
6142 6704 2.185350 CTCCGCATCCGTGAAGCT 59.815 61.111 0.00 0.00 0.00 3.74
6153 6715 3.393970 TGAAGCTCAGGCGGGAGG 61.394 66.667 10.50 0.00 44.37 4.30
6167 6729 2.711922 GGAGGCGACGATGGTCTGT 61.712 63.158 6.29 0.00 41.16 3.41
6168 6730 1.381928 GGAGGCGACGATGGTCTGTA 61.382 60.000 6.29 0.00 41.16 2.74
6185 6752 0.676782 GTACTGAACCGGCAAGGCAT 60.677 55.000 0.00 0.00 46.52 4.40
6283 6857 3.821995 TCGATGATGACGGCGAGA 58.178 55.556 16.62 0.00 0.00 4.04
6287 6861 0.179137 GATGATGACGGCGAGACACA 60.179 55.000 16.62 7.45 0.00 3.72
6288 6862 0.246360 ATGATGACGGCGAGACACAA 59.754 50.000 16.62 3.42 0.00 3.33
6372 6956 1.424493 GATGGCACGAGTAGCAGCAC 61.424 60.000 0.00 0.00 0.00 4.40
6376 6960 1.006220 CACGAGTAGCAGCACCACA 60.006 57.895 0.00 0.00 0.00 4.17
6397 6981 4.796231 GGAGCGGTGCGACACGAT 62.796 66.667 0.00 0.00 34.83 3.73
6400 6984 3.411351 GCGGTGCGACACGATGTT 61.411 61.111 0.00 0.00 34.83 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
263 300 6.458070 GCACATTTAGCAACACCAAAAATGTT 60.458 34.615 8.56 0.00 44.25 2.71
264 301 5.007528 GCACATTTAGCAACACCAAAAATGT 59.992 36.000 6.04 6.04 46.33 2.71
265 302 5.007430 TGCACATTTAGCAACACCAAAAATG 59.993 36.000 0.00 0.00 41.23 2.32
266 303 5.121811 TGCACATTTAGCAACACCAAAAAT 58.878 33.333 0.00 0.00 39.39 1.82
267 304 4.507710 TGCACATTTAGCAACACCAAAAA 58.492 34.783 0.00 0.00 39.39 1.94
268 305 4.128925 TGCACATTTAGCAACACCAAAA 57.871 36.364 0.00 0.00 39.39 2.44
269 306 3.808466 TGCACATTTAGCAACACCAAA 57.192 38.095 0.00 0.00 39.39 3.28
270 307 4.321601 GGTATGCACATTTAGCAACACCAA 60.322 41.667 13.91 0.00 46.27 3.67
271 308 3.192422 GGTATGCACATTTAGCAACACCA 59.808 43.478 13.91 0.00 46.27 4.17
272 309 3.730662 CGGTATGCACATTTAGCAACACC 60.731 47.826 10.51 10.51 46.27 4.16
273 310 3.425404 CGGTATGCACATTTAGCAACAC 58.575 45.455 0.00 0.00 46.27 3.32
274 311 2.159448 GCGGTATGCACATTTAGCAACA 60.159 45.455 0.00 0.00 46.27 3.33
275 312 2.450160 GCGGTATGCACATTTAGCAAC 58.550 47.619 0.00 0.00 46.27 4.17
276 313 2.842208 GCGGTATGCACATTTAGCAA 57.158 45.000 0.00 0.00 46.27 3.91
287 324 1.356624 GAGCCATGTTGCGGTATGC 59.643 57.895 0.00 0.00 46.70 3.14
288 325 1.775039 CGGAGCCATGTTGCGGTATG 61.775 60.000 0.00 0.00 36.02 2.39
289 326 1.523711 CGGAGCCATGTTGCGGTAT 60.524 57.895 0.00 0.00 36.02 2.73
290 327 2.125310 CGGAGCCATGTTGCGGTA 60.125 61.111 0.00 0.00 36.02 4.02
306 343 4.126390 CAAGCTCGTGTCGCAGCG 62.126 66.667 9.06 9.06 40.84 5.18
307 344 2.018582 GATCAAGCTCGTGTCGCAGC 62.019 60.000 0.00 0.00 35.73 5.25
308 345 1.416813 GGATCAAGCTCGTGTCGCAG 61.417 60.000 0.00 0.00 0.00 5.18
309 346 1.446099 GGATCAAGCTCGTGTCGCA 60.446 57.895 0.00 0.00 0.00 5.10
310 347 1.416813 CTGGATCAAGCTCGTGTCGC 61.417 60.000 0.00 0.00 0.00 5.19
311 348 1.416813 GCTGGATCAAGCTCGTGTCG 61.417 60.000 15.31 0.00 40.20 4.35
312 349 2.378028 GCTGGATCAAGCTCGTGTC 58.622 57.895 15.31 0.00 40.20 3.67
313 350 4.606071 GCTGGATCAAGCTCGTGT 57.394 55.556 15.31 0.00 40.20 4.49
319 356 1.817099 CCCACGAGCTGGATCAAGC 60.817 63.158 14.77 14.77 43.95 4.01
320 357 0.460987 GACCCACGAGCTGGATCAAG 60.461 60.000 1.44 0.00 43.95 3.02
321 358 1.596934 GACCCACGAGCTGGATCAA 59.403 57.895 1.44 0.00 43.95 2.57
322 359 2.710902 CGACCCACGAGCTGGATCA 61.711 63.158 1.44 0.00 43.95 2.92
323 360 2.105128 CGACCCACGAGCTGGATC 59.895 66.667 1.44 0.00 43.95 3.36
324 361 2.680352 ACGACCCACGAGCTGGAT 60.680 61.111 1.44 0.00 43.95 3.41
325 362 3.371063 GACGACCCACGAGCTGGA 61.371 66.667 1.44 0.00 43.95 3.86
326 363 4.778415 CGACGACCCACGAGCTGG 62.778 72.222 0.00 0.00 45.77 4.85
327 364 4.778415 CCGACGACCCACGAGCTG 62.778 72.222 0.00 0.00 45.77 4.24
330 367 4.415332 CACCCGACGACCCACGAG 62.415 72.222 0.00 0.00 45.77 4.18
335 372 3.819877 AAAGCACACCCGACGACCC 62.820 63.158 0.00 0.00 0.00 4.46
336 373 2.280592 AAAGCACACCCGACGACC 60.281 61.111 0.00 0.00 0.00 4.79
337 374 2.315386 GGAAAGCACACCCGACGAC 61.315 63.158 0.00 0.00 0.00 4.34
338 375 2.029964 GGAAAGCACACCCGACGA 59.970 61.111 0.00 0.00 0.00 4.20
339 376 3.411351 CGGAAAGCACACCCGACG 61.411 66.667 0.00 0.00 45.58 5.12
340 377 3.047877 CCGGAAAGCACACCCGAC 61.048 66.667 0.00 0.00 45.58 4.79
341 378 3.524648 GACCGGAAAGCACACCCGA 62.525 63.158 9.46 0.00 45.58 5.14
342 379 2.162338 TAGACCGGAAAGCACACCCG 62.162 60.000 9.46 0.00 42.64 5.28
343 380 0.391263 CTAGACCGGAAAGCACACCC 60.391 60.000 9.46 0.00 0.00 4.61
344 381 0.320697 ACTAGACCGGAAAGCACACC 59.679 55.000 9.46 0.00 0.00 4.16
345 382 2.490903 TCTACTAGACCGGAAAGCACAC 59.509 50.000 9.46 0.00 0.00 3.82
346 383 2.490903 GTCTACTAGACCGGAAAGCACA 59.509 50.000 9.46 0.00 39.28 4.57
347 384 3.148026 GTCTACTAGACCGGAAAGCAC 57.852 52.381 9.46 0.00 39.28 4.40
360 397 8.154856 ACTTTGAAATAACTGCAAGGTCTACTA 58.845 33.333 0.00 0.00 39.30 1.82
381 418 8.988064 TCTTGCTCTTACATCTACTAACTTTG 57.012 34.615 0.00 0.00 0.00 2.77
382 419 7.762159 GCTCTTGCTCTTACATCTACTAACTTT 59.238 37.037 0.00 0.00 36.03 2.66
464 568 2.516227 TAGAGACAGACAGGGACAGG 57.484 55.000 0.00 0.00 0.00 4.00
503 607 3.589988 CTGTGTTCTATTCCTTCACGCT 58.410 45.455 0.00 0.00 32.55 5.07
504 608 2.673368 CCTGTGTTCTATTCCTTCACGC 59.327 50.000 0.00 0.00 32.55 5.34
505 609 4.188247 TCCTGTGTTCTATTCCTTCACG 57.812 45.455 0.00 0.00 32.55 4.35
506 610 5.106515 GCTTTCCTGTGTTCTATTCCTTCAC 60.107 44.000 0.00 0.00 0.00 3.18
507 611 5.003804 GCTTTCCTGTGTTCTATTCCTTCA 58.996 41.667 0.00 0.00 0.00 3.02
509 613 4.336280 GGCTTTCCTGTGTTCTATTCCTT 58.664 43.478 0.00 0.00 0.00 3.36
511 615 2.678336 CGGCTTTCCTGTGTTCTATTCC 59.322 50.000 0.00 0.00 0.00 3.01
557 934 1.037998 CATCATCATCGTCGTCGTCG 58.962 55.000 5.50 5.50 38.33 5.12
559 936 0.595053 GGCATCATCATCGTCGTCGT 60.595 55.000 1.33 0.00 38.33 4.34
560 937 0.318191 AGGCATCATCATCGTCGTCG 60.318 55.000 0.00 0.00 38.55 5.12
563 940 0.032540 TCCAGGCATCATCATCGTCG 59.967 55.000 0.00 0.00 0.00 5.12
566 943 1.450025 CCATCCAGGCATCATCATCG 58.550 55.000 0.00 0.00 0.00 3.84
578 955 4.517934 CCTGCCCTGCCCATCCAG 62.518 72.222 0.00 0.00 0.00 3.86
690 1075 0.599204 GACTGCTCGTTTGGTTCGGA 60.599 55.000 0.00 0.00 0.00 4.55
691 1076 1.860078 GACTGCTCGTTTGGTTCGG 59.140 57.895 0.00 0.00 0.00 4.30
692 1077 1.487231 CGACTGCTCGTTTGGTTCG 59.513 57.895 0.00 0.00 35.00 3.95
693 1078 1.860078 CCGACTGCTCGTTTGGTTC 59.140 57.895 0.00 0.00 38.32 3.62
821 1219 4.973360 CGTTGGCGTTGGCGTTGG 62.973 66.667 0.00 0.00 41.24 3.77
822 1220 4.973360 CCGTTGGCGTTGGCGTTG 62.973 66.667 0.00 0.00 41.24 4.10
984 1389 2.982643 TACGGGTACGGCAGAGGGA 61.983 63.158 0.00 0.00 46.48 4.20
1100 1527 3.350031 AATTGGGGAGGCTCGGCTG 62.350 63.158 8.69 0.00 0.00 4.85
1101 1528 3.017581 AATTGGGGAGGCTCGGCT 61.018 61.111 8.69 0.00 0.00 5.52
1102 1529 2.517166 GAATTGGGGAGGCTCGGC 60.517 66.667 8.69 0.00 0.00 5.54
1103 1530 2.193248 GGAATTGGGGAGGCTCGG 59.807 66.667 8.69 0.00 0.00 4.63
1225 1654 2.820479 CAGAGCAGCAGCCTCAGC 60.820 66.667 0.00 0.00 43.56 4.26
1226 1655 2.806503 AAGCAGAGCAGCAGCCTCAG 62.807 60.000 0.00 0.00 43.56 3.35
1227 1656 2.799814 GAAGCAGAGCAGCAGCCTCA 62.800 60.000 0.00 0.00 43.56 3.86
1228 1657 2.046120 AAGCAGAGCAGCAGCCTC 60.046 61.111 0.00 0.00 43.56 4.70
1229 1658 2.046120 GAAGCAGAGCAGCAGCCT 60.046 61.111 0.00 0.00 43.56 4.58
1230 1659 2.359602 TGAAGCAGAGCAGCAGCC 60.360 61.111 0.00 0.00 43.56 4.85
1231 1660 1.671704 AGTGAAGCAGAGCAGCAGC 60.672 57.895 0.00 0.00 42.56 5.25
1255 1684 3.319198 GCCGGAAGTCACCAGGGA 61.319 66.667 5.05 0.00 0.00 4.20
1258 1687 2.266055 GAGGCCGGAAGTCACCAG 59.734 66.667 5.05 0.00 0.00 4.00
1294 1723 3.294493 GAAACCAAGCAGCCGCCA 61.294 61.111 0.00 0.00 39.83 5.69
1300 1729 2.978010 ACCGCCGAAACCAAGCAG 60.978 61.111 0.00 0.00 0.00 4.24
1450 1894 1.199615 CCTCCTCCTCTTCCTCCAAC 58.800 60.000 0.00 0.00 0.00 3.77
1459 1903 0.998945 CCTCCTCCTCCTCCTCCTCT 60.999 65.000 0.00 0.00 0.00 3.69
1468 1912 1.820481 CTCGTCGACCTCCTCCTCC 60.820 68.421 10.58 0.00 0.00 4.30
1614 2058 0.984230 ATTCGCCTTCCTCTTCACCA 59.016 50.000 0.00 0.00 0.00 4.17
1696 2140 2.547642 GCCAATCTCCTCATCTTCCTCG 60.548 54.545 0.00 0.00 0.00 4.63
1702 2146 1.786937 AGTCGCCAATCTCCTCATCT 58.213 50.000 0.00 0.00 0.00 2.90
1717 2161 2.288458 GTCGAGATCTTCCTGGTAGTCG 59.712 54.545 0.00 3.32 0.00 4.18
1718 2162 2.288458 CGTCGAGATCTTCCTGGTAGTC 59.712 54.545 0.00 0.00 0.00 2.59
1719 2163 2.093075 TCGTCGAGATCTTCCTGGTAGT 60.093 50.000 0.00 0.00 0.00 2.73
1720 2164 2.546368 CTCGTCGAGATCTTCCTGGTAG 59.454 54.545 17.52 0.00 0.00 3.18
1721 2165 2.562635 CTCGTCGAGATCTTCCTGGTA 58.437 52.381 17.52 0.00 0.00 3.25
1722 2166 1.384525 CTCGTCGAGATCTTCCTGGT 58.615 55.000 17.52 0.00 0.00 4.00
1723 2167 0.665835 CCTCGTCGAGATCTTCCTGG 59.334 60.000 23.74 0.14 0.00 4.45
1724 2168 1.669604 TCCTCGTCGAGATCTTCCTG 58.330 55.000 23.74 4.27 0.00 3.86
1725 2169 2.092861 TCTTCCTCGTCGAGATCTTCCT 60.093 50.000 23.74 0.00 0.00 3.36
1726 2170 2.289547 CTCTTCCTCGTCGAGATCTTCC 59.710 54.545 23.74 0.00 0.00 3.46
1813 2266 1.789506 GATTAGATCGCTGAGCCACC 58.210 55.000 0.00 0.00 0.00 4.61
1890 2343 0.972983 ATCTGTGTCCTCGTCCCCTG 60.973 60.000 0.00 0.00 0.00 4.45
1906 2359 3.370953 CCTCCAAATCAGGGTCGAAATCT 60.371 47.826 0.00 0.00 0.00 2.40
1942 2395 1.958579 TCCTCTTCGTCGTCCTCAAAA 59.041 47.619 0.00 0.00 0.00 2.44
1986 2442 4.460948 TTCTTAAGCCTCGGTATCGTTT 57.539 40.909 0.00 0.00 37.69 3.60
2110 2578 3.443037 CTCGATGACAGATCGCTTTCTT 58.557 45.455 0.00 0.00 40.95 2.52
2119 2587 2.289274 CTCGTAGTGCTCGATGACAGAT 59.711 50.000 0.00 0.00 36.73 2.90
2272 2740 6.728089 TCTGATGAGTCTGAATCAATAGCT 57.272 37.500 12.12 0.00 32.60 3.32
2296 2764 6.293626 CGTCTTCAGATGTTCCAAACTCAAAT 60.294 38.462 0.00 0.00 0.00 2.32
2353 2821 2.564524 CCTCCTTTTCCTCCCCTTCCTA 60.565 54.545 0.00 0.00 0.00 2.94
2483 2957 5.114780 CGAGACATGGAATTCAGAATCTGT 58.885 41.667 10.36 1.17 32.61 3.41
3019 3493 1.746239 CCACTCCATGATGCACGCA 60.746 57.895 0.00 0.00 0.00 5.24
3247 3722 9.853555 GATGTTTACCAATCATGTGTTGAATTA 57.146 29.630 12.91 2.34 38.03 1.40
3474 3949 6.891908 ACAAGTAATTCAGAACATATTGCCCT 59.108 34.615 0.00 0.00 0.00 5.19
3594 4069 5.582689 ATGCTTACAACATTAAAGAGCCC 57.417 39.130 0.00 0.00 0.00 5.19
3683 4158 5.723672 TTGACTGTAAGAACCTACTGAGG 57.276 43.478 0.00 0.00 43.42 3.86
3746 4221 7.992180 AAAAATCAACTGTCACAGAATTCAC 57.008 32.000 13.14 0.00 35.18 3.18
3923 4404 5.761726 GCCCAAACATACTAGGGTGTTATAC 59.238 44.000 13.31 3.56 43.42 1.47
3924 4405 5.429109 TGCCCAAACATACTAGGGTGTTATA 59.571 40.000 13.31 0.42 43.42 0.98
3925 4406 4.228666 TGCCCAAACATACTAGGGTGTTAT 59.771 41.667 13.31 4.38 43.42 1.89
3926 4407 3.587951 TGCCCAAACATACTAGGGTGTTA 59.412 43.478 13.31 0.00 43.42 2.41
3927 4408 2.377193 TGCCCAAACATACTAGGGTGTT 59.623 45.455 8.65 8.65 43.42 3.32
3928 4409 1.989586 TGCCCAAACATACTAGGGTGT 59.010 47.619 0.00 0.00 43.42 4.16
3929 4410 2.799126 TGCCCAAACATACTAGGGTG 57.201 50.000 0.00 0.00 43.42 4.61
3930 4411 4.749785 GCATATGCCCAAACATACTAGGGT 60.750 45.833 17.26 0.00 43.42 4.34
3931 4412 3.758554 GCATATGCCCAAACATACTAGGG 59.241 47.826 17.26 0.00 44.37 3.53
3932 4413 4.655963 AGCATATGCCCAAACATACTAGG 58.344 43.478 23.96 0.00 43.38 3.02
3933 4414 7.391554 ACATAAGCATATGCCCAAACATACTAG 59.608 37.037 23.96 3.52 42.26 2.57
3934 4415 7.230747 ACATAAGCATATGCCCAAACATACTA 58.769 34.615 23.96 1.52 42.26 1.82
3935 4416 6.070656 ACATAAGCATATGCCCAAACATACT 58.929 36.000 23.96 0.00 42.26 2.12
3936 4417 6.331369 ACATAAGCATATGCCCAAACATAC 57.669 37.500 23.96 0.00 42.26 2.39
3937 4418 6.777091 AGAACATAAGCATATGCCCAAACATA 59.223 34.615 23.96 6.79 42.26 2.29
3938 4419 5.599656 AGAACATAAGCATATGCCCAAACAT 59.400 36.000 23.96 5.63 42.26 2.71
3939 4420 4.955450 AGAACATAAGCATATGCCCAAACA 59.045 37.500 23.96 3.72 42.26 2.83
4120 4619 0.175989 GTACTTCTCTTCCCAGGCCG 59.824 60.000 0.00 0.00 0.00 6.13
4180 4679 1.688735 CTAGGATGCGTTGATCCCTCA 59.311 52.381 0.00 0.00 42.81 3.86
4433 4932 3.941483 TGCCTTTGTCTATCTAGCAAAGC 59.059 43.478 18.50 15.79 41.12 3.51
4434 4933 6.018098 CAGATGCCTTTGTCTATCTAGCAAAG 60.018 42.308 17.72 17.72 41.55 2.77
4578 5077 5.409214 CGATTTGGTTCAATTCTTGGCAAAT 59.591 36.000 0.00 0.00 0.00 2.32
4643 5142 2.419159 CCCGAATGTCATCAAGCAGAGA 60.419 50.000 0.00 0.00 0.00 3.10
4672 5171 4.677779 GCTTGAACAGAAGAAAAGCAACCA 60.678 41.667 0.00 0.00 42.19 3.67
4748 5247 2.849880 TTGCTGTTGACACTTTCTGC 57.150 45.000 0.00 0.00 0.00 4.26
4882 5410 8.937835 TGGAGTATTCATTCATTCAGGAGATTA 58.062 33.333 0.00 0.00 0.00 1.75
5067 5599 4.446371 AGAGCATTATCACAGTTACTGGC 58.554 43.478 17.21 8.21 35.51 4.85
5165 5697 9.480053 AAAAGGTTAATGAGAACATGTTCATTG 57.520 29.630 33.92 0.00 42.35 2.82
5220 5753 7.067372 TGTTTAGGACTGAATGAATGGCAATAG 59.933 37.037 0.00 0.00 0.00 1.73
5328 5861 2.378547 TGGAACTGGCTTTCCCAATACT 59.621 45.455 13.75 0.00 44.81 2.12
5438 5973 5.977489 AGTTAAATTAGCAAACACCTCCC 57.023 39.130 0.00 0.00 0.00 4.30
5439 5974 6.387465 GGAAGTTAAATTAGCAAACACCTCC 58.613 40.000 0.00 0.00 0.00 4.30
5511 6046 0.322456 CCCGTCTGGAGCATTTTCCA 60.322 55.000 0.00 0.00 44.84 3.53
5537 6072 4.424711 GGGCCTGTGGATTCGCCA 62.425 66.667 0.84 0.00 46.96 5.69
5553 6088 2.358737 GACAAGCCCGTGGTGAGG 60.359 66.667 0.00 0.00 0.00 3.86
5554 6089 2.738521 CGACAAGCCCGTGGTGAG 60.739 66.667 0.00 0.00 0.00 3.51
5555 6090 3.228017 TCGACAAGCCCGTGGTGA 61.228 61.111 0.00 0.00 0.00 4.02
5556 6091 3.041940 GTCGACAAGCCCGTGGTG 61.042 66.667 11.55 0.00 0.00 4.17
5557 6092 4.657824 CGTCGACAAGCCCGTGGT 62.658 66.667 17.16 0.00 0.00 4.16
5558 6093 3.851845 TTCGTCGACAAGCCCGTGG 62.852 63.158 17.16 0.00 0.00 4.94
5559 6094 2.355363 TTCGTCGACAAGCCCGTG 60.355 61.111 17.16 0.00 0.00 4.94
5560 6095 2.049433 CTTCGTCGACAAGCCCGT 60.049 61.111 17.16 0.00 0.00 5.28
5561 6096 3.479269 GCTTCGTCGACAAGCCCG 61.479 66.667 27.81 11.71 40.45 6.13
5567 6102 1.289066 CCTTCAGGCTTCGTCGACA 59.711 57.895 17.16 0.00 0.00 4.35
5573 6108 0.610687 ACTCTTCCCTTCAGGCTTCG 59.389 55.000 0.00 0.00 34.51 3.79
5582 6117 3.557264 CGGCTAGAACAAACTCTTCCCTT 60.557 47.826 0.00 0.00 0.00 3.95
5584 6119 2.347731 CGGCTAGAACAAACTCTTCCC 58.652 52.381 0.00 0.00 0.00 3.97
5587 6122 1.809684 GGCGGCTAGAACAAACTCTT 58.190 50.000 0.00 0.00 0.00 2.85
5597 6132 1.664321 GGTTTCTCTCGGCGGCTAGA 61.664 60.000 12.73 12.73 0.00 2.43
5598 6133 1.227002 GGTTTCTCTCGGCGGCTAG 60.227 63.158 7.21 5.64 0.00 3.42
5599 6134 2.890371 GGTTTCTCTCGGCGGCTA 59.110 61.111 7.21 0.00 0.00 3.93
5600 6135 4.436998 CGGTTTCTCTCGGCGGCT 62.437 66.667 7.21 0.00 0.00 5.52
5615 6150 4.981806 TTTATCCAAGCATTTTCTCCGG 57.018 40.909 0.00 0.00 0.00 5.14
5616 6151 6.389906 ACTTTTTATCCAAGCATTTTCTCCG 58.610 36.000 0.00 0.00 0.00 4.63
5672 6208 2.663423 GCCCTTGGCTGCTTTTTGCA 62.663 55.000 0.00 0.00 46.69 4.08
5673 6209 1.962822 GCCCTTGGCTGCTTTTTGC 60.963 57.895 0.00 0.00 46.69 3.68
5674 6210 4.366603 GCCCTTGGCTGCTTTTTG 57.633 55.556 0.00 0.00 46.69 2.44
5684 6220 1.750399 CCGTTGGAGATGCCCTTGG 60.750 63.158 0.00 0.00 34.97 3.61
5685 6221 2.409870 GCCGTTGGAGATGCCCTTG 61.410 63.158 0.00 0.00 34.97 3.61
5732 6269 2.463589 GAACTGACCCCATGTCCGCA 62.464 60.000 0.00 0.00 43.78 5.69
5740 6277 0.179067 GTGTTCACGAACTGACCCCA 60.179 55.000 11.01 0.00 41.67 4.96
5742 6279 1.219522 CCGTGTTCACGAACTGACCC 61.220 60.000 23.84 0.00 41.67 4.46
5745 6282 1.778334 CATCCGTGTTCACGAACTGA 58.222 50.000 23.84 13.85 41.67 3.41
5746 6283 0.163788 GCATCCGTGTTCACGAACTG 59.836 55.000 23.84 17.61 41.67 3.16
5755 6295 2.125512 GCCTCTCGCATCCGTGTT 60.126 61.111 0.00 0.00 37.47 3.32
5820 6361 4.699735 TGCGTTTACATGAGTTTCATCCAT 59.300 37.500 0.00 0.00 34.28 3.41
5821 6362 4.068599 TGCGTTTACATGAGTTTCATCCA 58.931 39.130 0.00 0.00 34.28 3.41
5836 6377 6.606234 TTTATATGAAATCCGCTGCGTTTA 57.394 33.333 21.59 6.06 0.00 2.01
5841 6382 4.024387 TCCGTTTTATATGAAATCCGCTGC 60.024 41.667 0.00 0.00 0.00 5.25
5916 6473 3.444805 GAGTGGAGCTCCTCGCGT 61.445 66.667 32.28 14.12 45.59 6.01
5950 6508 2.993899 CGGCCTTTTGTACACTAGTCTG 59.006 50.000 0.00 0.00 0.00 3.51
5952 6510 1.730612 GCGGCCTTTTGTACACTAGTC 59.269 52.381 0.00 0.00 0.00 2.59
5959 6517 4.454717 CGCCGCGGCCTTTTGTAC 62.455 66.667 42.07 14.11 37.98 2.90
5984 6542 1.271543 TGCCAGACATGGGAAAGACAG 60.272 52.381 0.00 0.00 45.14 3.51
6028 6586 6.062095 CACCGAAAGAATATATTTCCAGGGT 58.938 40.000 0.00 3.04 33.92 4.34
6036 6594 8.881262 AGGGAAGATACACCGAAAGAATATATT 58.119 33.333 0.00 0.00 0.00 1.28
6037 6595 8.437274 AGGGAAGATACACCGAAAGAATATAT 57.563 34.615 0.00 0.00 0.00 0.86
6049 6607 3.640029 TCCGAACATAGGGAAGATACACC 59.360 47.826 0.00 0.00 0.00 4.16
6050 6608 4.931661 TCCGAACATAGGGAAGATACAC 57.068 45.455 0.00 0.00 0.00 2.90
6103 6661 0.837272 CCTAATCCCCTCGGCTGAAA 59.163 55.000 0.00 0.00 0.00 2.69
6113 6671 1.128188 ATGCGGAGACCCTAATCCCC 61.128 60.000 0.00 0.00 31.43 4.81
6120 6679 3.461773 CACGGATGCGGAGACCCT 61.462 66.667 12.44 0.00 0.00 4.34
6153 6715 0.450583 TCAGTACAGACCATCGTCGC 59.549 55.000 0.00 0.00 44.28 5.19
6167 6729 0.676466 CATGCCTTGCCGGTTCAGTA 60.676 55.000 1.90 0.00 34.25 2.74
6168 6730 1.973281 CATGCCTTGCCGGTTCAGT 60.973 57.895 1.90 0.00 34.25 3.41
6182 6749 1.632046 CCGACGTACACAACCCATGC 61.632 60.000 0.00 0.00 0.00 4.06
6185 6752 2.029369 GCCGACGTACACAACCCA 59.971 61.111 0.00 0.00 0.00 4.51
6212 6779 2.933287 TCCCAGGAATGCCACCGT 60.933 61.111 0.00 0.00 36.29 4.83
6220 6787 2.677228 CGCTTGGGTCCCAGGAAT 59.323 61.111 23.95 0.00 31.89 3.01
6287 6861 2.719354 GCGGCTTCCAACACGTTT 59.281 55.556 0.00 0.00 0.00 3.60
6288 6862 3.645975 CGCGGCTTCCAACACGTT 61.646 61.111 0.00 0.00 0.00 3.99
6323 6903 3.376078 GTCCGTGACCGTGCCCTA 61.376 66.667 0.00 0.00 0.00 3.53
6372 6956 4.767255 GCACCGCTCCTCCTGTGG 62.767 72.222 0.00 0.00 40.62 4.17
6397 6981 4.182433 TGCCTGCCGTGGACAACA 62.182 61.111 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.