Multiple sequence alignment - TraesCS7B01G037400

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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 TraesCS7B01G037400 chr7B 100.000 2933 0 0 1 2933 36475241 36472309 0.000000e+00 5417.0
1 TraesCS7B01G037400 chr7B 86.289 671 70 13 1671 2328 36490927 36490266 0.000000e+00 710.0
2 TraesCS7B01G037400 chr7B 100.000 359 0 0 3313 3671 36471929 36471571 0.000000e+00 664.0
3 TraesCS7B01G037400 chr7B 86.005 393 48 4 976 1367 36491445 36491059 7.330000e-112 414.0
4 TraesCS7B01G037400 chr7B 80.964 394 69 6 1 391 680275817 680276207 1.280000e-79 307.0
5 TraesCS7B01G037400 chr7B 89.583 240 23 2 2601 2839 36469684 36469922 1.660000e-78 303.0
6 TraesCS7B01G037400 chr7B 93.233 133 9 0 2469 2601 36490155 36490023 2.890000e-46 196.0
7 TraesCS7B01G037400 chr7A 87.988 1665 127 34 734 2368 89037584 89035963 0.000000e+00 1899.0
8 TraesCS7B01G037400 chr7A 87.307 646 63 11 1687 2323 89044093 89043458 0.000000e+00 721.0
9 TraesCS7B01G037400 chr7A 84.302 516 73 4 844 1358 89044741 89044233 7.080000e-137 497.0
10 TraesCS7B01G037400 chr7A 88.261 230 18 4 2373 2601 89035912 89035691 2.170000e-67 267.0
11 TraesCS7B01G037400 chr7A 89.474 133 14 0 2469 2601 89043419 89043287 6.300000e-38 169.0
12 TraesCS7B01G037400 chr7A 87.313 134 14 3 1402 1532 705143287 705143420 2.280000e-32 150.0
13 TraesCS7B01G037400 chr7D 93.532 1206 62 5 1410 2601 87487250 87486047 0.000000e+00 1781.0
14 TraesCS7B01G037400 chr7D 91.481 763 53 4 647 1400 87489225 87488466 0.000000e+00 1038.0
15 TraesCS7B01G037400 chr7D 86.824 592 69 7 1683 2265 87506863 87506272 0.000000e+00 652.0
16 TraesCS7B01G037400 chr7D 82.081 692 85 18 1 656 87503442 87502754 4.140000e-154 555.0
17 TraesCS7B01G037400 chr7D 87.404 389 40 7 976 1362 87507412 87507031 4.350000e-119 438.0
18 TraesCS7B01G037400 chr7D 82.180 477 79 4 1 473 599881553 599882027 4.410000e-109 405.0
19 TraesCS7B01G037400 chr7D 81.748 389 64 5 1 386 582141372 582141756 5.920000e-83 318.0
20 TraesCS7B01G037400 chr7D 91.971 137 11 0 2465 2601 87506187 87506051 3.740000e-45 193.0
21 TraesCS7B01G037400 chr2B 78.905 749 128 15 1 723 39791503 39790759 7.130000e-132 481.0
22 TraesCS7B01G037400 chr3A 78.822 713 122 21 2 699 624428035 624427337 1.550000e-123 453.0
23 TraesCS7B01G037400 chr3A 90.756 238 21 1 2601 2838 569623910 569624146 2.130000e-82 316.0
24 TraesCS7B01G037400 chr3A 90.377 239 22 1 2601 2839 569625612 569625375 2.750000e-81 313.0
25 TraesCS7B01G037400 chr3A 85.764 288 37 4 2601 2886 646844750 646845035 5.960000e-78 302.0
26 TraesCS7B01G037400 chr3A 90.043 231 21 2 2602 2832 569625104 569624876 7.710000e-77 298.0
27 TraesCS7B01G037400 chr3A 85.887 248 32 3 3426 3671 569624603 569624357 1.010000e-65 261.0
28 TraesCS7B01G037400 chr3A 94.545 55 2 1 3618 3671 569625110 569625164 2.350000e-12 84.2
29 TraesCS7B01G037400 chr5A 79.398 665 114 20 2 652 382841739 382841084 7.230000e-122 448.0
30 TraesCS7B01G037400 chr4D 76.042 768 128 26 7 734 441813149 441812398 7.540000e-92 348.0
31 TraesCS7B01G037400 chr1D 84.663 326 49 1 1 325 424475604 424475929 1.270000e-84 324.0
32 TraesCS7B01G037400 chr1D 89.113 248 23 3 2594 2839 314655863 314656108 4.610000e-79 305.0
33 TraesCS7B01G037400 chr3B 86.014 286 37 3 2602 2886 616078668 616078951 1.660000e-78 303.0
34 TraesCS7B01G037400 chr2A 89.627 241 21 4 2601 2839 21142592 21142830 1.660000e-78 303.0
35 TraesCS7B01G037400 chr2A 85.338 266 34 5 2603 2866 740253265 740253003 1.680000e-68 270.0
36 TraesCS7B01G037400 chr2A 86.000 100 9 5 291 388 95055351 95055447 6.490000e-18 102.0
37 TraesCS7B01G037400 chr2D 88.983 236 24 2 3438 3671 528594155 528594390 1.290000e-74 291.0


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 TraesCS7B01G037400 chr7B 36471571 36475241 3670 True 3040.500000 5417 100.000000 1 3671 2 chr7B.!!$R1 3670
1 TraesCS7B01G037400 chr7B 36490023 36491445 1422 True 440.000000 710 88.509000 976 2601 3 chr7B.!!$R2 1625
2 TraesCS7B01G037400 chr7A 89035691 89037584 1893 True 1083.000000 1899 88.124500 734 2601 2 chr7A.!!$R1 1867
3 TraesCS7B01G037400 chr7A 89043287 89044741 1454 True 462.333333 721 87.027667 844 2601 3 chr7A.!!$R2 1757
4 TraesCS7B01G037400 chr7D 87486047 87489225 3178 True 1409.500000 1781 92.506500 647 2601 2 chr7D.!!$R1 1954
5 TraesCS7B01G037400 chr7D 87502754 87507412 4658 True 459.500000 652 87.070000 1 2601 4 chr7D.!!$R2 2600
6 TraesCS7B01G037400 chr2B 39790759 39791503 744 True 481.000000 481 78.905000 1 723 1 chr2B.!!$R1 722
7 TraesCS7B01G037400 chr3A 624427337 624428035 698 True 453.000000 453 78.822000 2 699 1 chr3A.!!$R1 697
8 TraesCS7B01G037400 chr3A 569624357 569625612 1255 True 290.666667 313 88.769000 2601 3671 3 chr3A.!!$R2 1070
9 TraesCS7B01G037400 chr3A 569623910 569625164 1254 False 200.100000 316 92.650500 2601 3671 2 chr3A.!!$F2 1070
10 TraesCS7B01G037400 chr5A 382841084 382841739 655 True 448.000000 448 79.398000 2 652 1 chr5A.!!$R1 650
11 TraesCS7B01G037400 chr4D 441812398 441813149 751 True 348.000000 348 76.042000 7 734 1 chr4D.!!$R1 727

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
159 163 0.606604 GCCCTCCTGAAGACGTGTAA 59.393 55.0 0.00 0.00 0.00 2.41 F
424 429 0.609406 CGGGCGATAGATCTGGGAGA 60.609 60.0 5.18 0.00 39.76 3.71 F
474 479 0.809241 GATCTGCACCTCGAAGCCTG 60.809 60.0 2.25 0.00 0.00 4.85 F
1856 3171 0.319383 CGAGCTGATCCAATCCCTCG 60.319 60.0 0.00 10.56 40.81 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1389 0.538118 AGTATGGTAGCCGGCGAAAA 59.462 50.0 23.20 9.28 0.00 2.29 R
1798 3113 0.673985 CGTGAGAGAAGGTGTGGACA 59.326 55.0 0.00 0.00 0.00 4.02 R
2140 3464 2.981784 CCTCCCAGGATCCATATGTTGA 59.018 50.0 15.82 2.11 37.67 3.18 R
3600 9046 0.108520 CAACATGCTTCCCACCATGC 60.109 55.0 0.00 0.00 41.88 4.06 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
40 41 2.092914 CCCTCCGCTTTACTGATCCTTT 60.093 50.000 0.00 0.00 0.00 3.11
46 47 4.878397 CCGCTTTACTGATCCTTTGATCTT 59.122 41.667 4.39 0.00 46.34 2.40
52 53 5.643421 ACTGATCCTTTGATCTTAGCCAT 57.357 39.130 4.39 0.00 46.34 4.40
62 63 7.147949 CCTTTGATCTTAGCCATCATGACTTTT 60.148 37.037 0.00 0.00 30.26 2.27
102 104 3.977427 TGGAAATCGAGATACCGACATG 58.023 45.455 0.00 0.00 41.70 3.21
104 106 4.142026 TGGAAATCGAGATACCGACATGTT 60.142 41.667 0.00 0.00 41.70 2.71
107 109 5.718649 AATCGAGATACCGACATGTTTTG 57.281 39.130 0.00 0.00 41.70 2.44
108 110 4.182693 TCGAGATACCGACATGTTTTGT 57.817 40.909 0.00 0.20 42.79 2.83
136 140 3.268013 ACAAACAACATAGCTTCACGC 57.732 42.857 0.00 0.00 39.57 5.34
159 163 0.606604 GCCCTCCTGAAGACGTGTAA 59.393 55.000 0.00 0.00 0.00 2.41
161 165 1.893801 CCCTCCTGAAGACGTGTAAGT 59.106 52.381 0.00 0.00 0.00 2.24
164 168 3.243771 CCTCCTGAAGACGTGTAAGTTGT 60.244 47.826 0.00 0.00 0.00 3.32
190 194 4.036852 TGGATGTGCACGACTAGATTCTAG 59.963 45.833 17.40 17.40 0.00 2.43
209 213 2.894731 AGCCGATCCAGATATCCTTGA 58.105 47.619 0.00 0.00 0.00 3.02
214 218 4.503817 CCGATCCAGATATCCTTGAGCAAA 60.504 45.833 0.00 0.00 0.00 3.68
233 237 4.326826 CAAAATCTCTGGCAGTAGTTCCA 58.673 43.478 15.27 0.00 0.00 3.53
255 259 1.215382 CTTGTCGACGGCCAGATCA 59.785 57.895 11.62 0.00 0.00 2.92
338 343 3.680786 CTGCCTCCACCACGTCGA 61.681 66.667 0.00 0.00 0.00 4.20
339 344 3.916392 CTGCCTCCACCACGTCGAC 62.916 68.421 5.18 5.18 0.00 4.20
344 349 4.735132 CCACCACGTCGACGCCAT 62.735 66.667 35.92 19.31 44.43 4.40
345 350 3.179265 CACCACGTCGACGCCATC 61.179 66.667 35.92 0.00 44.43 3.51
346 351 3.676605 ACCACGTCGACGCCATCA 61.677 61.111 35.92 0.00 44.43 3.07
347 352 3.179265 CCACGTCGACGCCATCAC 61.179 66.667 35.92 0.00 44.43 3.06
348 353 3.179265 CACGTCGACGCCATCACC 61.179 66.667 35.92 0.00 44.43 4.02
349 354 4.771356 ACGTCGACGCCATCACCG 62.771 66.667 35.92 11.31 44.43 4.94
355 360 4.634703 ACGCCATCACCGCCACAA 62.635 61.111 0.00 0.00 0.00 3.33
356 361 4.101790 CGCCATCACCGCCACAAC 62.102 66.667 0.00 0.00 0.00 3.32
357 362 4.101790 GCCATCACCGCCACAACG 62.102 66.667 0.00 0.00 0.00 4.10
365 370 3.041940 CGCCACAACGGAGGACAC 61.042 66.667 0.00 0.00 36.56 3.67
366 371 2.668550 GCCACAACGGAGGACACC 60.669 66.667 0.00 0.00 36.56 4.16
367 372 2.825982 CCACAACGGAGGACACCA 59.174 61.111 0.00 0.00 36.56 4.17
368 373 1.301716 CCACAACGGAGGACACCAG 60.302 63.158 0.00 0.00 36.56 4.00
369 374 1.301716 CACAACGGAGGACACCAGG 60.302 63.158 0.00 0.00 0.00 4.45
370 375 2.358737 CAACGGAGGACACCAGGC 60.359 66.667 0.00 0.00 0.00 4.85
371 376 3.637273 AACGGAGGACACCAGGCC 61.637 66.667 0.00 0.00 0.00 5.19
372 377 4.954118 ACGGAGGACACCAGGCCA 62.954 66.667 5.01 0.00 0.00 5.36
373 378 4.394712 CGGAGGACACCAGGCCAC 62.395 72.222 5.01 0.00 0.00 5.01
374 379 4.394712 GGAGGACACCAGGCCACG 62.395 72.222 5.01 0.00 0.00 4.94
378 383 4.626081 GACACCAGGCCACGCTGT 62.626 66.667 5.01 0.00 0.00 4.40
379 384 4.626081 ACACCAGGCCACGCTGTC 62.626 66.667 5.01 0.00 0.00 3.51
383 388 4.624364 CAGGCCACGCTGTCCACA 62.624 66.667 5.01 0.00 0.00 4.17
384 389 4.320456 AGGCCACGCTGTCCACAG 62.320 66.667 5.01 2.06 46.40 3.66
404 409 4.717629 CACGCCGCCGACTGAAGA 62.718 66.667 0.00 0.00 38.29 2.87
405 410 4.719369 ACGCCGCCGACTGAAGAC 62.719 66.667 0.00 0.00 38.29 3.01
414 419 3.553597 GACTGAAGACGGGCGATAG 57.446 57.895 0.00 0.00 0.00 2.08
415 420 1.022735 GACTGAAGACGGGCGATAGA 58.977 55.000 0.00 0.00 39.76 1.98
416 421 1.609555 GACTGAAGACGGGCGATAGAT 59.390 52.381 0.00 0.00 39.76 1.98
417 422 1.609555 ACTGAAGACGGGCGATAGATC 59.390 52.381 0.00 0.00 39.76 2.75
418 423 1.883275 CTGAAGACGGGCGATAGATCT 59.117 52.381 0.00 0.00 39.76 2.75
419 424 1.609072 TGAAGACGGGCGATAGATCTG 59.391 52.381 5.18 0.00 39.76 2.90
420 425 0.962489 AAGACGGGCGATAGATCTGG 59.038 55.000 5.18 0.00 39.76 3.86
421 426 0.896019 AGACGGGCGATAGATCTGGG 60.896 60.000 5.18 0.00 39.76 4.45
422 427 0.894184 GACGGGCGATAGATCTGGGA 60.894 60.000 5.18 0.00 39.76 4.37
423 428 0.896019 ACGGGCGATAGATCTGGGAG 60.896 60.000 5.18 0.00 39.76 4.30
424 429 0.609406 CGGGCGATAGATCTGGGAGA 60.609 60.000 5.18 0.00 39.76 3.71
425 430 1.633774 GGGCGATAGATCTGGGAGAA 58.366 55.000 5.18 0.00 39.76 2.87
426 431 2.183679 GGGCGATAGATCTGGGAGAAT 58.816 52.381 5.18 0.00 39.76 2.40
427 432 2.167487 GGGCGATAGATCTGGGAGAATC 59.833 54.545 5.18 0.00 39.76 2.52
438 443 2.049063 GAGAATCCCGATCCGCCG 60.049 66.667 0.00 0.00 0.00 6.46
439 444 4.301027 AGAATCCCGATCCGCCGC 62.301 66.667 0.00 0.00 0.00 6.53
458 463 4.899239 CCCCTCGCCTGCACGATC 62.899 72.222 0.00 0.00 42.02 3.69
459 464 3.842923 CCCTCGCCTGCACGATCT 61.843 66.667 0.00 0.00 42.02 2.75
460 465 2.584418 CCTCGCCTGCACGATCTG 60.584 66.667 0.00 0.00 42.02 2.90
468 473 2.181777 GCACGATCTGCACCTCGA 59.818 61.111 17.45 0.00 46.29 4.04
469 474 1.446099 GCACGATCTGCACCTCGAA 60.446 57.895 17.45 0.00 46.29 3.71
470 475 1.416813 GCACGATCTGCACCTCGAAG 61.417 60.000 17.45 11.20 46.29 3.79
471 476 1.153745 ACGATCTGCACCTCGAAGC 60.154 57.895 17.45 0.00 38.24 3.86
472 477 1.880340 CGATCTGCACCTCGAAGCC 60.880 63.158 7.25 0.00 37.05 4.35
473 478 1.519719 GATCTGCACCTCGAAGCCT 59.480 57.895 2.25 0.00 0.00 4.58
474 479 0.809241 GATCTGCACCTCGAAGCCTG 60.809 60.000 2.25 0.00 0.00 4.85
475 480 2.866085 ATCTGCACCTCGAAGCCTGC 62.866 60.000 2.25 0.00 0.00 4.85
476 481 4.704833 TGCACCTCGAAGCCTGCC 62.705 66.667 2.25 0.00 0.00 4.85
477 482 4.704833 GCACCTCGAAGCCTGCCA 62.705 66.667 0.00 0.00 0.00 4.92
478 483 2.270205 CACCTCGAAGCCTGCCAT 59.730 61.111 0.00 0.00 0.00 4.40
479 484 2.110967 CACCTCGAAGCCTGCCATG 61.111 63.158 0.00 0.00 0.00 3.66
480 485 3.207669 CCTCGAAGCCTGCCATGC 61.208 66.667 0.00 0.00 0.00 4.06
481 486 3.570638 CTCGAAGCCTGCCATGCG 61.571 66.667 0.00 0.00 0.00 4.73
525 530 4.309950 ACCACGGTGAACCTCGCC 62.310 66.667 10.28 0.00 43.41 5.54
530 535 3.195698 GGTGAACCTCGCCATCGC 61.196 66.667 1.32 0.00 46.03 4.58
549 554 4.699522 GTGTCCCGGTCCAGCCAC 62.700 72.222 0.00 0.00 36.97 5.01
557 562 4.699522 GTCCAGCCACCCCGTGAC 62.700 72.222 0.00 0.00 35.23 3.67
575 580 4.722700 GGAGGCCCTGCGCAAGAA 62.723 66.667 13.05 0.00 40.31 2.52
576 581 3.130160 GAGGCCCTGCGCAAGAAG 61.130 66.667 13.05 0.00 45.27 2.85
583 588 2.509845 CTGCGCAAGAAGGCAAAAC 58.490 52.632 13.05 0.00 40.33 2.43
584 589 1.270777 CTGCGCAAGAAGGCAAAACG 61.271 55.000 13.05 0.00 40.33 3.60
585 590 2.648318 GCGCAAGAAGGCAAAACGC 61.648 57.895 0.30 0.00 43.02 4.84
627 632 4.133796 GCTTTGCCCGGCCATGTC 62.134 66.667 7.03 0.00 0.00 3.06
628 633 3.451894 CTTTGCCCGGCCATGTCC 61.452 66.667 7.03 0.00 0.00 4.02
629 634 3.944250 CTTTGCCCGGCCATGTCCT 62.944 63.158 7.03 0.00 0.00 3.85
630 635 3.936772 TTTGCCCGGCCATGTCCTC 62.937 63.158 7.03 0.00 0.00 3.71
632 637 4.864334 GCCCGGCCATGTCCTCTG 62.864 72.222 2.24 0.00 0.00 3.35
633 638 4.181010 CCCGGCCATGTCCTCTGG 62.181 72.222 2.24 0.00 36.81 3.86
634 639 4.181010 CCGGCCATGTCCTCTGGG 62.181 72.222 2.24 0.00 34.16 4.45
635 640 4.181010 CGGCCATGTCCTCTGGGG 62.181 72.222 2.24 0.00 34.16 4.96
636 641 2.692368 GGCCATGTCCTCTGGGGA 60.692 66.667 0.00 0.00 42.77 4.81
651 656 1.458588 GGGACAGCTAGGGAGGAGG 60.459 68.421 0.00 0.00 0.00 4.30
669 674 2.766229 GAGGGAGAGGAGGGTGCC 60.766 72.222 0.00 0.00 0.00 5.01
708 713 3.727258 CTCCCCGTTGCCCATGGA 61.727 66.667 15.22 0.00 32.27 3.41
723 728 2.514824 GGAAGCGACATGGGAGGC 60.515 66.667 0.00 0.00 0.00 4.70
728 733 1.050988 AGCGACATGGGAGGCTATGT 61.051 55.000 1.09 1.09 40.04 2.29
755 760 4.684724 TCCCTATTGTCTTGTAGGTGAGT 58.315 43.478 0.00 0.00 36.54 3.41
805 813 6.034577 GGTTGACAAAGTTTTTGCTAACAGAC 59.965 38.462 16.32 8.17 0.00 3.51
808 816 7.319646 TGACAAAGTTTTTGCTAACAGACAAT 58.680 30.769 1.68 0.00 0.00 2.71
842 850 0.923403 CAATCGTGATCGCGACATGT 59.077 50.000 31.68 14.73 43.99 3.21
884 892 3.087031 CCATCTCAAACATTCACCTGCT 58.913 45.455 0.00 0.00 0.00 4.24
925 940 2.187946 CGCACACTCTCCCCATCC 59.812 66.667 0.00 0.00 0.00 3.51
1063 1087 7.864615 CATGTCCTCATGTGGTCAGTACCAG 62.865 52.000 16.73 2.59 44.84 4.00
1196 1226 2.267006 CCTGATGGTGCACGAGCT 59.733 61.111 17.99 0.00 42.74 4.09
1221 1251 4.383861 TCACTGCAGAGGCTGGCG 62.384 66.667 23.35 0.00 42.66 5.69
1281 1311 1.731613 CGCTACCGTCGTGCTTTCA 60.732 57.895 0.00 0.00 0.00 2.69
1305 1335 4.475135 GAGGCGGCCAAGGAGGTC 62.475 72.222 23.09 3.92 40.61 3.85
1337 1367 1.304630 ATGTCCATTGCTGCAGCCA 60.305 52.632 34.64 25.80 41.18 4.75
1359 1389 3.710722 CCCTCGCCAGGCAAGTCT 61.711 66.667 13.30 0.00 38.72 3.24
1634 2949 2.040012 TCGGTAATTTGGGTTGGTGCTA 59.960 45.455 0.00 0.00 0.00 3.49
1638 2953 5.612351 GGTAATTTGGGTTGGTGCTAAAAA 58.388 37.500 0.00 0.00 0.00 1.94
1798 3113 2.030562 CTCGTGGGGAGCAAACGT 59.969 61.111 0.00 0.00 38.43 3.99
1856 3171 0.319383 CGAGCTGATCCAATCCCTCG 60.319 60.000 0.00 10.56 40.81 4.63
2123 3447 6.786122 ACATTCCTAGAGATAGACTCCTACC 58.214 44.000 0.00 0.00 45.96 3.18
2179 3503 3.015516 GGTGAAGCCCGTGAAAGAA 57.984 52.632 0.00 0.00 0.00 2.52
2215 3539 3.394274 TGTTGATCAGTCTTTGGAAGGGA 59.606 43.478 0.00 0.00 0.00 4.20
2310 3634 8.860088 TCTGTAGCTTCTCAACTGCATATATAA 58.140 33.333 0.00 0.00 0.00 0.98
2428 3835 6.631088 GCGGAGGGAATACTTTTTAAGTAGGA 60.631 42.308 5.62 0.00 46.32 2.94
2544 3952 2.110578 TCCGAGCTGATCAAGAATCCA 58.889 47.619 0.00 0.00 33.01 3.41
2630 4038 2.234661 TGCACAAAACCACCACATTTGA 59.765 40.909 4.65 0.00 37.46 2.69
2684 4092 2.283884 AGTTTTTGCAAAAATCACCGCG 59.716 40.909 33.23 0.00 39.75 6.46
2686 4094 0.249238 TTTGCAAAAATCACCGCGCT 60.249 45.000 10.02 0.00 0.00 5.92
2690 4098 0.702383 CAAAAATCACCGCGCTTTCG 59.298 50.000 5.56 0.00 39.07 3.46
2770 4308 1.450312 GTGAGGCCGGATTGTCAGG 60.450 63.158 5.05 0.00 34.70 3.86
2774 5797 2.514824 GCCGGATTGTCAGGAGCC 60.515 66.667 5.05 0.00 33.29 4.70
2781 5804 0.976641 ATTGTCAGGAGCCGACTTGA 59.023 50.000 10.98 0.00 34.37 3.02
2799 5822 8.020819 CCGACTTGACAAAACATTTACATACAT 58.979 33.333 0.00 0.00 0.00 2.29
2803 5826 8.415950 TTGACAAAACATTTACATACATCCCT 57.584 30.769 0.00 0.00 0.00 4.20
2858 7081 3.827898 CCCTCCTCGCGACCTGTC 61.828 72.222 3.71 0.00 0.00 3.51
2859 7082 3.827898 CCTCCTCGCGACCTGTCC 61.828 72.222 3.71 0.00 0.00 4.02
2860 7083 3.827898 CTCCTCGCGACCTGTCCC 61.828 72.222 3.71 0.00 0.00 4.46
2867 7090 2.928396 CGACCTGTCCCCCACCTT 60.928 66.667 0.00 0.00 0.00 3.50
2868 7091 2.757077 GACCTGTCCCCCACCTTG 59.243 66.667 0.00 0.00 0.00 3.61
2869 7092 1.846124 GACCTGTCCCCCACCTTGA 60.846 63.158 0.00 0.00 0.00 3.02
2870 7093 2.125766 GACCTGTCCCCCACCTTGAC 62.126 65.000 0.00 0.00 0.00 3.18
2871 7094 2.757077 CTGTCCCCCACCTTGACC 59.243 66.667 0.00 0.00 0.00 4.02
2872 7095 2.039298 TGTCCCCCACCTTGACCA 60.039 61.111 0.00 0.00 0.00 4.02
2873 7096 2.129555 CTGTCCCCCACCTTGACCAG 62.130 65.000 0.00 0.00 0.00 4.00
2874 7097 3.256960 TCCCCCACCTTGACCAGC 61.257 66.667 0.00 0.00 0.00 4.85
2875 7098 4.366684 CCCCCACCTTGACCAGCC 62.367 72.222 0.00 0.00 0.00 4.85
2876 7099 4.366684 CCCCACCTTGACCAGCCC 62.367 72.222 0.00 0.00 0.00 5.19
2877 7100 4.722700 CCCACCTTGACCAGCCCG 62.723 72.222 0.00 0.00 0.00 6.13
2878 7101 3.636231 CCACCTTGACCAGCCCGA 61.636 66.667 0.00 0.00 0.00 5.14
2879 7102 2.358737 CACCTTGACCAGCCCGAC 60.359 66.667 0.00 0.00 0.00 4.79
2880 7103 3.637273 ACCTTGACCAGCCCGACC 61.637 66.667 0.00 0.00 0.00 4.79
2881 7104 3.322466 CCTTGACCAGCCCGACCT 61.322 66.667 0.00 0.00 0.00 3.85
2882 7105 2.266055 CTTGACCAGCCCGACCTC 59.734 66.667 0.00 0.00 0.00 3.85
2883 7106 3.649277 CTTGACCAGCCCGACCTCG 62.649 68.421 0.00 0.00 39.44 4.63
2884 7107 4.671590 TGACCAGCCCGACCTCGA 62.672 66.667 0.00 0.00 43.02 4.04
2885 7108 4.131088 GACCAGCCCGACCTCGAC 62.131 72.222 0.00 0.00 43.02 4.20
2888 7111 4.135153 CAGCCCGACCTCGACCAG 62.135 72.222 0.00 0.00 43.02 4.00
2910 7133 4.749310 CGCTGCCAGTCCGCTTCT 62.749 66.667 0.00 0.00 0.00 2.85
2911 7134 3.123620 GCTGCCAGTCCGCTTCTG 61.124 66.667 0.00 0.00 0.00 3.02
2913 7136 4.704833 TGCCAGTCCGCTTCTGCC 62.705 66.667 0.00 0.00 35.36 4.85
3331 7554 4.973360 CAAAACGCCACCGCACCG 62.973 66.667 0.00 0.00 38.22 4.94
3354 7577 3.732849 CCTTCCCCCTGGCCTCAC 61.733 72.222 3.32 0.00 0.00 3.51
3355 7578 3.732849 CTTCCCCCTGGCCTCACC 61.733 72.222 3.32 0.00 39.84 4.02
3423 7809 3.394836 AGTTGCCCTCTCCTCCGC 61.395 66.667 0.00 0.00 0.00 5.54
3424 7810 4.475135 GTTGCCCTCTCCTCCGCC 62.475 72.222 0.00 0.00 0.00 6.13
3443 8888 1.729470 CTGCTCGCCGTCTAGGTCAT 61.729 60.000 0.00 0.00 43.70 3.06
3449 8894 2.279517 CGTCTAGGTCATGCGGCC 60.280 66.667 0.00 0.00 0.00 6.13
3450 8895 2.900273 GTCTAGGTCATGCGGCCA 59.100 61.111 2.24 0.00 0.00 5.36
3474 8919 4.864334 GCATGGGGAGGCGACCTG 62.864 72.222 2.98 0.00 31.76 4.00
3529 8975 2.367486 GCCTACACTAGAGTTCGTCCT 58.633 52.381 0.00 0.00 0.00 3.85
3530 8976 2.355444 GCCTACACTAGAGTTCGTCCTC 59.645 54.545 0.00 0.00 0.00 3.71
3558 9004 3.144120 CTCCTCGGCGTGGATCCAG 62.144 68.421 28.45 14.70 32.56 3.86
3559 9005 3.461773 CCTCGGCGTGGATCCAGT 61.462 66.667 22.66 0.00 0.00 4.00
3577 9023 3.192422 CCAGTGAGTAGAGGAGACAACAG 59.808 52.174 0.00 0.00 0.00 3.16
3578 9024 2.823154 AGTGAGTAGAGGAGACAACAGC 59.177 50.000 0.00 0.00 0.00 4.40
3579 9025 1.813178 TGAGTAGAGGAGACAACAGCG 59.187 52.381 0.00 0.00 0.00 5.18
3580 9026 1.133407 GAGTAGAGGAGACAACAGCGG 59.867 57.143 0.00 0.00 0.00 5.52
3583 9029 1.115930 AGAGGAGACAACAGCGGTGT 61.116 55.000 15.81 15.81 39.19 4.16
3585 9031 1.961277 GGAGACAACAGCGGTGTGG 60.961 63.158 22.63 21.43 36.84 4.17
3613 9059 2.345760 CCTGTGCATGGTGGGAAGC 61.346 63.158 0.00 0.00 0.00 3.86
3614 9060 1.604308 CTGTGCATGGTGGGAAGCA 60.604 57.895 0.00 0.00 34.10 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 4.665833 TGTCGGTATCTCGATTTCCATT 57.334 40.909 0.00 0.00 41.40 3.16
102 104 6.994868 TGTTGTTTGTTGACACTACAAAAC 57.005 33.333 6.95 4.52 44.42 2.43
104 106 6.970043 GCTATGTTGTTTGTTGACACTACAAA 59.030 34.615 10.69 2.04 41.69 2.83
107 109 6.300354 AGCTATGTTGTTTGTTGACACTAC 57.700 37.500 0.00 0.00 0.00 2.73
108 110 6.540551 TGAAGCTATGTTGTTTGTTGACACTA 59.459 34.615 0.00 0.00 0.00 2.74
136 140 4.821589 GTCTTCAGGAGGGCGCGG 62.822 72.222 8.83 0.00 0.00 6.46
146 150 5.924254 TCCATAACAACTTACACGTCTTCAG 59.076 40.000 0.00 0.00 0.00 3.02
149 153 6.147164 CACATCCATAACAACTTACACGTCTT 59.853 38.462 0.00 0.00 0.00 3.01
152 156 4.153475 GCACATCCATAACAACTTACACGT 59.847 41.667 0.00 0.00 0.00 4.49
159 163 2.742053 GTCGTGCACATCCATAACAACT 59.258 45.455 18.64 0.00 0.00 3.16
161 165 3.052455 AGTCGTGCACATCCATAACAA 57.948 42.857 18.64 0.00 0.00 2.83
164 168 4.937201 ATCTAGTCGTGCACATCCATAA 57.063 40.909 18.64 0.00 0.00 1.90
190 194 2.676463 GCTCAAGGATATCTGGATCGGC 60.676 54.545 2.05 0.00 0.00 5.54
209 213 3.710209 ACTACTGCCAGAGATTTTGCT 57.290 42.857 0.00 0.00 0.00 3.91
233 237 1.006102 CTGGCCGTCGACAAGTTCT 60.006 57.895 17.16 0.00 0.00 3.01
238 242 0.389817 CTTGATCTGGCCGTCGACAA 60.390 55.000 17.16 0.07 0.00 3.18
239 243 1.215382 CTTGATCTGGCCGTCGACA 59.785 57.895 17.16 0.00 0.00 4.35
255 259 1.918262 TCTGCATGATTGGTCCTCCTT 59.082 47.619 0.00 0.00 34.23 3.36
327 332 4.735132 ATGGCGTCGACGTGGTGG 62.735 66.667 35.48 10.56 42.22 4.61
328 333 3.179265 GATGGCGTCGACGTGGTG 61.179 66.667 35.48 11.31 42.22 4.17
329 334 3.676605 TGATGGCGTCGACGTGGT 61.677 61.111 35.48 22.41 42.22 4.16
330 335 3.179265 GTGATGGCGTCGACGTGG 61.179 66.667 35.48 12.08 42.22 4.94
331 336 3.179265 GGTGATGGCGTCGACGTG 61.179 66.667 35.48 12.84 42.22 4.49
332 337 4.771356 CGGTGATGGCGTCGACGT 62.771 66.667 35.48 19.18 42.22 4.34
338 343 4.634703 TTGTGGCGGTGATGGCGT 62.635 61.111 0.00 0.00 37.19 5.68
339 344 4.101790 GTTGTGGCGGTGATGGCG 62.102 66.667 0.00 0.00 37.19 5.69
340 345 4.101790 CGTTGTGGCGGTGATGGC 62.102 66.667 0.00 0.00 0.00 4.40
341 346 3.430862 CCGTTGTGGCGGTGATGG 61.431 66.667 0.00 0.00 46.11 3.51
348 353 3.041940 GTGTCCTCCGTTGTGGCG 61.042 66.667 0.00 0.00 37.80 5.69
349 354 2.668550 GGTGTCCTCCGTTGTGGC 60.669 66.667 0.00 0.00 37.80 5.01
350 355 1.301716 CTGGTGTCCTCCGTTGTGG 60.302 63.158 0.00 0.00 40.09 4.17
351 356 1.301716 CCTGGTGTCCTCCGTTGTG 60.302 63.158 0.00 0.00 0.00 3.33
352 357 3.148084 CCTGGTGTCCTCCGTTGT 58.852 61.111 0.00 0.00 0.00 3.32
353 358 2.358737 GCCTGGTGTCCTCCGTTG 60.359 66.667 0.00 0.00 0.00 4.10
354 359 3.637273 GGCCTGGTGTCCTCCGTT 61.637 66.667 0.00 0.00 0.00 4.44
355 360 4.954118 TGGCCTGGTGTCCTCCGT 62.954 66.667 3.32 0.00 0.00 4.69
356 361 4.394712 GTGGCCTGGTGTCCTCCG 62.395 72.222 3.32 0.00 0.00 4.63
357 362 4.394712 CGTGGCCTGGTGTCCTCC 62.395 72.222 3.32 0.00 0.00 4.30
361 366 4.626081 ACAGCGTGGCCTGGTGTC 62.626 66.667 22.33 0.00 44.06 3.67
387 392 4.717629 TCTTCAGTCGGCGGCGTG 62.718 66.667 31.06 22.43 0.00 5.34
388 393 4.719369 GTCTTCAGTCGGCGGCGT 62.719 66.667 31.06 10.38 0.00 5.68
391 396 4.796231 CCCGTCTTCAGTCGGCGG 62.796 72.222 7.21 0.00 43.57 6.13
394 399 1.721664 TATCGCCCGTCTTCAGTCGG 61.722 60.000 5.61 5.61 44.31 4.79
395 400 0.317103 CTATCGCCCGTCTTCAGTCG 60.317 60.000 0.00 0.00 0.00 4.18
396 401 1.022735 TCTATCGCCCGTCTTCAGTC 58.977 55.000 0.00 0.00 0.00 3.51
397 402 1.609555 GATCTATCGCCCGTCTTCAGT 59.390 52.381 0.00 0.00 0.00 3.41
398 403 1.883275 AGATCTATCGCCCGTCTTCAG 59.117 52.381 0.00 0.00 0.00 3.02
399 404 1.609072 CAGATCTATCGCCCGTCTTCA 59.391 52.381 0.00 0.00 0.00 3.02
400 405 1.068194 CCAGATCTATCGCCCGTCTTC 60.068 57.143 0.00 0.00 0.00 2.87
401 406 0.962489 CCAGATCTATCGCCCGTCTT 59.038 55.000 0.00 0.00 0.00 3.01
402 407 0.896019 CCCAGATCTATCGCCCGTCT 60.896 60.000 0.00 0.00 0.00 4.18
403 408 0.894184 TCCCAGATCTATCGCCCGTC 60.894 60.000 0.00 0.00 0.00 4.79
404 409 0.896019 CTCCCAGATCTATCGCCCGT 60.896 60.000 0.00 0.00 0.00 5.28
405 410 0.609406 TCTCCCAGATCTATCGCCCG 60.609 60.000 0.00 0.00 0.00 6.13
406 411 1.633774 TTCTCCCAGATCTATCGCCC 58.366 55.000 0.00 0.00 0.00 6.13
407 412 2.167487 GGATTCTCCCAGATCTATCGCC 59.833 54.545 0.00 0.00 0.00 5.54
408 413 3.518634 GGATTCTCCCAGATCTATCGC 57.481 52.381 0.00 0.00 0.00 4.58
420 425 2.344129 GGCGGATCGGGATTCTCC 59.656 66.667 2.13 0.00 35.23 3.71
421 426 2.049063 CGGCGGATCGGGATTCTC 60.049 66.667 0.00 0.00 0.00 2.87
422 427 4.301027 GCGGCGGATCGGGATTCT 62.301 66.667 9.78 0.00 0.00 2.40
441 446 4.899239 GATCGTGCAGGCGAGGGG 62.899 72.222 5.62 0.00 44.43 4.79
442 447 3.842923 AGATCGTGCAGGCGAGGG 61.843 66.667 5.62 0.00 44.43 4.30
443 448 2.584418 CAGATCGTGCAGGCGAGG 60.584 66.667 5.62 0.00 44.43 4.63
452 457 1.416813 GCTTCGAGGTGCAGATCGTG 61.417 60.000 17.31 13.15 39.86 4.35
453 458 1.153745 GCTTCGAGGTGCAGATCGT 60.154 57.895 17.31 0.00 39.86 3.73
454 459 1.880340 GGCTTCGAGGTGCAGATCG 60.880 63.158 13.02 13.02 40.26 3.69
455 460 0.809241 CAGGCTTCGAGGTGCAGATC 60.809 60.000 8.86 0.00 0.00 2.75
456 461 1.220206 CAGGCTTCGAGGTGCAGAT 59.780 57.895 8.86 0.00 0.00 2.90
457 462 2.659016 CAGGCTTCGAGGTGCAGA 59.341 61.111 8.86 0.00 0.00 4.26
458 463 3.123620 GCAGGCTTCGAGGTGCAG 61.124 66.667 5.41 0.00 35.91 4.41
459 464 4.704833 GGCAGGCTTCGAGGTGCA 62.705 66.667 11.39 0.00 37.68 4.57
460 465 3.984193 ATGGCAGGCTTCGAGGTGC 62.984 63.158 1.97 1.97 35.07 5.01
461 466 2.110967 CATGGCAGGCTTCGAGGTG 61.111 63.158 0.00 0.00 0.00 4.00
462 467 2.270205 CATGGCAGGCTTCGAGGT 59.730 61.111 0.00 0.00 0.00 3.85
463 468 3.207669 GCATGGCAGGCTTCGAGG 61.208 66.667 18.07 0.00 0.00 4.63
464 469 3.570638 CGCATGGCAGGCTTCGAG 61.571 66.667 22.62 1.74 0.00 4.04
502 507 3.645975 GTTCACCGTGGTGTGGCG 61.646 66.667 18.05 0.00 45.55 5.69
503 508 3.284449 GGTTCACCGTGGTGTGGC 61.284 66.667 18.05 9.59 45.55 5.01
504 509 1.597027 GAGGTTCACCGTGGTGTGG 60.597 63.158 18.05 0.00 45.55 4.17
505 510 1.954146 CGAGGTTCACCGTGGTGTG 60.954 63.158 18.05 0.00 45.55 3.82
506 511 2.420043 CGAGGTTCACCGTGGTGT 59.580 61.111 18.05 0.00 45.55 4.16
507 512 3.041940 GCGAGGTTCACCGTGGTG 61.042 66.667 12.91 12.91 46.64 4.17
508 513 4.309950 GGCGAGGTTCACCGTGGT 62.310 66.667 0.00 0.00 42.08 4.16
509 514 3.605749 ATGGCGAGGTTCACCGTGG 62.606 63.158 0.00 0.00 42.08 4.94
510 515 2.047274 ATGGCGAGGTTCACCGTG 60.047 61.111 0.00 0.00 42.08 4.94
511 516 2.264794 GATGGCGAGGTTCACCGT 59.735 61.111 0.00 0.00 42.08 4.83
512 517 2.885644 CGATGGCGAGGTTCACCG 60.886 66.667 0.00 0.00 42.08 4.94
513 518 3.195698 GCGATGGCGAGGTTCACC 61.196 66.667 0.00 0.00 40.82 4.02
532 537 4.699522 GTGGCTGGACCGGGACAC 62.700 72.222 6.32 1.68 43.94 3.67
540 545 4.699522 GTCACGGGGTGGCTGGAC 62.700 72.222 0.00 0.00 35.05 4.02
558 563 4.722700 TTCTTGCGCAGGGCCTCC 62.723 66.667 20.24 0.00 42.61 4.30
559 564 3.130160 CTTCTTGCGCAGGGCCTC 61.130 66.667 20.24 0.00 42.61 4.70
560 565 4.729918 CCTTCTTGCGCAGGGCCT 62.730 66.667 20.24 0.00 42.61 5.19
563 568 2.086251 TTTTGCCTTCTTGCGCAGGG 62.086 55.000 20.24 16.43 36.14 4.45
564 569 0.940991 GTTTTGCCTTCTTGCGCAGG 60.941 55.000 14.22 14.22 36.14 4.85
565 570 1.270777 CGTTTTGCCTTCTTGCGCAG 61.271 55.000 11.31 5.25 36.14 5.18
566 571 1.299014 CGTTTTGCCTTCTTGCGCA 60.299 52.632 5.66 5.66 0.00 6.09
567 572 2.648318 GCGTTTTGCCTTCTTGCGC 61.648 57.895 0.00 0.00 37.76 6.09
568 573 3.526029 GCGTTTTGCCTTCTTGCG 58.474 55.556 0.00 0.00 37.76 4.85
610 615 4.133796 GACATGGCCGGGCAAAGC 62.134 66.667 36.08 21.80 0.00 3.51
611 616 3.451894 GGACATGGCCGGGCAAAG 61.452 66.667 36.08 30.02 0.00 2.77
612 617 3.936772 GAGGACATGGCCGGGCAAA 62.937 63.158 36.08 13.58 0.00 3.68
613 618 4.424711 GAGGACATGGCCGGGCAA 62.425 66.667 36.08 18.63 0.00 4.52
615 620 4.864334 CAGAGGACATGGCCGGGC 62.864 72.222 23.42 23.42 0.00 6.13
616 621 4.181010 CCAGAGGACATGGCCGGG 62.181 72.222 13.29 11.95 0.00 5.73
617 622 4.181010 CCCAGAGGACATGGCCGG 62.181 72.222 13.29 7.59 36.43 6.13
618 623 4.181010 CCCCAGAGGACATGGCCG 62.181 72.222 13.29 0.00 38.24 6.13
619 624 2.692368 TCCCCAGAGGACATGGCC 60.692 66.667 10.65 10.65 40.93 5.36
626 631 1.311403 CCTAGCTGTCCCCAGAGGA 59.689 63.158 0.00 0.00 44.91 3.71
627 632 1.764054 CCCTAGCTGTCCCCAGAGG 60.764 68.421 0.00 0.00 41.50 3.69
628 633 0.758685 CTCCCTAGCTGTCCCCAGAG 60.759 65.000 0.00 0.00 41.50 3.35
629 634 1.311403 CTCCCTAGCTGTCCCCAGA 59.689 63.158 0.00 0.00 41.50 3.86
630 635 1.764054 CCTCCCTAGCTGTCCCCAG 60.764 68.421 0.00 0.00 41.91 4.45
631 636 2.243774 CTCCTCCCTAGCTGTCCCCA 62.244 65.000 0.00 0.00 0.00 4.96
632 637 1.458588 CTCCTCCCTAGCTGTCCCC 60.459 68.421 0.00 0.00 0.00 4.81
633 638 1.458588 CCTCCTCCCTAGCTGTCCC 60.459 68.421 0.00 0.00 0.00 4.46
634 639 1.458588 CCCTCCTCCCTAGCTGTCC 60.459 68.421 0.00 0.00 0.00 4.02
635 640 0.469144 CTCCCTCCTCCCTAGCTGTC 60.469 65.000 0.00 0.00 0.00 3.51
636 641 1.623625 CTCCCTCCTCCCTAGCTGT 59.376 63.158 0.00 0.00 0.00 4.40
637 642 1.152355 CCTCCCTCCTCCCTAGCTG 60.152 68.421 0.00 0.00 0.00 4.24
638 643 2.408203 CCCTCCCTCCTCCCTAGCT 61.408 68.421 0.00 0.00 0.00 3.32
639 644 2.202899 CCCTCCCTCCTCCCTAGC 59.797 72.222 0.00 0.00 0.00 3.42
640 645 0.703056 TCTCCCTCCCTCCTCCCTAG 60.703 65.000 0.00 0.00 0.00 3.02
641 646 0.703056 CTCTCCCTCCCTCCTCCCTA 60.703 65.000 0.00 0.00 0.00 3.53
642 647 2.018086 CTCTCCCTCCCTCCTCCCT 61.018 68.421 0.00 0.00 0.00 4.20
643 648 2.612251 CTCTCCCTCCCTCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
644 649 2.015726 TCCTCTCCCTCCCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
645 650 1.541672 CTCCTCTCCCTCCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
651 656 2.766229 GCACCCTCCTCTCCCTCC 60.766 72.222 0.00 0.00 0.00 4.30
697 702 1.315257 ATGTCGCTTCCATGGGCAAC 61.315 55.000 13.02 4.37 0.00 4.17
699 704 1.750018 CATGTCGCTTCCATGGGCA 60.750 57.895 13.02 0.00 36.81 5.36
705 710 2.989639 CCTCCCATGTCGCTTCCA 59.010 61.111 0.00 0.00 0.00 3.53
708 713 0.107456 CATAGCCTCCCATGTCGCTT 59.893 55.000 0.00 0.00 32.76 4.68
723 728 7.060383 ACAAGACAATAGGGATCTCACATAG 57.940 40.000 0.00 0.00 0.00 2.23
728 733 5.363868 CACCTACAAGACAATAGGGATCTCA 59.636 44.000 0.00 0.00 42.11 3.27
755 760 2.668185 TTTCGCGGTTGCTTCCCTCA 62.668 55.000 6.13 0.00 39.65 3.86
777 782 4.123497 AGCAAAAACTTTGTCAACCCTC 57.877 40.909 1.45 0.00 0.00 4.30
778 783 5.046950 TGTTAGCAAAAACTTTGTCAACCCT 60.047 36.000 11.79 0.63 0.00 4.34
805 813 6.520790 CACGATTGTGTTGTCATACTCAATTG 59.479 38.462 4.78 17.50 43.01 2.32
808 816 5.293560 TCACGATTGTGTTGTCATACTCAA 58.706 37.500 12.90 0.00 46.49 3.02
842 850 3.181451 GGCTATGGAGGATTGACATGTCA 60.181 47.826 24.56 24.56 37.91 3.58
884 892 0.607217 CACTGATTGGGCTGTGCAGA 60.607 55.000 3.02 0.00 32.34 4.26
925 940 8.358148 GGATATATGGTTATATACACACGGAGG 58.642 40.741 0.00 0.00 35.22 4.30
956 980 1.691219 CCAATGGGGCACAGTAGGT 59.309 57.895 0.00 0.00 0.00 3.08
1196 1226 1.475169 CCTCTGCAGTGACTGGTGGA 61.475 60.000 17.19 0.00 31.21 4.02
1202 1232 3.067091 CCAGCCTCTGCAGTGACT 58.933 61.111 17.19 8.12 41.13 3.41
1260 1290 2.410638 AAAGCACGACGGTAGCGACA 62.411 55.000 22.88 0.00 0.00 4.35
1266 1296 1.074319 GCGATGAAAGCACGACGGTA 61.074 55.000 0.00 0.00 34.19 4.02
1305 1335 1.293924 GGACATCATGCGTCTTGAGG 58.706 55.000 12.92 6.07 33.73 3.86
1359 1389 0.538118 AGTATGGTAGCCGGCGAAAA 59.462 50.000 23.20 9.28 0.00 2.29
1570 2833 6.147656 CCAAAAGGCCAAAATATTCACTTGAC 59.852 38.462 5.01 0.00 0.00 3.18
1638 2953 8.699130 AGGATTTCAGTTTCAGTTTCAGAATTT 58.301 29.630 0.00 0.00 0.00 1.82
1639 2954 8.242729 AGGATTTCAGTTTCAGTTTCAGAATT 57.757 30.769 0.00 0.00 0.00 2.17
1640 2955 7.830099 AGGATTTCAGTTTCAGTTTCAGAAT 57.170 32.000 0.00 0.00 0.00 2.40
1798 3113 0.673985 CGTGAGAGAAGGTGTGGACA 59.326 55.000 0.00 0.00 0.00 4.02
2134 3458 4.346127 CCAGGATCCATATGTTGAGTGAGA 59.654 45.833 15.82 0.00 0.00 3.27
2139 3463 3.008813 CCTCCCAGGATCCATATGTTGAG 59.991 52.174 15.82 10.94 37.67 3.02
2140 3464 2.981784 CCTCCCAGGATCCATATGTTGA 59.018 50.000 15.82 2.11 37.67 3.18
2172 3496 4.136796 CACATCCACAAGGTCTTCTTTCA 58.863 43.478 0.00 0.00 32.41 2.69
2179 3503 3.072915 TGATCAACACATCCACAAGGTCT 59.927 43.478 0.00 0.00 35.89 3.85
2215 3539 3.498661 GGTCCTTTGTGATCTTCCCTTGT 60.499 47.826 0.00 0.00 0.00 3.16
2403 3810 5.526479 CCTACTTAAAAAGTATTCCCTCCGC 59.474 44.000 0.28 0.00 42.69 5.54
2544 3952 0.674895 GTGCCTTCTTCATCACCGCT 60.675 55.000 0.00 0.00 0.00 5.52
2664 4072 2.623705 CGCGGTGATTTTTGCAAAAAC 58.376 42.857 33.34 26.06 40.33 2.43
2684 4092 3.552604 TGCAACAAGATTACCGAAAGC 57.447 42.857 0.00 0.00 0.00 3.51
2686 4094 5.233263 GCTTTTTGCAACAAGATTACCGAAA 59.767 36.000 25.67 6.89 42.31 3.46
2714 4122 8.479689 TGATTAAATGACCTAAATCACTCGGTA 58.520 33.333 0.00 0.00 34.34 4.02
2716 4124 7.786178 TGATTAAATGACCTAAATCACTCGG 57.214 36.000 0.00 0.00 34.34 4.63
2755 4293 3.036429 GCTCCTGACAATCCGGCCT 62.036 63.158 0.00 0.00 0.00 5.19
2770 4308 3.626028 AATGTTTTGTCAAGTCGGCTC 57.374 42.857 0.00 0.00 0.00 4.70
2774 5797 8.948853 ATGTATGTAAATGTTTTGTCAAGTCG 57.051 30.769 0.00 0.00 0.00 4.18
2781 5804 8.650143 AAGAGGGATGTATGTAAATGTTTTGT 57.350 30.769 0.00 0.00 0.00 2.83
2799 5822 8.793592 GCTTTTTGTTTTTAGATCTAAGAGGGA 58.206 33.333 14.63 0.00 0.00 4.20
2851 7074 1.846124 TCAAGGTGGGGGACAGGTC 60.846 63.158 0.00 0.00 0.00 3.85
2853 7076 2.757077 GTCAAGGTGGGGGACAGG 59.243 66.667 0.00 0.00 0.00 4.00
2854 7077 2.129555 CTGGTCAAGGTGGGGGACAG 62.130 65.000 0.00 0.00 33.26 3.51
2855 7078 2.039298 TGGTCAAGGTGGGGGACA 60.039 61.111 0.00 0.00 33.26 4.02
2857 7080 3.256960 GCTGGTCAAGGTGGGGGA 61.257 66.667 0.00 0.00 0.00 4.81
2858 7081 4.366684 GGCTGGTCAAGGTGGGGG 62.367 72.222 0.00 0.00 0.00 5.40
2859 7082 4.366684 GGGCTGGTCAAGGTGGGG 62.367 72.222 0.00 0.00 0.00 4.96
2860 7083 4.722700 CGGGCTGGTCAAGGTGGG 62.723 72.222 0.00 0.00 0.00 4.61
2863 7086 3.637273 GGTCGGGCTGGTCAAGGT 61.637 66.667 0.00 0.00 0.00 3.50
2864 7087 3.316573 GAGGTCGGGCTGGTCAAGG 62.317 68.421 0.00 0.00 0.00 3.61
2865 7088 2.266055 GAGGTCGGGCTGGTCAAG 59.734 66.667 0.00 0.00 0.00 3.02
2867 7090 4.671590 TCGAGGTCGGGCTGGTCA 62.672 66.667 0.00 0.00 40.29 4.02
2868 7091 4.131088 GTCGAGGTCGGGCTGGTC 62.131 72.222 0.00 0.00 40.29 4.02
2871 7094 4.135153 CTGGTCGAGGTCGGGCTG 62.135 72.222 0.00 0.00 40.29 4.85
2893 7116 4.749310 AGAAGCGGACTGGCAGCG 62.749 66.667 15.89 12.35 42.89 5.18
2894 7117 3.123620 CAGAAGCGGACTGGCAGC 61.124 66.667 15.89 7.42 38.03 5.25
2895 7118 3.123620 GCAGAAGCGGACTGGCAG 61.124 66.667 14.16 14.16 36.09 4.85
2900 7123 3.394836 GAGGGGCAGAAGCGGACT 61.395 66.667 0.00 0.00 43.41 3.85
3314 7537 4.973360 CGGTGCGGTGGCGTTTTG 62.973 66.667 0.00 0.00 44.10 2.44
3337 7560 3.732849 GTGAGGCCAGGGGGAAGG 61.733 72.222 5.01 0.00 35.59 3.46
3338 7561 3.732849 GGTGAGGCCAGGGGGAAG 61.733 72.222 5.01 0.00 37.17 3.46
3403 7626 2.674220 GGAGGAGAGGGCAACTGGG 61.674 68.421 0.00 0.00 0.00 4.45
3404 7627 2.993853 GGAGGAGAGGGCAACTGG 59.006 66.667 0.00 0.00 0.00 4.00
3405 7628 2.581354 CGGAGGAGAGGGCAACTG 59.419 66.667 0.00 0.00 0.00 3.16
3406 7629 3.394836 GCGGAGGAGAGGGCAACT 61.395 66.667 0.00 0.00 0.00 3.16
3413 7799 3.898509 CGAGCAGGCGGAGGAGAG 61.899 72.222 0.00 0.00 0.00 3.20
3423 7809 3.127352 GACCTAGACGGCGAGCAGG 62.127 68.421 16.62 18.05 35.61 4.85
3424 7810 1.729470 ATGACCTAGACGGCGAGCAG 61.729 60.000 16.62 6.66 35.61 4.24
3449 8894 3.592814 CTCCCCATGCATGCGCTG 61.593 66.667 21.69 12.85 39.64 5.18
3450 8895 4.889112 CCTCCCCATGCATGCGCT 62.889 66.667 21.69 0.00 39.64 5.92
3455 8900 4.195334 GGTCGCCTCCCCATGCAT 62.195 66.667 0.00 0.00 0.00 3.96
3502 8947 1.310904 CTCTAGTGTAGGCCGGAGAC 58.689 60.000 5.05 0.00 0.00 3.36
3503 8948 0.917533 ACTCTAGTGTAGGCCGGAGA 59.082 55.000 5.05 0.00 0.00 3.71
3507 8952 1.063764 GACGAACTCTAGTGTAGGCCG 59.936 57.143 0.00 3.31 0.00 6.13
3508 8953 1.404748 GGACGAACTCTAGTGTAGGCC 59.595 57.143 8.80 8.80 0.00 5.19
3529 8975 2.044252 CGAGGAGGGGGAAGTCGA 60.044 66.667 0.00 0.00 32.32 4.20
3530 8976 3.148279 CCGAGGAGGGGGAAGTCG 61.148 72.222 0.00 0.00 35.97 4.18
3549 8995 2.955660 CTCCTCTACTCACTGGATCCAC 59.044 54.545 11.44 0.00 0.00 4.02
3550 8996 2.853077 TCTCCTCTACTCACTGGATCCA 59.147 50.000 15.27 15.27 0.00 3.41
3551 8997 3.219281 GTCTCCTCTACTCACTGGATCC 58.781 54.545 4.20 4.20 0.00 3.36
3558 9004 2.414824 CGCTGTTGTCTCCTCTACTCAC 60.415 54.545 0.00 0.00 0.00 3.51
3559 9005 1.813178 CGCTGTTGTCTCCTCTACTCA 59.187 52.381 0.00 0.00 0.00 3.41
3593 9039 4.720902 TCCCACCATGCACAGGCG 62.721 66.667 6.93 0.00 45.35 5.52
3600 9046 0.108520 CAACATGCTTCCCACCATGC 60.109 55.000 0.00 0.00 41.88 4.06
3602 9048 0.409092 TCCAACATGCTTCCCACCAT 59.591 50.000 0.00 0.00 0.00 3.55
3606 9052 0.322816 GCTCTCCAACATGCTTCCCA 60.323 55.000 0.00 0.00 0.00 4.37
3613 9059 3.197790 CCGCCGCTCTCCAACATG 61.198 66.667 0.00 0.00 0.00 3.21
3614 9060 4.473520 CCCGCCGCTCTCCAACAT 62.474 66.667 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.