Multiple sequence alignment - TraesCS2D01G112700

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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 TraesCS2D01G112700 chr2D 100.000 6192 0 0 1 6192 62406833 62400642 0.000000e+00 11435.0
1 TraesCS2D01G112700 chr2D 96.520 431 14 1 5762 6192 473090096 473090525 0.000000e+00 712.0
2 TraesCS2D01G112700 chr2D 90.852 317 27 2 5423 5737 473089796 473090112 2.060000e-114 424.0
3 TraesCS2D01G112700 chr2D 89.967 299 27 3 247 543 328796243 328796540 3.500000e-102 383.0
4 TraesCS2D01G112700 chr2D 94.340 53 3 0 5359 5411 20348843 20348895 1.430000e-11 82.4
5 TraesCS2D01G112700 chr2A 95.246 2482 72 24 2887 5356 63361683 63359236 0.000000e+00 3888.0
6 TraesCS2D01G112700 chr2A 90.320 1529 86 30 533 2035 63364058 63362566 0.000000e+00 1947.0
7 TraesCS2D01G112700 chr2A 97.689 779 18 0 5414 6192 63357420 63356642 0.000000e+00 1339.0
8 TraesCS2D01G112700 chr2A 89.481 770 30 18 2160 2898 63362465 63361716 0.000000e+00 926.0
9 TraesCS2D01G112700 chr2A 83.968 761 77 22 1086 1836 628726118 628725393 0.000000e+00 688.0
10 TraesCS2D01G112700 chr2A 84.211 722 70 25 1127 1836 610180518 610179829 0.000000e+00 662.0
11 TraesCS2D01G112700 chr2A 94.340 212 12 0 4 215 63364265 63364054 5.990000e-85 326.0
12 TraesCS2D01G112700 chr2A 92.793 222 16 0 5762 5983 614574654 614574875 7.740000e-84 322.0
13 TraesCS2D01G112700 chr2A 86.447 273 29 6 5469 5737 614574402 614574670 6.070000e-75 292.0
14 TraesCS2D01G112700 chr2A 93.923 181 11 0 5982 6162 614574957 614575137 2.200000e-69 274.0
15 TraesCS2D01G112700 chr2A 91.667 168 11 3 1885 2050 63362646 63362480 4.830000e-56 230.0
16 TraesCS2D01G112700 chr2A 100.000 30 0 0 6163 6192 614575572 614575601 8.670000e-04 56.5
17 TraesCS2D01G112700 chr2A 100.000 28 0 0 3014 3041 16611943 16611970 1.100000e-02 52.8
18 TraesCS2D01G112700 chr2A 100.000 28 0 0 3014 3041 16625686 16625713 1.100000e-02 52.8
19 TraesCS2D01G112700 chr2B 90.416 2786 157 62 1877 4606 97955910 97953179 0.000000e+00 3565.0
20 TraesCS2D01G112700 chr2B 88.513 1419 70 30 647 2035 97957247 97955892 0.000000e+00 1631.0
21 TraesCS2D01G112700 chr2B 96.816 534 14 2 5414 5945 97950746 97950214 0.000000e+00 889.0
22 TraesCS2D01G112700 chr2B 90.755 530 17 11 4652 5171 97953187 97952680 0.000000e+00 678.0
23 TraesCS2D01G112700 chr2B 98.268 231 4 0 5962 6192 97950129 97949899 7.470000e-109 405.0
24 TraesCS2D01G112700 chr2B 93.204 206 13 1 5988 6192 552425807 552426012 1.010000e-77 302.0
25 TraesCS2D01G112700 chr2B 92.357 157 12 0 3 159 97958800 97958644 2.250000e-54 224.0
26 TraesCS2D01G112700 chr2B 93.750 144 9 0 1892 2035 97955965 97955822 3.760000e-52 217.0
27 TraesCS2D01G112700 chr2B 96.667 120 3 1 5205 5324 97952679 97952561 1.360000e-46 198.0
28 TraesCS2D01G112700 chr2B 100.000 34 0 0 5323 5356 97952343 97952310 5.180000e-06 63.9
29 TraesCS2D01G112700 chr7A 83.871 775 69 31 1086 1836 471564528 471565270 0.000000e+00 688.0
30 TraesCS2D01G112700 chr6A 84.605 721 68 23 1128 1836 17964081 17964770 0.000000e+00 676.0
31 TraesCS2D01G112700 chr6A 85.009 527 48 13 1319 1836 554798270 554798774 1.990000e-139 507.0
32 TraesCS2D01G112700 chr6A 79.681 251 26 17 1086 1321 554794659 554794899 2.310000e-34 158.0
33 TraesCS2D01G112700 chr6A 93.182 44 2 1 5526 5569 609026027 609026069 5.180000e-06 63.9
34 TraesCS2D01G112700 chr4A 83.549 772 72 29 1086 1836 625650533 625649796 0.000000e+00 671.0
35 TraesCS2D01G112700 chr4A 80.952 777 78 28 1086 1836 395049319 395048587 9.070000e-153 551.0
36 TraesCS2D01G112700 chr4A 97.222 36 1 0 5359 5394 688324487 688324522 1.860000e-05 62.1
37 TraesCS2D01G112700 chr7B 94.158 291 13 4 251 538 697030748 697030459 2.050000e-119 440.0
38 TraesCS2D01G112700 chr6D 91.582 297 23 2 248 542 327021863 327022159 5.780000e-110 409.0
39 TraesCS2D01G112700 chr3D 91.667 288 22 2 253 538 255424391 255424678 1.250000e-106 398.0
40 TraesCS2D01G112700 chr3B 91.667 288 21 3 253 538 377115119 377115405 4.500000e-106 396.0
41 TraesCS2D01G112700 chr3B 85.994 357 36 13 204 551 39465201 39464850 2.730000e-98 370.0
42 TraesCS2D01G112700 chr3A 91.349 289 22 3 253 538 319962311 319962599 5.820000e-105 392.0
43 TraesCS2D01G112700 chr1A 91.034 290 24 2 254 541 478212079 478211790 2.090000e-104 390.0
44 TraesCS2D01G112700 chr5D 88.415 328 29 9 221 540 132472957 132472631 2.710000e-103 387.0
45 TraesCS2D01G112700 chr5D 92.453 53 4 0 5359 5411 529823925 529823977 6.660000e-10 76.8
46 TraesCS2D01G112700 chrUn 92.157 51 4 0 5359 5409 29750339 29750389 8.610000e-09 73.1
47 TraesCS2D01G112700 chr1B 90.566 53 5 0 5359 5411 658448357 658448409 3.100000e-08 71.3
48 TraesCS2D01G112700 chr1B 91.489 47 4 0 5359 5405 610016126 610016172 1.440000e-06 65.8
49 TraesCS2D01G112700 chr4D 95.122 41 2 0 5371 5411 13329923 13329963 1.440000e-06 65.8


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 TraesCS2D01G112700 chr2D 62400642 62406833 6191 True 11435.000000 11435 100.000000 1 6192 1 chr2D.!!$R1 6191
1 TraesCS2D01G112700 chr2D 473089796 473090525 729 False 568.000000 712 93.686000 5423 6192 2 chr2D.!!$F3 769
2 TraesCS2D01G112700 chr2A 63356642 63364265 7623 True 1442.666667 3888 93.123833 4 6192 6 chr2A.!!$R3 6188
3 TraesCS2D01G112700 chr2A 628725393 628726118 725 True 688.000000 688 83.968000 1086 1836 1 chr2A.!!$R2 750
4 TraesCS2D01G112700 chr2A 610179829 610180518 689 True 662.000000 662 84.211000 1127 1836 1 chr2A.!!$R1 709
5 TraesCS2D01G112700 chr2A 614574402 614575601 1199 False 236.125000 322 93.290750 5469 6192 4 chr2A.!!$F3 723
6 TraesCS2D01G112700 chr2B 97949899 97958800 8901 True 874.544444 3565 94.171333 3 6192 9 chr2B.!!$R1 6189
7 TraesCS2D01G112700 chr7A 471564528 471565270 742 False 688.000000 688 83.871000 1086 1836 1 chr7A.!!$F1 750
8 TraesCS2D01G112700 chr6A 17964081 17964770 689 False 676.000000 676 84.605000 1128 1836 1 chr6A.!!$F1 708
9 TraesCS2D01G112700 chr6A 554794659 554798774 4115 False 332.500000 507 82.345000 1086 1836 2 chr6A.!!$F3 750
10 TraesCS2D01G112700 chr4A 625649796 625650533 737 True 671.000000 671 83.549000 1086 1836 1 chr4A.!!$R2 750
11 TraesCS2D01G112700 chr4A 395048587 395049319 732 True 551.000000 551 80.952000 1086 1836 1 chr4A.!!$R1 750


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
536 777 0.316937 AACGCACGTGCATTGTTCAG 60.317 50.000 37.03 21.56 42.21 3.02 F
1560 6222 0.250166 AGGTTAGTGTTGGCACCGAC 60.250 55.000 0.00 0.00 46.35 4.79 F
1881 6570 1.795768 ATTACACCGATGCGCATAGG 58.204 50.000 38.08 38.08 39.19 2.57 F
2240 7071 2.407340 TGGGGCAGGGTAATTTGTTT 57.593 45.000 0.00 0.00 0.00 2.83 F
3842 8804 1.279846 TGAGATGTGCATGCCTCTTGA 59.720 47.619 16.68 3.40 0.00 3.02 F
4060 9022 0.388659 ATCAGATGCTCACTCGCCTC 59.611 55.000 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2209 7040 0.179113 CTGCCCCAAAACACACACAC 60.179 55.0 0.00 0.00 0.00 3.82 R
2453 7302 1.247567 CAAATGCTTCCCGTCCAAGT 58.752 50.0 0.00 0.00 0.00 3.16 R
2818 7696 1.549203 GATGGCAAACAGACCACCAT 58.451 50.0 0.00 0.00 43.72 3.55 R
4045 9007 0.809241 CCTTGAGGCGAGTGAGCATC 60.809 60.0 0.00 0.00 46.74 3.91 R
4929 9893 0.179070 GCCTCCGGAACTCCTCATTC 60.179 60.0 5.23 0.00 0.00 2.67 R
5664 13530 0.443869 GTAATGTGCTGCAGTCACGG 59.556 55.0 25.65 1.04 37.26 4.94 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
25 26 4.811557 GCACCCGAATTAGAGATATATGCC 59.188 45.833 0.00 0.00 0.00 4.40
63 64 3.004734 ACTTTGGCTCTTCAAAATGGTCG 59.995 43.478 0.00 0.00 36.37 4.79
71 72 4.714632 TCTTCAAAATGGTCGAACCTTCT 58.285 39.130 0.00 0.00 39.58 2.85
93 94 2.083774 GTCTGGTGCAATCGGATTTCA 58.916 47.619 0.00 0.00 0.00 2.69
94 95 2.083774 TCTGGTGCAATCGGATTTCAC 58.916 47.619 20.55 20.55 0.00 3.18
96 97 2.083774 TGGTGCAATCGGATTTCACTC 58.916 47.619 25.22 18.11 0.00 3.51
151 152 4.885426 ATCACCGCATGATCACCC 57.115 55.556 0.00 0.00 45.52 4.61
240 481 9.991906 TCTTTATCTCTACTTCTCTAGCTCTAC 57.008 37.037 0.00 0.00 0.00 2.59
241 482 9.998106 CTTTATCTCTACTTCTCTAGCTCTACT 57.002 37.037 0.00 0.00 0.00 2.57
243 484 9.991906 TTATCTCTACTTCTCTAGCTCTACTTC 57.008 37.037 0.00 0.00 0.00 3.01
244 485 7.670605 TCTCTACTTCTCTAGCTCTACTTCT 57.329 40.000 0.00 0.00 0.00 2.85
245 486 7.723324 TCTCTACTTCTCTAGCTCTACTTCTC 58.277 42.308 0.00 0.00 0.00 2.87
246 487 7.563924 TCTCTACTTCTCTAGCTCTACTTCTCT 59.436 40.741 0.00 0.00 0.00 3.10
247 488 8.771521 TCTACTTCTCTAGCTCTACTTCTCTA 57.228 38.462 0.00 0.00 0.00 2.43
248 489 9.375974 TCTACTTCTCTAGCTCTACTTCTCTAT 57.624 37.037 0.00 0.00 0.00 1.98
249 490 9.640963 CTACTTCTCTAGCTCTACTTCTCTATC 57.359 40.741 0.00 0.00 0.00 2.08
250 491 8.263854 ACTTCTCTAGCTCTACTTCTCTATCT 57.736 38.462 0.00 0.00 0.00 1.98
251 492 8.368668 ACTTCTCTAGCTCTACTTCTCTATCTC 58.631 40.741 0.00 0.00 0.00 2.75
252 493 8.492415 TTCTCTAGCTCTACTTCTCTATCTCT 57.508 38.462 0.00 0.00 0.00 3.10
253 494 9.596308 TTCTCTAGCTCTACTTCTCTATCTCTA 57.404 37.037 0.00 0.00 0.00 2.43
254 495 9.769677 TCTCTAGCTCTACTTCTCTATCTCTAT 57.230 37.037 0.00 0.00 0.00 1.98
256 497 9.769677 TCTAGCTCTACTTCTCTATCTCTATCT 57.230 37.037 0.00 0.00 0.00 1.98
258 499 8.671987 AGCTCTACTTCTCTATCTCTATCTCT 57.328 38.462 0.00 0.00 0.00 3.10
259 500 9.769677 AGCTCTACTTCTCTATCTCTATCTCTA 57.230 37.037 0.00 0.00 0.00 2.43
260 501 9.804758 GCTCTACTTCTCTATCTCTATCTCTAC 57.195 40.741 0.00 0.00 0.00 2.59
293 534 2.786777 ACGTAAGGTTCCCATTTCACC 58.213 47.619 0.00 0.00 46.39 4.02
294 535 2.374170 ACGTAAGGTTCCCATTTCACCT 59.626 45.455 0.00 0.00 43.17 4.00
296 537 3.824443 CGTAAGGTTCCCATTTCACCTTT 59.176 43.478 8.08 0.00 46.85 3.11
297 538 4.279922 CGTAAGGTTCCCATTTCACCTTTT 59.720 41.667 8.08 0.00 46.85 2.27
298 539 5.221362 CGTAAGGTTCCCATTTCACCTTTTT 60.221 40.000 8.08 0.00 46.85 1.94
314 555 2.668144 TTTTTCCACCATCCCTTCGT 57.332 45.000 0.00 0.00 0.00 3.85
315 556 2.194201 TTTTCCACCATCCCTTCGTC 57.806 50.000 0.00 0.00 0.00 4.20
316 557 0.326927 TTTCCACCATCCCTTCGTCC 59.673 55.000 0.00 0.00 0.00 4.79
317 558 0.838554 TTCCACCATCCCTTCGTCCA 60.839 55.000 0.00 0.00 0.00 4.02
318 559 0.838554 TCCACCATCCCTTCGTCCAA 60.839 55.000 0.00 0.00 0.00 3.53
319 560 0.676782 CCACCATCCCTTCGTCCAAC 60.677 60.000 0.00 0.00 0.00 3.77
320 561 0.676782 CACCATCCCTTCGTCCAACC 60.677 60.000 0.00 0.00 0.00 3.77
321 562 0.840722 ACCATCCCTTCGTCCAACCT 60.841 55.000 0.00 0.00 0.00 3.50
322 563 0.328258 CCATCCCTTCGTCCAACCTT 59.672 55.000 0.00 0.00 0.00 3.50
323 564 1.679032 CCATCCCTTCGTCCAACCTTC 60.679 57.143 0.00 0.00 0.00 3.46
324 565 0.618981 ATCCCTTCGTCCAACCTTCC 59.381 55.000 0.00 0.00 0.00 3.46
325 566 0.765135 TCCCTTCGTCCAACCTTCCA 60.765 55.000 0.00 0.00 0.00 3.53
326 567 0.328258 CCCTTCGTCCAACCTTCCAT 59.672 55.000 0.00 0.00 0.00 3.41
327 568 1.453155 CCTTCGTCCAACCTTCCATG 58.547 55.000 0.00 0.00 0.00 3.66
328 569 1.271379 CCTTCGTCCAACCTTCCATGT 60.271 52.381 0.00 0.00 0.00 3.21
329 570 2.027561 CCTTCGTCCAACCTTCCATGTA 60.028 50.000 0.00 0.00 0.00 2.29
330 571 3.370527 CCTTCGTCCAACCTTCCATGTAT 60.371 47.826 0.00 0.00 0.00 2.29
331 572 4.141801 CCTTCGTCCAACCTTCCATGTATA 60.142 45.833 0.00 0.00 0.00 1.47
332 573 5.454755 CCTTCGTCCAACCTTCCATGTATAT 60.455 44.000 0.00 0.00 0.00 0.86
333 574 4.956085 TCGTCCAACCTTCCATGTATATG 58.044 43.478 0.00 0.00 0.00 1.78
334 575 4.651962 TCGTCCAACCTTCCATGTATATGA 59.348 41.667 0.25 0.00 36.36 2.15
335 576 5.306937 TCGTCCAACCTTCCATGTATATGAT 59.693 40.000 0.25 0.00 36.36 2.45
336 577 6.495526 TCGTCCAACCTTCCATGTATATGATA 59.504 38.462 0.25 0.00 36.36 2.15
337 578 7.015779 TCGTCCAACCTTCCATGTATATGATAA 59.984 37.037 0.25 0.00 36.36 1.75
338 579 7.824289 CGTCCAACCTTCCATGTATATGATAAT 59.176 37.037 0.25 0.00 36.36 1.28
339 580 9.167311 GTCCAACCTTCCATGTATATGATAATC 57.833 37.037 0.25 0.00 36.36 1.75
340 581 8.889445 TCCAACCTTCCATGTATATGATAATCA 58.111 33.333 0.25 0.00 36.36 2.57
341 582 9.519191 CCAACCTTCCATGTATATGATAATCAA 57.481 33.333 0.25 0.00 36.36 2.57
369 610 9.687210 CACCTTAATTTACTTACCTTTTGAACC 57.313 33.333 0.00 0.00 0.00 3.62
370 611 9.423964 ACCTTAATTTACTTACCTTTTGAACCA 57.576 29.630 0.00 0.00 0.00 3.67
375 616 9.772973 AATTTACTTACCTTTTGAACCAATTCC 57.227 29.630 0.00 0.00 33.49 3.01
376 617 7.899648 TTACTTACCTTTTGAACCAATTCCA 57.100 32.000 0.00 0.00 33.49 3.53
377 618 6.156748 ACTTACCTTTTGAACCAATTCCAC 57.843 37.500 0.00 0.00 33.49 4.02
378 619 5.897250 ACTTACCTTTTGAACCAATTCCACT 59.103 36.000 0.00 0.00 33.49 4.00
379 620 6.382859 ACTTACCTTTTGAACCAATTCCACTT 59.617 34.615 0.00 0.00 33.49 3.16
380 621 5.692115 ACCTTTTGAACCAATTCCACTTT 57.308 34.783 0.00 0.00 33.49 2.66
381 622 6.800072 ACCTTTTGAACCAATTCCACTTTA 57.200 33.333 0.00 0.00 33.49 1.85
382 623 7.189079 ACCTTTTGAACCAATTCCACTTTAA 57.811 32.000 0.00 0.00 33.49 1.52
383 624 7.801104 ACCTTTTGAACCAATTCCACTTTAAT 58.199 30.769 0.00 0.00 33.49 1.40
384 625 8.271458 ACCTTTTGAACCAATTCCACTTTAATT 58.729 29.630 0.00 0.00 33.49 1.40
385 626 9.119418 CCTTTTGAACCAATTCCACTTTAATTT 57.881 29.630 0.00 0.00 33.49 1.82
388 629 8.804688 TTGAACCAATTCCACTTTAATTTACG 57.195 30.769 0.00 0.00 33.49 3.18
389 630 7.942990 TGAACCAATTCCACTTTAATTTACGT 58.057 30.769 0.00 0.00 33.49 3.57
390 631 9.064706 TGAACCAATTCCACTTTAATTTACGTA 57.935 29.630 0.00 0.00 33.49 3.57
393 634 9.233649 ACCAATTCCACTTTAATTTACGTATCA 57.766 29.630 0.00 0.00 0.00 2.15
435 676 6.683974 AAGGTAATTCATGGTCAGAATTCG 57.316 37.500 4.60 0.00 42.82 3.34
436 677 5.989477 AGGTAATTCATGGTCAGAATTCGA 58.011 37.500 4.60 0.00 42.82 3.71
437 678 6.595682 AGGTAATTCATGGTCAGAATTCGAT 58.404 36.000 4.60 0.00 42.82 3.59
438 679 6.484643 AGGTAATTCATGGTCAGAATTCGATG 59.515 38.462 4.60 0.00 42.82 3.84
439 680 6.483307 GGTAATTCATGGTCAGAATTCGATGA 59.517 38.462 4.60 0.00 42.82 2.92
440 681 7.012327 GGTAATTCATGGTCAGAATTCGATGAA 59.988 37.037 15.67 15.67 42.82 2.57
441 682 5.801350 TTCATGGTCAGAATTCGATGAAC 57.199 39.130 5.92 5.92 35.22 3.18
442 683 4.831107 TCATGGTCAGAATTCGATGAACA 58.169 39.130 15.46 15.46 46.51 3.18
447 688 7.864108 TGGTCAGAATTCGATGAACATTTAT 57.136 32.000 10.52 0.00 38.20 1.40
448 689 8.279970 TGGTCAGAATTCGATGAACATTTATT 57.720 30.769 10.52 0.00 38.20 1.40
449 690 8.739039 TGGTCAGAATTCGATGAACATTTATTT 58.261 29.630 10.52 0.00 38.20 1.40
459 700 9.381027 TCGATGAACATTTATTTATTCAATCGC 57.619 29.630 0.00 0.00 34.88 4.58
460 701 9.168353 CGATGAACATTTATTTATTCAATCGCA 57.832 29.630 0.00 0.00 34.88 5.10
471 712 7.928908 TTTATTCAATCGCATTATTCTTGGC 57.071 32.000 0.00 0.00 0.00 4.52
472 713 4.979943 TTCAATCGCATTATTCTTGGCA 57.020 36.364 0.00 0.00 0.00 4.92
473 714 4.979943 TCAATCGCATTATTCTTGGCAA 57.020 36.364 0.00 0.00 0.00 4.52
474 715 4.923893 TCAATCGCATTATTCTTGGCAAG 58.076 39.130 21.17 21.17 0.00 4.01
475 716 4.398988 TCAATCGCATTATTCTTGGCAAGT 59.601 37.500 25.39 11.09 0.00 3.16
476 717 5.588246 TCAATCGCATTATTCTTGGCAAGTA 59.412 36.000 25.39 17.65 0.00 2.24
477 718 6.094742 TCAATCGCATTATTCTTGGCAAGTAA 59.905 34.615 25.39 17.75 0.00 2.24
478 719 5.888691 TCGCATTATTCTTGGCAAGTAAA 57.111 34.783 25.39 17.66 0.00 2.01
479 720 6.449635 TCGCATTATTCTTGGCAAGTAAAT 57.550 33.333 25.39 19.98 0.00 1.40
480 721 6.494842 TCGCATTATTCTTGGCAAGTAAATC 58.505 36.000 25.39 12.49 0.00 2.17
481 722 6.094742 TCGCATTATTCTTGGCAAGTAAATCA 59.905 34.615 25.39 11.61 0.00 2.57
482 723 6.197096 CGCATTATTCTTGGCAAGTAAATCAC 59.803 38.462 25.39 15.10 0.00 3.06
483 724 7.035004 GCATTATTCTTGGCAAGTAAATCACA 58.965 34.615 25.39 8.36 0.00 3.58
484 725 7.545265 GCATTATTCTTGGCAAGTAAATCACAA 59.455 33.333 25.39 11.13 0.00 3.33
485 726 9.421806 CATTATTCTTGGCAAGTAAATCACAAA 57.578 29.630 25.39 10.44 0.00 2.83
486 727 8.810652 TTATTCTTGGCAAGTAAATCACAAAC 57.189 30.769 25.39 0.00 0.00 2.93
487 728 6.463995 TTCTTGGCAAGTAAATCACAAACT 57.536 33.333 25.39 0.00 0.00 2.66
488 729 7.575414 TTCTTGGCAAGTAAATCACAAACTA 57.425 32.000 25.39 0.00 0.00 2.24
489 730 7.575414 TCTTGGCAAGTAAATCACAAACTAA 57.425 32.000 25.39 0.00 0.00 2.24
490 731 7.422399 TCTTGGCAAGTAAATCACAAACTAAC 58.578 34.615 25.39 0.00 0.00 2.34
491 732 6.701145 TGGCAAGTAAATCACAAACTAACA 57.299 33.333 0.00 0.00 0.00 2.41
492 733 7.283625 TGGCAAGTAAATCACAAACTAACAT 57.716 32.000 0.00 0.00 0.00 2.71
493 734 8.397575 TGGCAAGTAAATCACAAACTAACATA 57.602 30.769 0.00 0.00 0.00 2.29
494 735 8.293867 TGGCAAGTAAATCACAAACTAACATAC 58.706 33.333 0.00 0.00 0.00 2.39
495 736 8.512138 GGCAAGTAAATCACAAACTAACATACT 58.488 33.333 0.00 0.00 0.00 2.12
528 769 2.621542 CGTTGTAACGCACGTGCA 59.378 55.556 37.03 18.05 46.06 4.57
529 770 1.203065 CGTTGTAACGCACGTGCAT 59.797 52.632 37.03 27.35 46.06 3.96
530 771 0.383737 CGTTGTAACGCACGTGCATT 60.384 50.000 37.03 31.72 46.06 3.56
531 772 1.041726 GTTGTAACGCACGTGCATTG 58.958 50.000 37.03 24.38 42.21 2.82
532 773 0.658368 TTGTAACGCACGTGCATTGT 59.342 45.000 37.03 25.05 42.21 2.71
533 774 0.658368 TGTAACGCACGTGCATTGTT 59.342 45.000 37.03 31.54 42.21 2.83
534 775 1.314581 GTAACGCACGTGCATTGTTC 58.685 50.000 37.03 20.09 42.21 3.18
535 776 0.938008 TAACGCACGTGCATTGTTCA 59.062 45.000 37.03 13.37 42.21 3.18
536 777 0.316937 AACGCACGTGCATTGTTCAG 60.317 50.000 37.03 21.56 42.21 3.02
537 778 1.279539 CGCACGTGCATTGTTCAGT 59.720 52.632 37.03 0.00 42.21 3.41
604 845 1.605232 CCCCGTGACTTGTTTGGTTAC 59.395 52.381 0.00 0.00 0.00 2.50
610 851 3.625764 GTGACTTGTTTGGTTACAGCAGA 59.374 43.478 0.00 0.00 0.00 4.26
617 858 3.838244 TTGGTTACAGCAGAGACTTGT 57.162 42.857 0.00 0.00 0.00 3.16
660 1893 9.780186 AATAGCAGATTATAACCCTCAAACTAC 57.220 33.333 0.00 0.00 0.00 2.73
665 1905 7.438459 CAGATTATAACCCTCAAACTACGAAGG 59.562 40.741 0.00 0.00 0.00 3.46
693 1933 5.717078 AAAACTCCTTTATTCCCCGAAAC 57.283 39.130 0.00 0.00 0.00 2.78
726 1969 5.086104 TGCTTCATAAGGTAGGAGTGAAC 57.914 43.478 0.00 0.00 0.00 3.18
815 2058 5.907197 TCTTCGAGCAGTTAAAAGTTCAG 57.093 39.130 0.00 0.00 0.00 3.02
816 2059 5.597806 TCTTCGAGCAGTTAAAAGTTCAGA 58.402 37.500 0.00 0.00 0.00 3.27
844 2088 1.843992 AAACAAGAACTACGCGTCGT 58.156 45.000 18.63 14.34 44.35 4.34
937 2181 3.367395 GGAAACTCCAAAATACTGCAGCC 60.367 47.826 15.27 0.00 36.28 4.85
939 2183 2.440409 ACTCCAAAATACTGCAGCCTG 58.560 47.619 15.27 3.92 0.00 4.85
943 2187 1.089920 AAAATACTGCAGCCTGAGCG 58.910 50.000 15.27 0.00 46.67 5.03
1046 2291 1.191489 GCAGCCTCCTCCTATCTCCC 61.191 65.000 0.00 0.00 0.00 4.30
1163 2437 2.939022 GTGTTCGTGGCTGCTGTC 59.061 61.111 0.00 0.00 0.00 3.51
1308 2591 1.912371 GCTGGTGCTACTTTCGTGCC 61.912 60.000 0.00 0.00 36.03 5.01
1409 6069 6.936900 TGAGCCTAATTGAAATAGTAGATGGC 59.063 38.462 0.00 0.00 36.11 4.40
1446 6107 1.403780 CCGTTTGGTTCCTACGAGGAG 60.404 57.143 14.77 0.00 46.73 3.69
1461 6122 2.739932 CGAGGAGTTAATCAGCTGGTGG 60.740 54.545 15.13 0.00 0.00 4.61
1560 6222 0.250166 AGGTTAGTGTTGGCACCGAC 60.250 55.000 0.00 0.00 46.35 4.79
1595 6262 3.374745 CAAAGATTAATGACATGGCCGC 58.625 45.455 0.00 0.00 0.00 6.53
1732 6402 2.237392 CCTTAGCCAACTCTGGTAGCTT 59.763 50.000 0.00 0.00 45.53 3.74
1875 6564 5.706916 ACCTTACTATATTACACCGATGCG 58.293 41.667 0.00 0.00 0.00 4.73
1881 6570 1.795768 ATTACACCGATGCGCATAGG 58.204 50.000 38.08 38.08 39.19 2.57
2056 6886 3.795488 GCCGCAAGTTCTAATAATTGGGC 60.795 47.826 0.00 0.00 35.10 5.36
2098 6929 2.562298 GAGCCCCAATTGTGACAATTCA 59.438 45.455 19.77 0.00 0.00 2.57
2101 6932 3.509575 GCCCCAATTGTGACAATTCAGTA 59.490 43.478 19.77 0.00 30.10 2.74
2102 6933 4.160252 GCCCCAATTGTGACAATTCAGTAT 59.840 41.667 19.77 0.00 30.10 2.12
2103 6934 5.359576 GCCCCAATTGTGACAATTCAGTATA 59.640 40.000 19.77 0.00 30.10 1.47
2125 6956 4.490743 ACCGAGGTTTTGTTTTTCTGTTG 58.509 39.130 0.00 0.00 0.00 3.33
2139 6970 7.556275 TGTTTTTCTGTTGAGAGTTTACCATCT 59.444 33.333 0.00 0.00 0.00 2.90
2209 7040 5.231702 TGGAATGAATTTGATGTTGCTGTG 58.768 37.500 0.00 0.00 0.00 3.66
2240 7071 2.407340 TGGGGCAGGGTAATTTGTTT 57.593 45.000 0.00 0.00 0.00 2.83
2315 7164 5.706916 CTGATTCCTGATGTTTTGAACAGG 58.293 41.667 0.00 0.00 45.95 4.00
2369 7218 3.202818 TGGGTGGAAGCAACTATGATGAT 59.797 43.478 0.00 0.00 34.77 2.45
2576 7426 6.346096 TGTTATTGATACACCAGGTAAGAGC 58.654 40.000 0.00 0.00 35.14 4.09
2597 7447 6.986231 AGAGCGTTTTGGATCTTTTGAATTTT 59.014 30.769 0.00 0.00 0.00 1.82
2650 7505 9.961265 TTTTGAACCTACGATGTCTATATAGTG 57.039 33.333 9.58 0.00 0.00 2.74
2882 7834 9.430399 AATTTCCTGAGTAATGATCCATGATTT 57.570 29.630 0.00 0.00 0.00 2.17
2883 7835 8.455903 TTTCCTGAGTAATGATCCATGATTTC 57.544 34.615 0.00 0.00 0.00 2.17
2884 7836 6.537355 TCCTGAGTAATGATCCATGATTTCC 58.463 40.000 0.00 0.00 0.00 3.13
2885 7837 6.101588 TCCTGAGTAATGATCCATGATTTCCA 59.898 38.462 0.00 0.00 0.00 3.53
2886 7838 6.206243 CCTGAGTAATGATCCATGATTTCCAC 59.794 42.308 0.00 0.00 0.00 4.02
2887 7839 6.903516 TGAGTAATGATCCATGATTTCCACT 58.096 36.000 0.00 0.00 0.00 4.00
2888 7840 8.033178 TGAGTAATGATCCATGATTTCCACTA 57.967 34.615 0.00 0.00 0.00 2.74
2889 7841 8.663167 TGAGTAATGATCCATGATTTCCACTAT 58.337 33.333 0.00 0.00 0.00 2.12
2890 7842 9.512588 GAGTAATGATCCATGATTTCCACTATT 57.487 33.333 0.00 0.00 0.00 1.73
2891 7843 9.872684 AGTAATGATCCATGATTTCCACTATTT 57.127 29.630 0.00 0.00 0.00 1.40
2950 7904 6.756542 GGTTGTTGTTTATTCTAATCCCATGC 59.243 38.462 0.00 0.00 0.00 4.06
2998 7954 2.700371 TGAGACTCCGCCACATGATTAT 59.300 45.455 0.00 0.00 0.00 1.28
3133 8092 9.643693 AATGTATTGCTCCTTATTTTGACTTTG 57.356 29.630 0.00 0.00 0.00 2.77
3173 8132 3.130340 GCGTTGGATGTTGTATTGGGAAT 59.870 43.478 0.00 0.00 0.00 3.01
3320 8279 5.741982 GTGAAAGCAGCTTCGTAAAGAAAAA 59.258 36.000 8.48 0.00 38.57 1.94
3377 8336 9.615295 GCTAATCGTGTTTTTAGGAAAATGTTA 57.385 29.630 0.00 0.00 37.12 2.41
3415 8374 3.009033 TCACCAATGTGGAAACTAGGGAG 59.991 47.826 0.18 0.00 40.96 4.30
3437 8396 5.506708 AGCCGGTAAATTTATCTTCCTTGT 58.493 37.500 1.90 0.00 0.00 3.16
3443 8402 7.273381 CGGTAAATTTATCTTCCTTGTTGCAAG 59.727 37.037 0.00 2.16 0.00 4.01
3510 8471 9.675464 ATGTTTTGCTAATCATCCATTTCATTT 57.325 25.926 0.00 0.00 0.00 2.32
3540 8501 6.710744 GGATAGGATTATTTGACATGACCGTT 59.289 38.462 0.00 0.00 0.00 4.44
3732 8693 7.159372 TGGTCTTAGTTTTCACTTATGGAGAC 58.841 38.462 0.00 0.00 34.06 3.36
3835 8797 2.602878 CCAAACTTGAGATGTGCATGC 58.397 47.619 11.82 11.82 0.00 4.06
3840 8802 2.290768 ACTTGAGATGTGCATGCCTCTT 60.291 45.455 16.68 6.65 0.00 2.85
3841 8803 1.746470 TGAGATGTGCATGCCTCTTG 58.254 50.000 16.68 0.00 0.00 3.02
3842 8804 1.279846 TGAGATGTGCATGCCTCTTGA 59.720 47.619 16.68 3.40 0.00 3.02
3861 8823 7.118535 CCTCTTGATGAATCATATGAGCTTGAG 59.881 40.741 11.78 9.51 36.56 3.02
3862 8824 7.732996 TCTTGATGAATCATATGAGCTTGAGA 58.267 34.615 11.78 5.88 36.56 3.27
3863 8825 8.376270 TCTTGATGAATCATATGAGCTTGAGAT 58.624 33.333 11.78 0.00 36.56 2.75
4045 9007 4.884164 GGAGGAAACCCATTTACAGATCAG 59.116 45.833 0.00 0.00 30.03 2.90
4060 9022 0.388659 ATCAGATGCTCACTCGCCTC 59.611 55.000 0.00 0.00 0.00 4.70
4363 9325 9.868160 CCAGAAACTTATCCCCTTCTTTATAAT 57.132 33.333 0.00 0.00 0.00 1.28
4546 9510 2.406401 GCGATGCACACAGCCATC 59.594 61.111 0.00 0.00 44.83 3.51
4623 9587 9.227777 GTTGTTGGAAAAAGTACTAGGACATAT 57.772 33.333 8.10 0.00 0.00 1.78
4629 9593 9.968870 GGAAAAAGTACTAGGACATATCTGTAG 57.031 37.037 8.10 0.00 35.14 2.74
4666 9630 5.860941 TCCAGCTTTGTTTGGACATTTTA 57.139 34.783 0.00 0.00 38.53 1.52
4708 9672 5.241662 CCAGAACTATCTAAATAGCTGCCC 58.758 45.833 0.00 0.00 38.81 5.36
4710 9674 6.471146 CAGAACTATCTAAATAGCTGCCCAT 58.529 40.000 0.00 0.00 38.81 4.00
4809 9773 1.294659 CGGTGGAGAAGCTGCAAGTC 61.295 60.000 1.02 0.00 32.80 3.01
4929 9893 0.395036 TCGAGAAGGCTCAGGAGGAG 60.395 60.000 0.00 0.00 46.93 3.69
5078 10048 5.890110 CAGATATACTGTACTTGGTTGCG 57.110 43.478 0.00 0.00 41.30 4.85
5119 10092 0.038166 GTTGAATGCCTGGGGAGTCA 59.962 55.000 7.16 7.16 38.65 3.41
5120 10093 0.776810 TTGAATGCCTGGGGAGTCAA 59.223 50.000 17.32 17.32 45.24 3.18
5121 10094 0.776810 TGAATGCCTGGGGAGTCAAA 59.223 50.000 8.69 0.00 37.59 2.69
5289 10264 3.742013 GCCAATGGGTTTATGCTTGGATG 60.742 47.826 0.00 0.00 38.92 3.51
5356 10550 1.513158 CCTCGTACTGGTGCCAGAG 59.487 63.158 23.55 13.96 46.30 3.35
5373 10859 3.611113 CCAGAGTAATCAAACCACGTACG 59.389 47.826 15.01 15.01 0.00 3.67
5374 10860 3.060363 CAGAGTAATCAAACCACGTACGC 59.940 47.826 16.72 0.00 0.00 4.42
5375 10861 2.988493 GAGTAATCAAACCACGTACGCA 59.012 45.455 16.72 0.00 0.00 5.24
5376 10862 2.991190 AGTAATCAAACCACGTACGCAG 59.009 45.455 16.72 9.51 0.00 5.18
5377 10863 1.153353 AATCAAACCACGTACGCAGG 58.847 50.000 21.68 21.68 0.00 4.85
5383 10869 3.172575 CACGTACGCAGGAGCACG 61.173 66.667 16.72 0.00 43.37 5.34
5388 10874 3.076258 TACGCAGGAGCACGGATGG 62.076 63.158 0.00 0.00 42.27 3.51
5569 13432 2.861462 TCCTTTGTTTCAAACGGCAG 57.139 45.000 0.00 0.00 0.00 4.85
5617 13483 6.254281 TCGATTCTCCAAAATTCCTTTGAC 57.746 37.500 0.00 0.00 46.35 3.18
5620 13486 6.749118 CGATTCTCCAAAATTCCTTTGACATC 59.251 38.462 0.00 0.00 46.35 3.06
5642 13508 3.506810 CCGCTGTTTCAACTTTCAAACA 58.493 40.909 0.00 0.00 39.61 2.83
5664 13530 1.531578 GGTCTGAGAACGGAAACAAGC 59.468 52.381 0.00 0.00 32.84 4.01
6057 14074 2.123726 CCTGCAATGGGTAGGGCC 60.124 66.667 0.00 0.00 44.95 5.80
6097 14115 0.984995 AGCTCTAAGGGCTCGGTTTT 59.015 50.000 0.00 0.00 34.70 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.395768 GCATATATCTCTAATTCGGGTGCCT 60.396 44.000 0.00 0.00 0.00 4.75
1 2 4.811557 GCATATATCTCTAATTCGGGTGCC 59.188 45.833 0.00 0.00 0.00 5.01
25 26 6.243900 AGCCAAAGTCATATCTCCCATTATG 58.756 40.000 0.00 0.00 0.00 1.90
63 64 3.402628 TTGCACCAGACTAGAAGGTTC 57.597 47.619 0.00 0.00 32.15 3.62
71 72 3.055458 TGAAATCCGATTGCACCAGACTA 60.055 43.478 0.00 0.00 0.00 2.59
151 152 8.817100 CATGAACATCTTTGATTTCATTGATGG 58.183 33.333 18.71 8.35 36.72 3.51
215 456 9.998106 AGTAGAGCTAGAGAAGTAGAGATAAAG 57.002 37.037 0.00 0.00 0.00 1.85
217 458 9.991906 GAAGTAGAGCTAGAGAAGTAGAGATAA 57.008 37.037 0.00 0.00 0.00 1.75
218 459 9.375974 AGAAGTAGAGCTAGAGAAGTAGAGATA 57.624 37.037 0.00 0.00 0.00 1.98
219 460 8.263854 AGAAGTAGAGCTAGAGAAGTAGAGAT 57.736 38.462 0.00 0.00 0.00 2.75
220 461 7.563924 AGAGAAGTAGAGCTAGAGAAGTAGAGA 59.436 40.741 0.00 0.00 0.00 3.10
221 462 7.727181 AGAGAAGTAGAGCTAGAGAAGTAGAG 58.273 42.308 0.00 0.00 0.00 2.43
222 463 7.670605 AGAGAAGTAGAGCTAGAGAAGTAGA 57.329 40.000 0.00 0.00 0.00 2.59
223 464 9.640963 GATAGAGAAGTAGAGCTAGAGAAGTAG 57.359 40.741 0.00 0.00 0.00 2.57
224 465 9.375974 AGATAGAGAAGTAGAGCTAGAGAAGTA 57.624 37.037 0.00 0.00 0.00 2.24
225 466 8.263854 AGATAGAGAAGTAGAGCTAGAGAAGT 57.736 38.462 0.00 0.00 0.00 3.01
226 467 8.589338 AGAGATAGAGAAGTAGAGCTAGAGAAG 58.411 40.741 0.00 0.00 0.00 2.85
227 468 8.492415 AGAGATAGAGAAGTAGAGCTAGAGAA 57.508 38.462 0.00 0.00 0.00 2.87
228 469 9.769677 ATAGAGATAGAGAAGTAGAGCTAGAGA 57.230 37.037 0.00 0.00 0.00 3.10
230 471 9.769677 AGATAGAGATAGAGAAGTAGAGCTAGA 57.230 37.037 0.00 0.00 0.00 2.43
232 473 9.769677 AGAGATAGAGATAGAGAAGTAGAGCTA 57.230 37.037 0.00 0.00 0.00 3.32
233 474 8.671987 AGAGATAGAGATAGAGAAGTAGAGCT 57.328 38.462 0.00 0.00 0.00 4.09
234 475 9.804758 GTAGAGATAGAGATAGAGAAGTAGAGC 57.195 40.741 0.00 0.00 0.00 4.09
255 496 9.905171 ACCTTACGTTCTTTTTAAGTAGTAGAG 57.095 33.333 0.00 0.00 0.00 2.43
295 536 2.510613 GACGAAGGGATGGTGGAAAAA 58.489 47.619 0.00 0.00 0.00 1.94
296 537 1.271707 GGACGAAGGGATGGTGGAAAA 60.272 52.381 0.00 0.00 0.00 2.29
297 538 0.326927 GGACGAAGGGATGGTGGAAA 59.673 55.000 0.00 0.00 0.00 3.13
298 539 0.838554 TGGACGAAGGGATGGTGGAA 60.839 55.000 0.00 0.00 0.00 3.53
299 540 0.838554 TTGGACGAAGGGATGGTGGA 60.839 55.000 0.00 0.00 0.00 4.02
300 541 0.676782 GTTGGACGAAGGGATGGTGG 60.677 60.000 0.00 0.00 0.00 4.61
301 542 0.676782 GGTTGGACGAAGGGATGGTG 60.677 60.000 0.00 0.00 0.00 4.17
302 543 0.840722 AGGTTGGACGAAGGGATGGT 60.841 55.000 0.00 0.00 0.00 3.55
303 544 0.328258 AAGGTTGGACGAAGGGATGG 59.672 55.000 0.00 0.00 0.00 3.51
304 545 1.679032 GGAAGGTTGGACGAAGGGATG 60.679 57.143 0.00 0.00 0.00 3.51
305 546 0.618981 GGAAGGTTGGACGAAGGGAT 59.381 55.000 0.00 0.00 0.00 3.85
306 547 0.765135 TGGAAGGTTGGACGAAGGGA 60.765 55.000 0.00 0.00 0.00 4.20
307 548 0.328258 ATGGAAGGTTGGACGAAGGG 59.672 55.000 0.00 0.00 0.00 3.95
308 549 1.271379 ACATGGAAGGTTGGACGAAGG 60.271 52.381 0.00 0.00 0.00 3.46
309 550 2.185004 ACATGGAAGGTTGGACGAAG 57.815 50.000 0.00 0.00 0.00 3.79
310 551 3.992943 ATACATGGAAGGTTGGACGAA 57.007 42.857 0.00 0.00 28.09 3.85
311 552 4.651962 TCATATACATGGAAGGTTGGACGA 59.348 41.667 0.00 0.00 32.61 4.20
312 553 4.956085 TCATATACATGGAAGGTTGGACG 58.044 43.478 0.00 0.00 32.61 4.79
313 554 9.167311 GATTATCATATACATGGAAGGTTGGAC 57.833 37.037 0.00 0.00 32.61 4.02
314 555 8.889445 TGATTATCATATACATGGAAGGTTGGA 58.111 33.333 0.00 0.00 32.61 3.53
315 556 9.519191 TTGATTATCATATACATGGAAGGTTGG 57.481 33.333 0.00 0.00 32.61 3.77
343 584 9.687210 GGTTCAAAAGGTAAGTAAATTAAGGTG 57.313 33.333 0.00 0.00 0.00 4.00
344 585 9.423964 TGGTTCAAAAGGTAAGTAAATTAAGGT 57.576 29.630 0.00 0.00 0.00 3.50
349 590 9.772973 GGAATTGGTTCAAAAGGTAAGTAAATT 57.227 29.630 0.00 0.00 36.01 1.82
350 591 8.929487 TGGAATTGGTTCAAAAGGTAAGTAAAT 58.071 29.630 0.00 0.00 36.01 1.40
351 592 8.198778 GTGGAATTGGTTCAAAAGGTAAGTAAA 58.801 33.333 0.00 0.00 36.01 2.01
352 593 7.562088 AGTGGAATTGGTTCAAAAGGTAAGTAA 59.438 33.333 0.00 0.00 36.01 2.24
353 594 7.064229 AGTGGAATTGGTTCAAAAGGTAAGTA 58.936 34.615 0.00 0.00 36.01 2.24
354 595 5.897250 AGTGGAATTGGTTCAAAAGGTAAGT 59.103 36.000 0.00 0.00 36.01 2.24
355 596 6.405278 AGTGGAATTGGTTCAAAAGGTAAG 57.595 37.500 0.00 0.00 36.01 2.34
356 597 6.800072 AAGTGGAATTGGTTCAAAAGGTAA 57.200 33.333 0.00 0.00 36.01 2.85
357 598 6.800072 AAAGTGGAATTGGTTCAAAAGGTA 57.200 33.333 0.00 0.00 36.01 3.08
358 599 5.692115 AAAGTGGAATTGGTTCAAAAGGT 57.308 34.783 0.00 0.00 36.01 3.50
359 600 8.675705 AATTAAAGTGGAATTGGTTCAAAAGG 57.324 30.769 0.00 0.00 36.01 3.11
362 603 9.250624 CGTAAATTAAAGTGGAATTGGTTCAAA 57.749 29.630 0.00 0.00 36.01 2.69
363 604 8.414778 ACGTAAATTAAAGTGGAATTGGTTCAA 58.585 29.630 0.00 0.00 36.01 2.69
364 605 7.942990 ACGTAAATTAAAGTGGAATTGGTTCA 58.057 30.769 0.00 0.00 36.01 3.18
367 608 9.233649 TGATACGTAAATTAAAGTGGAATTGGT 57.766 29.630 0.00 0.00 0.00 3.67
409 650 9.489084 CGAATTCTGACCATGAATTACCTTATA 57.511 33.333 3.52 0.00 42.17 0.98
410 651 8.210946 TCGAATTCTGACCATGAATTACCTTAT 58.789 33.333 3.52 0.00 42.17 1.73
411 652 7.561251 TCGAATTCTGACCATGAATTACCTTA 58.439 34.615 3.52 0.00 42.17 2.69
412 653 6.414732 TCGAATTCTGACCATGAATTACCTT 58.585 36.000 3.52 0.00 42.17 3.50
413 654 5.989477 TCGAATTCTGACCATGAATTACCT 58.011 37.500 3.52 0.00 42.17 3.08
414 655 6.483307 TCATCGAATTCTGACCATGAATTACC 59.517 38.462 3.52 0.00 42.17 2.85
415 656 7.482654 TCATCGAATTCTGACCATGAATTAC 57.517 36.000 3.52 0.00 42.17 1.89
416 657 7.552330 TGTTCATCGAATTCTGACCATGAATTA 59.448 33.333 3.52 2.60 42.17 1.40
417 658 6.375174 TGTTCATCGAATTCTGACCATGAATT 59.625 34.615 3.52 0.00 44.01 2.17
418 659 5.882000 TGTTCATCGAATTCTGACCATGAAT 59.118 36.000 3.52 0.00 33.89 2.57
419 660 5.244755 TGTTCATCGAATTCTGACCATGAA 58.755 37.500 3.52 7.15 0.00 2.57
420 661 4.831107 TGTTCATCGAATTCTGACCATGA 58.169 39.130 3.52 1.84 0.00 3.07
421 662 5.746307 ATGTTCATCGAATTCTGACCATG 57.254 39.130 6.86 1.82 0.00 3.66
422 663 6.764308 AAATGTTCATCGAATTCTGACCAT 57.236 33.333 3.52 3.17 0.00 3.55
423 664 7.864108 ATAAATGTTCATCGAATTCTGACCA 57.136 32.000 3.52 0.78 0.00 4.02
433 674 9.381027 GCGATTGAATAAATAAATGTTCATCGA 57.619 29.630 15.72 0.00 35.79 3.59
434 675 9.168353 TGCGATTGAATAAATAAATGTTCATCG 57.832 29.630 0.00 0.00 36.23 3.84
445 686 9.624697 GCCAAGAATAATGCGATTGAATAAATA 57.375 29.630 0.00 0.00 0.00 1.40
446 687 8.143193 TGCCAAGAATAATGCGATTGAATAAAT 58.857 29.630 0.00 0.00 0.00 1.40
447 688 7.487484 TGCCAAGAATAATGCGATTGAATAAA 58.513 30.769 0.00 0.00 0.00 1.40
448 689 7.036996 TGCCAAGAATAATGCGATTGAATAA 57.963 32.000 0.00 0.00 0.00 1.40
449 690 6.631971 TGCCAAGAATAATGCGATTGAATA 57.368 33.333 0.00 0.00 0.00 1.75
450 691 5.518848 TGCCAAGAATAATGCGATTGAAT 57.481 34.783 0.00 0.00 0.00 2.57
451 692 4.979943 TGCCAAGAATAATGCGATTGAA 57.020 36.364 0.00 0.00 0.00 2.69
452 693 4.398988 ACTTGCCAAGAATAATGCGATTGA 59.601 37.500 12.25 0.00 0.00 2.57
453 694 4.675510 ACTTGCCAAGAATAATGCGATTG 58.324 39.130 12.25 0.00 0.00 2.67
454 695 4.989279 ACTTGCCAAGAATAATGCGATT 57.011 36.364 12.25 0.00 0.00 3.34
455 696 6.449635 TTTACTTGCCAAGAATAATGCGAT 57.550 33.333 12.25 0.00 0.00 4.58
456 697 5.888691 TTTACTTGCCAAGAATAATGCGA 57.111 34.783 12.25 0.00 0.00 5.10
457 698 6.197096 GTGATTTACTTGCCAAGAATAATGCG 59.803 38.462 12.25 0.00 0.00 4.73
458 699 7.035004 TGTGATTTACTTGCCAAGAATAATGC 58.965 34.615 12.25 4.14 0.00 3.56
459 700 8.984891 TTGTGATTTACTTGCCAAGAATAATG 57.015 30.769 12.25 0.00 0.00 1.90
460 701 9.423061 GTTTGTGATTTACTTGCCAAGAATAAT 57.577 29.630 12.25 7.22 0.00 1.28
461 702 8.637986 AGTTTGTGATTTACTTGCCAAGAATAA 58.362 29.630 12.25 2.54 0.00 1.40
462 703 8.177119 AGTTTGTGATTTACTTGCCAAGAATA 57.823 30.769 12.25 0.00 0.00 1.75
463 704 7.054491 AGTTTGTGATTTACTTGCCAAGAAT 57.946 32.000 12.25 0.96 0.00 2.40
464 705 6.463995 AGTTTGTGATTTACTTGCCAAGAA 57.536 33.333 12.25 0.00 0.00 2.52
465 706 7.067615 TGTTAGTTTGTGATTTACTTGCCAAGA 59.932 33.333 12.25 0.00 0.00 3.02
466 707 7.199766 TGTTAGTTTGTGATTTACTTGCCAAG 58.800 34.615 2.11 2.11 0.00 3.61
467 708 7.101652 TGTTAGTTTGTGATTTACTTGCCAA 57.898 32.000 0.00 0.00 0.00 4.52
468 709 6.701145 TGTTAGTTTGTGATTTACTTGCCA 57.299 33.333 0.00 0.00 0.00 4.92
469 710 8.512138 AGTATGTTAGTTTGTGATTTACTTGCC 58.488 33.333 0.00 0.00 0.00 4.52
518 759 1.279539 CTGAACAATGCACGTGCGT 59.720 52.632 33.22 31.21 45.83 5.24
519 760 0.510790 TACTGAACAATGCACGTGCG 59.489 50.000 33.22 22.30 45.83 5.34
520 761 1.798223 TCTACTGAACAATGCACGTGC 59.202 47.619 33.11 33.11 42.50 5.34
521 762 4.668576 ATTCTACTGAACAATGCACGTG 57.331 40.909 12.28 12.28 34.71 4.49
522 763 9.411801 CTATATATTCTACTGAACAATGCACGT 57.588 33.333 0.00 0.00 34.71 4.49
523 764 9.626045 TCTATATATTCTACTGAACAATGCACG 57.374 33.333 0.00 0.00 34.71 5.34
556 797 1.666553 CCGTACGAGCAAGCCAACA 60.667 57.895 18.76 0.00 0.00 3.33
557 798 3.023591 GCCGTACGAGCAAGCCAAC 62.024 63.158 18.76 0.00 0.00 3.77
588 829 3.625764 TCTGCTGTAACCAAACAAGTCAC 59.374 43.478 0.00 0.00 0.00 3.67
604 845 4.694037 TGATGAATGAACAAGTCTCTGCTG 59.306 41.667 0.00 0.00 0.00 4.41
610 851 8.853077 TTACAAGATGATGAATGAACAAGTCT 57.147 30.769 0.00 0.00 0.00 3.24
617 858 9.788889 ATCTGCTATTACAAGATGATGAATGAA 57.211 29.630 0.00 0.00 0.00 2.57
693 1933 4.082787 ACCTTATGAAGCAAATCGTGTTGG 60.083 41.667 3.62 0.00 0.00 3.77
726 1969 5.351465 ACTGATTTACAATAGCAACAGACCG 59.649 40.000 0.00 0.00 0.00 4.79
853 2097 9.947669 GACTACAAAATATTTCTAGTAGCTCGA 57.052 33.333 22.41 0.00 33.96 4.04
854 2098 9.731819 TGACTACAAAATATTTCTAGTAGCTCG 57.268 33.333 22.41 10.32 33.96 5.03
868 2112 4.142227 GCCCGTCTCTCTGACTACAAAATA 60.142 45.833 0.00 0.00 43.25 1.40
869 2113 3.368531 GCCCGTCTCTCTGACTACAAAAT 60.369 47.826 0.00 0.00 43.25 1.82
870 2114 2.029290 GCCCGTCTCTCTGACTACAAAA 60.029 50.000 0.00 0.00 43.25 2.44
873 2117 0.680280 GGCCCGTCTCTCTGACTACA 60.680 60.000 0.00 0.00 43.25 2.74
1308 2591 1.064296 CCTACGACTAGCACAGCCG 59.936 63.158 0.00 0.00 0.00 5.52
1369 6025 2.435805 AGGCTCATCGATTCCTGCTTAA 59.564 45.455 9.20 0.00 0.00 1.85
1376 6033 6.566197 ATTTCAATTAGGCTCATCGATTCC 57.434 37.500 0.00 0.00 0.00 3.01
1409 6069 2.328099 GGACGTGGCTTGCTCCAAG 61.328 63.158 0.00 0.74 43.57 3.61
1421 6082 1.142474 GTAGGAACCAAACGGACGTG 58.858 55.000 0.00 0.00 0.00 4.49
1446 6107 1.305219 TGCGCCACCAGCTGATTAAC 61.305 55.000 17.39 0.20 40.39 2.01
1461 6122 1.060937 CCGATGCTAAACACTGCGC 59.939 57.895 0.00 0.00 0.00 6.09
1539 6201 1.234615 CGGTGCCAACACTAACCTGG 61.235 60.000 0.00 0.00 46.57 4.45
1560 6222 4.376340 AATCTTTGCGCCTATTTTCCTG 57.624 40.909 4.18 0.00 0.00 3.86
1595 6262 0.948678 CACCAAACTGGGTAACACCG 59.051 55.000 0.00 0.00 43.37 4.94
1732 6402 3.586470 TTCCTTTTCCAGTACCAAGCA 57.414 42.857 0.00 0.00 0.00 3.91
1875 6564 3.688673 GCTCCAGAGAAATATGCCTATGC 59.311 47.826 0.00 0.00 38.26 3.14
1881 6570 2.947127 AGGGCTCCAGAGAAATATGC 57.053 50.000 0.00 0.00 0.00 3.14
2056 6886 3.455910 TCTCTGGAATAGACACAATGGGG 59.544 47.826 0.00 0.00 0.00 4.96
2098 6929 6.769341 ACAGAAAAACAAAACCTCGGTATACT 59.231 34.615 2.25 0.00 0.00 2.12
2101 6932 6.095720 TCAACAGAAAAACAAAACCTCGGTAT 59.904 34.615 0.00 0.00 0.00 2.73
2102 6933 5.415077 TCAACAGAAAAACAAAACCTCGGTA 59.585 36.000 0.00 0.00 0.00 4.02
2103 6934 4.218852 TCAACAGAAAAACAAAACCTCGGT 59.781 37.500 0.00 0.00 0.00 4.69
2209 7040 0.179113 CTGCCCCAAAACACACACAC 60.179 55.000 0.00 0.00 0.00 3.82
2240 7071 7.934665 TCCTAAATTGCTATATGCGACCTTTTA 59.065 33.333 0.00 0.00 46.63 1.52
2315 7164 4.603231 TGGTAACGAACACTCACAAAAC 57.397 40.909 0.00 0.00 42.51 2.43
2453 7302 1.247567 CAAATGCTTCCCGTCCAAGT 58.752 50.000 0.00 0.00 0.00 3.16
2620 7475 9.832445 ATATAGACATCGTAGGTTCAAAACATT 57.168 29.630 0.00 0.00 0.00 2.71
2669 7546 7.539034 ACAACTTAGCATAACCAGGAAAAAT 57.461 32.000 0.00 0.00 0.00 1.82
2764 7642 5.997129 TGTTAAGAATGAGTGCAACAGATGA 59.003 36.000 0.00 0.00 41.43 2.92
2771 7649 8.539770 TTTTGTTTTGTTAAGAATGAGTGCAA 57.460 26.923 0.00 0.00 0.00 4.08
2818 7696 1.549203 GATGGCAAACAGACCACCAT 58.451 50.000 0.00 0.00 43.72 3.55
2890 7842 9.194271 GCAAAACCATAAAATACGACCTAAAAA 57.806 29.630 0.00 0.00 0.00 1.94
2891 7843 8.578151 AGCAAAACCATAAAATACGACCTAAAA 58.422 29.630 0.00 0.00 0.00 1.52
2892 7844 8.113173 AGCAAAACCATAAAATACGACCTAAA 57.887 30.769 0.00 0.00 0.00 1.85
2893 7845 7.690952 AGCAAAACCATAAAATACGACCTAA 57.309 32.000 0.00 0.00 0.00 2.69
2894 7846 8.967664 ATAGCAAAACCATAAAATACGACCTA 57.032 30.769 0.00 0.00 0.00 3.08
2895 7847 7.875327 ATAGCAAAACCATAAAATACGACCT 57.125 32.000 0.00 0.00 0.00 3.85
2896 7848 8.920509 AAATAGCAAAACCATAAAATACGACC 57.079 30.769 0.00 0.00 0.00 4.79
2903 7855 9.482627 CAACCTGTAAATAGCAAAACCATAAAA 57.517 29.630 0.00 0.00 0.00 1.52
2904 7856 8.643324 ACAACCTGTAAATAGCAAAACCATAAA 58.357 29.630 0.00 0.00 0.00 1.40
2905 7857 8.184304 ACAACCTGTAAATAGCAAAACCATAA 57.816 30.769 0.00 0.00 0.00 1.90
2906 7858 7.768807 ACAACCTGTAAATAGCAAAACCATA 57.231 32.000 0.00 0.00 0.00 2.74
2907 7859 6.664428 ACAACCTGTAAATAGCAAAACCAT 57.336 33.333 0.00 0.00 0.00 3.55
2908 7860 6.127310 ACAACAACCTGTAAATAGCAAAACCA 60.127 34.615 0.00 0.00 0.00 3.67
2909 7861 6.277605 ACAACAACCTGTAAATAGCAAAACC 58.722 36.000 0.00 0.00 0.00 3.27
2910 7862 7.764695 AACAACAACCTGTAAATAGCAAAAC 57.235 32.000 0.00 0.00 0.00 2.43
2913 7865 9.685828 GAATAAACAACAACCTGTAAATAGCAA 57.314 29.630 0.00 0.00 0.00 3.91
2923 7875 7.461182 TGGGATTAGAATAAACAACAACCTG 57.539 36.000 0.00 0.00 0.00 4.00
2950 7904 2.855209 TCCATGGCCACAAAAATTGG 57.145 45.000 8.16 10.81 37.17 3.16
3081 8040 8.175925 TGTAATTCACAAAATGAGATTCACCA 57.824 30.769 0.00 0.00 38.99 4.17
3110 8069 9.346725 CTTCAAAGTCAAAATAAGGAGCAATAC 57.653 33.333 0.00 0.00 0.00 1.89
3133 8092 4.946784 ACGCTCCAATTGTGATAACTTC 57.053 40.909 4.43 0.00 0.00 3.01
3173 8132 2.355108 GCTCTCCTACATTTCAGTGGCA 60.355 50.000 0.00 0.00 0.00 4.92
3212 8171 7.980662 ACAGCTGCAAAATATAAAACATGCATA 59.019 29.630 15.27 0.00 42.25 3.14
3415 8374 5.830000 ACAAGGAAGATAAATTTACCGGC 57.170 39.130 0.00 0.00 0.00 6.13
3437 8396 2.073117 TAACGCGATCAGTCTTGCAA 57.927 45.000 15.93 0.00 0.00 4.08
3510 8471 9.778741 GTCATGTCAAATAATCCTATCCAAGTA 57.221 33.333 0.00 0.00 0.00 2.24
3540 8501 2.072487 GCCAGCATCCTCAGGGGTA 61.072 63.158 0.00 0.00 36.25 3.69
3835 8797 6.935208 TCAAGCTCATATGATTCATCAAGAGG 59.065 38.462 5.72 0.00 40.69 3.69
3840 8802 7.387948 CACATCTCAAGCTCATATGATTCATCA 59.612 37.037 5.72 0.00 41.70 3.07
3841 8803 7.624554 GCACATCTCAAGCTCATATGATTCATC 60.625 40.741 5.72 0.00 0.00 2.92
3842 8804 6.149640 GCACATCTCAAGCTCATATGATTCAT 59.850 38.462 5.72 4.28 0.00 2.57
3861 8823 9.787532 ACATACAAATGTAACTATTTGCACATC 57.212 29.630 10.23 0.00 44.66 3.06
3863 8825 9.619316 GAACATACAAATGTAACTATTTGCACA 57.381 29.630 10.23 0.00 45.79 4.57
4045 9007 0.809241 CCTTGAGGCGAGTGAGCATC 60.809 60.000 0.00 0.00 46.74 3.91
4117 9079 9.202273 CCTACAAGATGAGATAAGCATAAGAAC 57.798 37.037 0.00 0.00 0.00 3.01
4546 9510 9.853177 AATATCAACTTATGTAGAAAGGGAAGG 57.147 33.333 0.00 0.00 0.00 3.46
4596 9560 6.416415 TGTCCTAGTACTTTTTCCAACAACA 58.584 36.000 0.00 0.00 0.00 3.33
4623 9587 5.305902 TGGATGTGTAAACAGAACCTACAGA 59.694 40.000 7.83 0.00 33.97 3.41
4629 9593 3.412386 AGCTGGATGTGTAAACAGAACC 58.588 45.455 0.23 0.23 33.53 3.62
4666 9630 7.780271 AGTTCTGGGAAAGTTAAAACAATCTCT 59.220 33.333 0.00 0.00 0.00 3.10
4708 9672 6.424509 ACTTGGAAACACATGCATGTAAAATG 59.575 34.615 30.92 20.40 42.67 2.32
4710 9674 5.911752 ACTTGGAAACACATGCATGTAAAA 58.088 33.333 30.92 16.81 42.67 1.52
4891 9855 1.002868 GCCTCTCCTTGAGCTTGCA 60.003 57.895 0.00 0.00 41.35 4.08
4929 9893 0.179070 GCCTCCGGAACTCCTCATTC 60.179 60.000 5.23 0.00 0.00 2.67
4932 9896 1.984570 CAGCCTCCGGAACTCCTCA 60.985 63.158 5.23 0.00 0.00 3.86
5078 10048 6.297694 ACTTCTACCAATATACGAGACGAC 57.702 41.667 0.00 0.00 0.00 4.34
5156 10129 5.627367 GTCGCAAGTGCTACTAATATGAGAG 59.373 44.000 1.21 0.00 39.32 3.20
5289 10264 9.673454 ATTAAAAACGATCAGACAAACTAAACC 57.327 29.630 0.00 0.00 0.00 3.27
5317 10292 3.418995 GGTTTCAAGGGAGAGTTAACCC 58.581 50.000 0.88 0.00 45.88 4.11
5356 10550 2.093152 CCTGCGTACGTGGTTTGATTAC 59.907 50.000 17.90 0.00 0.00 1.89
5399 10885 1.589414 ATTCTTACTGCCTGCTCCCT 58.411 50.000 0.00 0.00 0.00 4.20
5402 10888 3.198872 GGTGTATTCTTACTGCCTGCTC 58.801 50.000 0.00 0.00 0.00 4.26
5411 10897 8.391106 CAAATAGCAAGTCTGGTGTATTCTTAC 58.609 37.037 0.00 0.00 34.40 2.34
5412 10898 7.552687 CCAAATAGCAAGTCTGGTGTATTCTTA 59.447 37.037 0.00 0.00 34.40 2.10
5583 13448 7.938140 TTTTGGAGAATCGAATTCCTACATT 57.062 32.000 12.59 0.00 40.13 2.71
5617 13483 2.293122 TGAAAGTTGAAACAGCGGGATG 59.707 45.455 0.00 0.00 0.00 3.51
5620 13486 2.857748 GTTTGAAAGTTGAAACAGCGGG 59.142 45.455 1.85 0.00 34.94 6.13
5642 13508 1.420430 TGTTTCCGTTCTCAGACCCT 58.580 50.000 0.00 0.00 0.00 4.34
5664 13530 0.443869 GTAATGTGCTGCAGTCACGG 59.556 55.000 25.65 1.04 37.26 4.94
5804 13670 2.569404 GTCCAGGGCCTAGATATTGGAG 59.431 54.545 5.28 0.00 35.55 3.86
5863 13729 2.280628 GGCCCTGAGTCAAGATAAACG 58.719 52.381 0.00 0.00 0.00 3.60



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

AutoCloner maintained by Alex Coulton.