Multiple sequence alignment - TraesCS2B01G386000

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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 TraesCS2B01G386000 chr2B 100.000 3587 0 0 1 3587 549250274 549246688 0.000000e+00 6625.0
1 TraesCS2B01G386000 chr2B 78.201 656 82 38 1 642 612870425 612871033 2.630000e-96 363.0
2 TraesCS2B01G386000 chr2D 93.933 1846 94 9 828 2659 470240554 470238713 0.000000e+00 2772.0
3 TraesCS2B01G386000 chr2D 90.961 697 62 1 2890 3585 277528456 277529152 0.000000e+00 937.0
4 TraesCS2B01G386000 chr2D 89.255 698 74 1 2890 3587 277601295 277601991 0.000000e+00 872.0
5 TraesCS2B01G386000 chr2D 89.100 211 19 3 2670 2876 277601035 277601245 3.550000e-65 259.0
6 TraesCS2B01G386000 chr2D 87.736 212 21 4 2669 2876 277528195 277528405 3.580000e-60 243.0
7 TraesCS2B01G386000 chr2D 82.996 247 31 6 1 244 446965968 446966206 2.810000e-51 213.0
8 TraesCS2B01G386000 chr2A 90.232 1894 121 19 803 2668 612080074 612078217 0.000000e+00 2414.0
9 TraesCS2B01G386000 chr2A 86.531 1715 181 23 905 2597 611999641 611997955 0.000000e+00 1842.0
10 TraesCS2B01G386000 chr1D 91.248 697 60 1 2891 3587 293609747 293610442 0.000000e+00 948.0
11 TraesCS2B01G386000 chr1D 74.510 1683 335 60 916 2548 340983938 340982300 0.000000e+00 645.0
12 TraesCS2B01G386000 chr1D 76.139 461 100 5 1040 1493 341021125 341020668 2.150000e-57 233.0
13 TraesCS2B01G386000 chr4A 87.661 697 86 0 2891 3587 361716450 361717146 0.000000e+00 811.0
14 TraesCS2B01G386000 chr6B 86.667 690 89 3 2899 3587 156403360 156402673 0.000000e+00 761.0
15 TraesCS2B01G386000 chr6B 73.364 1498 286 81 1043 2481 615092506 615091063 5.460000e-123 451.0
16 TraesCS2B01G386000 chr6B 78.698 676 85 38 1 655 702239431 702240068 2.600000e-106 396.0
17 TraesCS2B01G386000 chr5B 85.366 697 102 0 2891 3587 390521850 390521154 0.000000e+00 723.0
18 TraesCS2B01G386000 chr5B 85.122 699 100 2 2891 3587 390400985 390400289 0.000000e+00 712.0
19 TraesCS2B01G386000 chr5B 79.192 668 81 34 1 655 498033166 498033788 9.270000e-111 411.0
20 TraesCS2B01G386000 chr5B 78.060 670 94 40 1 653 641669780 641670413 1.220000e-99 374.0
21 TraesCS2B01G386000 chr5B 83.965 343 43 11 1 338 419729392 419729057 5.780000e-83 318.0
22 TraesCS2B01G386000 chr1B 74.911 1686 330 59 916 2553 456433815 456432175 0.000000e+00 684.0
23 TraesCS2B01G386000 chr1B 86.351 359 39 8 1 356 676300891 676300540 2.020000e-102 383.0
24 TraesCS2B01G386000 chr1B 84.259 216 27 5 1 213 497283796 497284007 1.690000e-48 204.0
25 TraesCS2B01G386000 chr1B 83.146 178 24 6 480 654 676300449 676300275 1.330000e-34 158.0
26 TraesCS2B01G386000 chr1A 74.659 1614 326 54 916 2481 440669775 440668197 3.910000e-179 638.0
27 TraesCS2B01G386000 chr1A 83.146 267 35 6 3 267 500868838 500869096 5.990000e-58 235.0
28 TraesCS2B01G386000 chr7B 85.033 608 90 1 2891 3498 18961012 18961618 5.090000e-173 617.0
29 TraesCS2B01G386000 chr7A 82.739 701 112 9 2891 3587 459463630 459464325 1.830000e-172 616.0
30 TraesCS2B01G386000 chr7A 86.905 84 7 4 576 655 123276430 123276347 1.370000e-14 91.6
31 TraesCS2B01G386000 chr3D 73.870 1527 326 43 972 2478 338581209 338582682 3.150000e-150 542.0
32 TraesCS2B01G386000 chr3D 71.979 1531 326 68 1073 2550 562178549 562180029 4.400000e-94 355.0
33 TraesCS2B01G386000 chr6D 73.200 1500 296 72 1043 2481 409493417 409491963 2.540000e-121 446.0
34 TraesCS2B01G386000 chr6D 72.715 1488 302 73 1043 2481 409481486 409480054 1.550000e-108 403.0
35 TraesCS2B01G386000 chr3B 72.608 1526 325 66 1073 2550 749485018 749486498 1.990000e-112 416.0
36 TraesCS2B01G386000 chr3B 71.782 1173 251 45 1337 2478 436837670 436838793 3.550000e-65 259.0
37 TraesCS2B01G386000 chr3B 82.418 182 20 9 482 654 727851295 727851117 8.020000e-32 148.0
38 TraesCS2B01G386000 chr3B 90.541 74 5 2 592 664 662499503 662499575 2.950000e-16 97.1
39 TraesCS2B01G386000 chr3B 87.342 79 7 3 583 658 8530947 8530869 1.770000e-13 87.9
40 TraesCS2B01G386000 chr3A 73.897 1088 212 44 1415 2475 456807765 456808807 1.570000e-98 370.0
41 TraesCS2B01G386000 chr5D 84.186 215 27 7 2664 2871 510034183 510034397 6.070000e-48 202.0
42 TraesCS2B01G386000 chr4B 87.952 83 5 5 576 654 40430162 40430243 3.810000e-15 93.5
43 TraesCS2B01G386000 chr6A 86.364 88 7 5 576 660 52370696 52370611 1.370000e-14 91.6


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 TraesCS2B01G386000 chr2B 549246688 549250274 3586 True 6625.0 6625 100.0000 1 3587 1 chr2B.!!$R1 3586
1 TraesCS2B01G386000 chr2B 612870425 612871033 608 False 363.0 363 78.2010 1 642 1 chr2B.!!$F1 641
2 TraesCS2B01G386000 chr2D 470238713 470240554 1841 True 2772.0 2772 93.9330 828 2659 1 chr2D.!!$R1 1831
3 TraesCS2B01G386000 chr2D 277528195 277529152 957 False 590.0 937 89.3485 2669 3585 2 chr2D.!!$F2 916
4 TraesCS2B01G386000 chr2D 277601035 277601991 956 False 565.5 872 89.1775 2670 3587 2 chr2D.!!$F3 917
5 TraesCS2B01G386000 chr2A 612078217 612080074 1857 True 2414.0 2414 90.2320 803 2668 1 chr2A.!!$R2 1865
6 TraesCS2B01G386000 chr2A 611997955 611999641 1686 True 1842.0 1842 86.5310 905 2597 1 chr2A.!!$R1 1692
7 TraesCS2B01G386000 chr1D 293609747 293610442 695 False 948.0 948 91.2480 2891 3587 1 chr1D.!!$F1 696
8 TraesCS2B01G386000 chr1D 340982300 340983938 1638 True 645.0 645 74.5100 916 2548 1 chr1D.!!$R1 1632
9 TraesCS2B01G386000 chr4A 361716450 361717146 696 False 811.0 811 87.6610 2891 3587 1 chr4A.!!$F1 696
10 TraesCS2B01G386000 chr6B 156402673 156403360 687 True 761.0 761 86.6670 2899 3587 1 chr6B.!!$R1 688
11 TraesCS2B01G386000 chr6B 615091063 615092506 1443 True 451.0 451 73.3640 1043 2481 1 chr6B.!!$R2 1438
12 TraesCS2B01G386000 chr6B 702239431 702240068 637 False 396.0 396 78.6980 1 655 1 chr6B.!!$F1 654
13 TraesCS2B01G386000 chr5B 390521154 390521850 696 True 723.0 723 85.3660 2891 3587 1 chr5B.!!$R2 696
14 TraesCS2B01G386000 chr5B 390400289 390400985 696 True 712.0 712 85.1220 2891 3587 1 chr5B.!!$R1 696
15 TraesCS2B01G386000 chr5B 498033166 498033788 622 False 411.0 411 79.1920 1 655 1 chr5B.!!$F1 654
16 TraesCS2B01G386000 chr5B 641669780 641670413 633 False 374.0 374 78.0600 1 653 1 chr5B.!!$F2 652
17 TraesCS2B01G386000 chr1B 456432175 456433815 1640 True 684.0 684 74.9110 916 2553 1 chr1B.!!$R1 1637
18 TraesCS2B01G386000 chr1B 676300275 676300891 616 True 270.5 383 84.7485 1 654 2 chr1B.!!$R2 653
19 TraesCS2B01G386000 chr1A 440668197 440669775 1578 True 638.0 638 74.6590 916 2481 1 chr1A.!!$R1 1565
20 TraesCS2B01G386000 chr7B 18961012 18961618 606 False 617.0 617 85.0330 2891 3498 1 chr7B.!!$F1 607
21 TraesCS2B01G386000 chr7A 459463630 459464325 695 False 616.0 616 82.7390 2891 3587 1 chr7A.!!$F1 696
22 TraesCS2B01G386000 chr3D 338581209 338582682 1473 False 542.0 542 73.8700 972 2478 1 chr3D.!!$F1 1506
23 TraesCS2B01G386000 chr3D 562178549 562180029 1480 False 355.0 355 71.9790 1073 2550 1 chr3D.!!$F2 1477
24 TraesCS2B01G386000 chr6D 409491963 409493417 1454 True 446.0 446 73.2000 1043 2481 1 chr6D.!!$R2 1438
25 TraesCS2B01G386000 chr6D 409480054 409481486 1432 True 403.0 403 72.7150 1043 2481 1 chr6D.!!$R1 1438
26 TraesCS2B01G386000 chr3B 749485018 749486498 1480 False 416.0 416 72.6080 1073 2550 1 chr3B.!!$F3 1477
27 TraesCS2B01G386000 chr3B 436837670 436838793 1123 False 259.0 259 71.7820 1337 2478 1 chr3B.!!$F1 1141
28 TraesCS2B01G386000 chr3A 456807765 456808807 1042 False 370.0 370 73.8970 1415 2475 1 chr3A.!!$F1 1060

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
723 745 0.034337 TGGTTTGCGAGTAGGGTGAC 59.966 55.0 0.0 0.0 0.0 3.67 F
827 849 0.041238 TCCCCACACTCGAATCTCCT 59.959 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1597 1718 1.493311 CGAGTTTGAGGCTTCGCAC 59.507 57.895 0.0 0.0 0.0 5.34 R
2731 2945 1.209898 CGCATTCGTGCCACACATT 59.790 52.632 0.0 0.0 33.4 2.71 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
49 50 4.497291 GGGTTAATGATCCCTGTGTACA 57.503 45.455 0.00 0.00 40.48 2.90
63 65 5.393027 CCCTGTGTACATGTTAATTTGCTCC 60.393 44.000 2.30 0.00 0.00 4.70
65 67 6.071952 CCTGTGTACATGTTAATTTGCTCCTT 60.072 38.462 2.30 0.00 0.00 3.36
144 146 1.276421 GAGGCAGGAGTGAAGCAAGTA 59.724 52.381 0.00 0.00 0.00 2.24
145 147 1.699634 AGGCAGGAGTGAAGCAAGTAA 59.300 47.619 0.00 0.00 0.00 2.24
237 241 4.704540 TGACCAAAAAGCTTCAAGTCTTCA 59.295 37.500 0.00 0.00 0.00 3.02
238 242 5.163622 TGACCAAAAAGCTTCAAGTCTTCAG 60.164 40.000 0.00 0.00 0.00 3.02
254 258 2.627515 TCAGGGATCTATGTTGCTGC 57.372 50.000 0.00 0.00 0.00 5.25
283 289 1.207570 CTCAGAGGCAGCAAGATCACT 59.792 52.381 0.00 0.00 0.00 3.41
286 292 0.540923 GAGGCAGCAAGATCACTCCT 59.459 55.000 0.00 0.00 0.00 3.69
287 293 0.252479 AGGCAGCAAGATCACTCCTG 59.748 55.000 0.00 0.00 0.00 3.86
288 294 1.375098 GGCAGCAAGATCACTCCTGC 61.375 60.000 15.14 15.14 45.99 4.85
293 299 4.005650 CAGCAAGATCACTCCTGCTTTTA 58.994 43.478 0.00 0.00 37.90 1.52
298 304 6.127786 GCAAGATCACTCCTGCTTTTATTTCT 60.128 38.462 0.00 0.00 30.08 2.52
313 319 9.521503 GCTTTTATTTCTCTCTGTTCTTTTGTT 57.478 29.630 0.00 0.00 0.00 2.83
318 324 6.515272 TTCTCTCTGTTCTTTTGTTGCTTT 57.485 33.333 0.00 0.00 0.00 3.51
319 325 7.624360 TTCTCTCTGTTCTTTTGTTGCTTTA 57.376 32.000 0.00 0.00 0.00 1.85
320 326 7.624360 TCTCTCTGTTCTTTTGTTGCTTTAA 57.376 32.000 0.00 0.00 0.00 1.52
321 327 7.697691 TCTCTCTGTTCTTTTGTTGCTTTAAG 58.302 34.615 0.00 0.00 0.00 1.85
348 357 3.713764 CCTGAGAGGGGATTATCTGTTGT 59.286 47.826 0.00 0.00 0.00 3.32
349 358 4.444022 CCTGAGAGGGGATTATCTGTTGTG 60.444 50.000 0.00 0.00 0.00 3.33
350 359 4.361783 TGAGAGGGGATTATCTGTTGTGA 58.638 43.478 0.00 0.00 0.00 3.58
353 362 4.785376 AGAGGGGATTATCTGTTGTGAGTT 59.215 41.667 0.00 0.00 0.00 3.01
370 379 5.135330 GTGAGTTCGATGTTAAAAACGGTC 58.865 41.667 0.00 0.00 0.00 4.79
371 380 4.084952 TGAGTTCGATGTTAAAAACGGTCG 60.085 41.667 9.65 9.65 40.90 4.79
372 381 3.184986 AGTTCGATGTTAAAAACGGTCGG 59.815 43.478 13.64 0.00 40.35 4.79
373 382 2.067766 TCGATGTTAAAAACGGTCGGG 58.932 47.619 13.64 0.00 40.35 5.14
374 383 1.799994 CGATGTTAAAAACGGTCGGGT 59.200 47.619 8.58 0.00 38.01 5.28
375 384 2.159801 CGATGTTAAAAACGGTCGGGTC 60.160 50.000 8.58 0.00 38.01 4.46
391 400 0.580104 GGTCTGTGTTCGTTTGGTCG 59.420 55.000 0.00 0.00 0.00 4.79
402 411 2.756760 TCGTTTGGTCGCCTAGATACTT 59.243 45.455 0.00 0.00 0.00 2.24
415 426 7.889073 TCGCCTAGATACTTTCTGGTCTATTAT 59.111 37.037 0.00 0.00 35.79 1.28
416 427 9.175312 CGCCTAGATACTTTCTGGTCTATTATA 57.825 37.037 0.00 0.00 35.79 0.98
441 452 1.822990 TCTGTTACGCTGGTTCTAGGG 59.177 52.381 0.00 0.00 36.75 3.53
443 454 0.248289 GTTACGCTGGTTCTAGGGCA 59.752 55.000 0.00 0.00 34.28 5.36
444 455 0.535335 TTACGCTGGTTCTAGGGCAG 59.465 55.000 0.00 0.00 34.28 4.85
449 460 1.229496 TGGTTCTAGGGCAGGCTCA 60.229 57.895 0.00 0.00 0.00 4.26
454 466 0.189574 TCTAGGGCAGGCTCATAGCT 59.810 55.000 0.00 0.00 41.99 3.32
468 480 2.773661 TCATAGCTCAGGCCTTTGATCA 59.226 45.455 0.00 0.00 39.73 2.92
470 482 0.034670 AGCTCAGGCCTTTGATCACC 60.035 55.000 0.00 0.00 39.73 4.02
472 484 0.622665 CTCAGGCCTTTGATCACCCT 59.377 55.000 0.00 0.00 0.00 4.34
473 485 0.329261 TCAGGCCTTTGATCACCCTG 59.671 55.000 0.00 18.19 43.40 4.45
474 486 0.682209 CAGGCCTTTGATCACCCTGG 60.682 60.000 0.00 9.42 39.45 4.45
475 487 2.054453 GGCCTTTGATCACCCTGGC 61.054 63.158 15.16 15.16 39.61 4.85
476 488 2.409870 GCCTTTGATCACCCTGGCG 61.410 63.158 0.00 0.00 0.00 5.69
477 489 1.750399 CCTTTGATCACCCTGGCGG 60.750 63.158 0.00 0.00 37.81 6.13
495 507 2.256461 CTGGCGGCACTGCTTTTC 59.744 61.111 7.97 0.00 34.52 2.29
534 546 1.414866 GGATGGCTCCCCTTCCTCTC 61.415 65.000 7.25 0.00 46.81 3.20
538 550 1.414866 GGCTCCCCTTCCTCTCCATC 61.415 65.000 0.00 0.00 0.00 3.51
542 554 1.081174 TCCCCTTCCTCTCCATCTGTT 59.919 52.381 0.00 0.00 0.00 3.16
550 562 3.776969 TCCTCTCCATCTGTTTAGTGCAT 59.223 43.478 0.00 0.00 0.00 3.96
561 573 0.546122 TTAGTGCATTGCCGGGAGAT 59.454 50.000 2.18 0.00 0.00 2.75
568 580 0.323725 ATTGCCGGGAGATGTTGCTT 60.324 50.000 2.18 0.00 0.00 3.91
578 590 4.280929 GGGAGATGTTGCTTTGGTAGTTTT 59.719 41.667 0.00 0.00 0.00 2.43
579 591 5.475564 GGGAGATGTTGCTTTGGTAGTTTTA 59.524 40.000 0.00 0.00 0.00 1.52
586 598 8.468720 TGTTGCTTTGGTAGTTTTAGTTTTTC 57.531 30.769 0.00 0.00 0.00 2.29
631 653 7.612065 TTCTATTAATGGAAATCGGAGAGGA 57.388 36.000 11.45 0.00 43.63 3.71
632 654 7.612065 TCTATTAATGGAAATCGGAGAGGAA 57.388 36.000 0.00 0.00 43.63 3.36
633 655 8.029782 TCTATTAATGGAAATCGGAGAGGAAA 57.970 34.615 0.00 0.00 43.63 3.13
634 656 6.944234 ATTAATGGAAATCGGAGAGGAAAC 57.056 37.500 0.00 0.00 43.63 2.78
635 657 4.576330 AATGGAAATCGGAGAGGAAACT 57.424 40.909 0.00 0.00 43.63 2.66
673 695 6.696441 AAAAATGTTTTGACCAATGTGCAT 57.304 29.167 0.00 0.00 0.00 3.96
674 696 5.927954 AAATGTTTTGACCAATGTGCATC 57.072 34.783 0.00 0.00 0.00 3.91
675 697 3.383620 TGTTTTGACCAATGTGCATCC 57.616 42.857 0.00 0.00 0.00 3.51
676 698 2.288091 TGTTTTGACCAATGTGCATCCG 60.288 45.455 0.00 0.00 0.00 4.18
677 699 1.902938 TTTGACCAATGTGCATCCGA 58.097 45.000 0.00 0.00 0.00 4.55
678 700 1.902938 TTGACCAATGTGCATCCGAA 58.097 45.000 0.00 0.00 0.00 4.30
679 701 1.902938 TGACCAATGTGCATCCGAAA 58.097 45.000 0.00 0.00 0.00 3.46
680 702 1.539388 TGACCAATGTGCATCCGAAAC 59.461 47.619 0.00 0.00 0.00 2.78
681 703 0.521291 ACCAATGTGCATCCGAAACG 59.479 50.000 0.00 0.00 0.00 3.60
682 704 0.798009 CCAATGTGCATCCGAAACGC 60.798 55.000 0.00 0.00 0.00 4.84
683 705 0.109827 CAATGTGCATCCGAAACGCA 60.110 50.000 0.00 0.00 0.00 5.24
684 706 0.595588 AATGTGCATCCGAAACGCAA 59.404 45.000 0.00 0.00 37.41 4.85
685 707 0.168788 ATGTGCATCCGAAACGCAAG 59.831 50.000 0.00 0.00 37.41 4.01
700 722 3.405170 CGCAAGTTCTGTGAACAGTTT 57.595 42.857 10.14 2.04 44.12 2.66
701 723 3.758300 CGCAAGTTCTGTGAACAGTTTT 58.242 40.909 10.14 1.73 44.12 2.43
702 724 4.165779 CGCAAGTTCTGTGAACAGTTTTT 58.834 39.130 10.14 1.42 44.12 1.94
703 725 4.262976 CGCAAGTTCTGTGAACAGTTTTTC 59.737 41.667 10.14 0.00 44.12 2.29
704 726 5.402398 GCAAGTTCTGTGAACAGTTTTTCT 58.598 37.500 10.14 1.49 44.12 2.52
705 727 7.852449 CGCAAGTTCTGTGAACAGTTTTTCTG 61.852 42.308 10.14 3.83 44.12 3.02
708 730 5.476945 AGTTCTGTGAACAGTTTTTCTGGTT 59.523 36.000 10.14 0.00 45.06 3.67
709 731 5.975693 TCTGTGAACAGTTTTTCTGGTTT 57.024 34.783 10.14 0.00 45.06 3.27
710 732 5.708948 TCTGTGAACAGTTTTTCTGGTTTG 58.291 37.500 10.14 0.00 45.06 2.93
711 733 4.241681 TGTGAACAGTTTTTCTGGTTTGC 58.758 39.130 0.00 0.00 45.06 3.68
712 734 3.303229 GTGAACAGTTTTTCTGGTTTGCG 59.697 43.478 0.00 0.00 45.06 4.85
713 735 3.191581 TGAACAGTTTTTCTGGTTTGCGA 59.808 39.130 0.00 0.00 45.06 5.10
714 736 3.769536 AACAGTTTTTCTGGTTTGCGAG 58.230 40.909 0.00 0.00 42.00 5.03
715 737 3.192633 AACAGTTTTTCTGGTTTGCGAGT 59.807 39.130 0.00 0.00 42.00 4.18
716 738 4.396790 AACAGTTTTTCTGGTTTGCGAGTA 59.603 37.500 0.00 0.00 42.00 2.59
717 739 4.527564 CAGTTTTTCTGGTTTGCGAGTAG 58.472 43.478 0.00 0.00 40.23 2.57
718 740 3.564225 AGTTTTTCTGGTTTGCGAGTAGG 59.436 43.478 0.00 0.00 0.00 3.18
719 741 2.178912 TTTCTGGTTTGCGAGTAGGG 57.821 50.000 0.00 0.00 0.00 3.53
720 742 1.053424 TTCTGGTTTGCGAGTAGGGT 58.947 50.000 0.00 0.00 0.00 4.34
721 743 0.320374 TCTGGTTTGCGAGTAGGGTG 59.680 55.000 0.00 0.00 0.00 4.61
722 744 0.320374 CTGGTTTGCGAGTAGGGTGA 59.680 55.000 0.00 0.00 0.00 4.02
723 745 0.034337 TGGTTTGCGAGTAGGGTGAC 59.966 55.000 0.00 0.00 0.00 3.67
724 746 0.320697 GGTTTGCGAGTAGGGTGACT 59.679 55.000 0.00 0.00 0.00 3.41
725 747 1.547372 GGTTTGCGAGTAGGGTGACTA 59.453 52.381 0.00 0.00 0.00 2.59
726 748 2.028748 GGTTTGCGAGTAGGGTGACTAA 60.029 50.000 0.00 0.00 32.37 2.24
727 749 3.555586 GGTTTGCGAGTAGGGTGACTAAA 60.556 47.826 0.00 0.00 32.37 1.85
728 750 3.587797 TTGCGAGTAGGGTGACTAAAG 57.412 47.619 0.00 0.00 32.37 1.85
729 751 2.522185 TGCGAGTAGGGTGACTAAAGT 58.478 47.619 0.00 0.00 32.37 2.66
730 752 2.230508 TGCGAGTAGGGTGACTAAAGTG 59.769 50.000 0.00 0.00 32.37 3.16
731 753 2.230750 GCGAGTAGGGTGACTAAAGTGT 59.769 50.000 0.00 0.00 32.37 3.55
732 754 3.441572 GCGAGTAGGGTGACTAAAGTGTA 59.558 47.826 0.00 0.00 32.37 2.90
733 755 4.673841 GCGAGTAGGGTGACTAAAGTGTAC 60.674 50.000 0.00 0.00 32.37 2.90
734 756 4.142513 CGAGTAGGGTGACTAAAGTGTACC 60.143 50.000 5.10 5.10 32.37 3.34
735 757 4.092279 AGTAGGGTGACTAAAGTGTACCC 58.908 47.826 18.22 18.22 45.39 3.69
736 758 2.980548 AGGGTGACTAAAGTGTACCCA 58.019 47.619 23.86 1.00 46.48 4.51
737 759 3.527937 AGGGTGACTAAAGTGTACCCAT 58.472 45.455 23.86 12.69 46.48 4.00
738 760 3.518303 AGGGTGACTAAAGTGTACCCATC 59.482 47.826 23.86 3.63 46.48 3.51
739 761 3.262405 GGGTGACTAAAGTGTACCCATCA 59.738 47.826 19.89 0.00 44.86 3.07
740 762 4.251268 GGTGACTAAAGTGTACCCATCAC 58.749 47.826 0.00 0.00 35.56 3.06
741 763 4.262721 GGTGACTAAAGTGTACCCATCACA 60.263 45.833 0.00 0.00 37.53 3.58
742 764 4.689345 GTGACTAAAGTGTACCCATCACAC 59.311 45.833 0.00 0.00 45.36 3.82
750 772 5.046910 GTGTACCCATCACACAAATTCTG 57.953 43.478 0.92 0.00 44.58 3.02
751 773 4.518970 GTGTACCCATCACACAAATTCTGT 59.481 41.667 0.92 0.00 44.58 3.41
761 783 3.402628 ACAAATTCTGTGACCGCTAGT 57.597 42.857 0.00 0.00 36.69 2.57
762 784 3.067106 ACAAATTCTGTGACCGCTAGTG 58.933 45.455 0.00 0.00 36.69 2.74
763 785 1.726853 AATTCTGTGACCGCTAGTGC 58.273 50.000 0.00 0.00 0.00 4.40
776 798 3.768468 GCTAGTGCGATCTACCCTATC 57.232 52.381 0.00 0.00 0.00 2.08
777 799 2.096174 GCTAGTGCGATCTACCCTATCG 59.904 54.545 0.00 0.00 46.94 2.92
778 800 1.535833 AGTGCGATCTACCCTATCGG 58.464 55.000 7.49 0.00 44.92 4.18
796 818 7.904205 CCTATCGGGGAAAATATAACTGTACT 58.096 38.462 0.00 0.00 0.00 2.73
797 819 9.028284 CCTATCGGGGAAAATATAACTGTACTA 57.972 37.037 0.00 0.00 0.00 1.82
798 820 9.852091 CTATCGGGGAAAATATAACTGTACTAC 57.148 37.037 0.00 0.00 0.00 2.73
799 821 7.658525 TCGGGGAAAATATAACTGTACTACA 57.341 36.000 0.00 0.00 0.00 2.74
800 822 8.076910 TCGGGGAAAATATAACTGTACTACAA 57.923 34.615 0.00 0.00 0.00 2.41
801 823 8.538701 TCGGGGAAAATATAACTGTACTACAAA 58.461 33.333 0.00 0.00 0.00 2.83
813 835 6.607019 ACTGTACTACAAAATTTTCTCCCCA 58.393 36.000 0.00 0.00 0.00 4.96
827 849 0.041238 TCCCCACACTCGAATCTCCT 59.959 55.000 0.00 0.00 0.00 3.69
829 851 0.101399 CCCACACTCGAATCTCCTCG 59.899 60.000 0.00 0.00 40.25 4.63
832 854 1.107114 ACACTCGAATCTCCTCGCAT 58.893 50.000 0.00 0.00 38.73 4.73
870 892 6.553524 GGATACTATTTCTACTCCGATTCCG 58.446 44.000 0.00 0.00 0.00 4.30
893 917 3.303791 GGTCGTTGATCCACACAAACTTC 60.304 47.826 0.00 0.00 0.00 3.01
896 920 3.559655 CGTTGATCCACACAAACTTCTCA 59.440 43.478 0.00 0.00 0.00 3.27
897 921 4.214119 CGTTGATCCACACAAACTTCTCAT 59.786 41.667 0.00 0.00 0.00 2.90
899 923 6.073276 CGTTGATCCACACAAACTTCTCATAA 60.073 38.462 0.00 0.00 0.00 1.90
946 973 2.734670 TGCCGACGGTCTATTTAATCG 58.265 47.619 16.73 0.00 0.00 3.34
947 974 1.454653 GCCGACGGTCTATTTAATCGC 59.545 52.381 16.73 0.00 0.00 4.58
948 975 2.056577 CCGACGGTCTATTTAATCGCC 58.943 52.381 5.48 0.00 0.00 5.54
949 976 2.544277 CCGACGGTCTATTTAATCGCCA 60.544 50.000 5.48 0.00 0.00 5.69
950 977 2.470257 CGACGGTCTATTTAATCGCCAC 59.530 50.000 6.57 0.00 0.00 5.01
951 978 2.798847 GACGGTCTATTTAATCGCCACC 59.201 50.000 0.00 0.00 0.00 4.61
952 979 1.790623 CGGTCTATTTAATCGCCACCG 59.209 52.381 0.00 0.00 39.38 4.94
953 980 1.529865 GGTCTATTTAATCGCCACCGC 59.470 52.381 0.00 0.00 0.00 5.68
995 1048 2.982130 CGCTGGTGGAGGTAGCTT 59.018 61.111 0.00 0.00 35.36 3.74
1374 1456 2.743928 GCCTTGACCAGCTCCGTG 60.744 66.667 0.00 0.00 0.00 4.94
1855 2011 1.067776 GCGTCGGGTTCATAGGGATAG 60.068 57.143 0.00 0.00 0.00 2.08
1884 2040 4.521062 CTTCCCAGGCTCGAGCGG 62.521 72.222 29.81 24.94 43.26 5.52
2109 2289 1.445582 GATCGTGCCGTCCGTTTCT 60.446 57.895 0.00 0.00 0.00 2.52
2485 2692 4.303993 TGACGCAGCAGCAGCAGA 62.304 61.111 10.77 0.00 45.49 4.26
2505 2715 3.052620 CTCGCAGTGGACCGACGAT 62.053 63.158 0.00 0.00 31.59 3.73
2568 2778 0.321671 CTTCCTCAACCGCTTCTCCA 59.678 55.000 0.00 0.00 0.00 3.86
2591 2801 6.311200 CCAGTTATAGTTTTTGGCTGATTTGC 59.689 38.462 0.00 0.00 0.00 3.68
2598 2808 5.928264 AGTTTTTGGCTGATTTGCTGTAATC 59.072 36.000 0.00 0.00 35.54 1.75
2624 2834 3.006940 TCCATCCATAACGTGAAAGTGC 58.993 45.455 0.00 0.00 0.00 4.40
2625 2835 2.223021 CCATCCATAACGTGAAAGTGCG 60.223 50.000 0.00 0.00 0.00 5.34
2634 2844 1.055338 GTGAAAGTGCGAGCATTTGC 58.945 50.000 6.59 5.54 42.49 3.68
2662 2872 3.934457 ATTTGTAGGCTTCCGGTTTTG 57.066 42.857 0.00 0.00 0.00 2.44
2663 2873 2.642154 TTGTAGGCTTCCGGTTTTGA 57.358 45.000 0.00 0.00 0.00 2.69
2697 2907 3.630769 TCGAGAGTACATCAAAGGCGTAT 59.369 43.478 0.00 0.00 0.00 3.06
2741 2955 7.403312 AAGCATAACTATAAAATGTGTGGCA 57.597 32.000 0.00 0.00 0.00 4.92
2767 2981 1.827315 CGAACATTCGGCACACACGT 61.827 55.000 6.11 0.00 46.30 4.49
2771 2985 1.262151 ACATTCGGCACACACGTTTAC 59.738 47.619 0.00 0.00 0.00 2.01
2787 3001 0.465824 TTACCCCAACACCAACACCG 60.466 55.000 0.00 0.00 0.00 4.94
2788 3002 1.633915 TACCCCAACACCAACACCGT 61.634 55.000 0.00 0.00 0.00 4.83
2789 3003 1.755008 CCCCAACACCAACACCGTT 60.755 57.895 0.00 0.00 0.00 4.44
2804 3018 2.230508 CACCGTTCAAGCTACACCTAGA 59.769 50.000 0.00 0.00 0.00 2.43
2812 3026 5.567430 TCAAGCTACACCTAGACTAACTCA 58.433 41.667 0.00 0.00 0.00 3.41
2820 3034 7.246171 ACACCTAGACTAACTCATCACAAAT 57.754 36.000 0.00 0.00 0.00 2.32
2829 3043 8.547967 ACTAACTCATCACAAATCGTTGTAAT 57.452 30.769 0.00 0.00 46.47 1.89
2867 3081 1.301677 GCTTGCCACCACTCTGCTAC 61.302 60.000 0.00 0.00 0.00 3.58
2876 3090 4.279671 CCACCACTCTGCTACCTCTATTAG 59.720 50.000 0.00 0.00 0.00 1.73
2966 3217 1.070289 GTCAAAACCTCTCCTGTCCGT 59.930 52.381 0.00 0.00 0.00 4.69
3186 3437 1.127343 GCCTAGCCCTTCTGTCTGAT 58.873 55.000 0.00 0.00 0.00 2.90
3196 3447 4.554292 CCTTCTGTCTGATGTCCATATCG 58.446 47.826 0.00 0.00 0.00 2.92
3209 3460 2.621526 TCCATATCGTGTACTGCATCGT 59.378 45.455 0.00 0.00 0.00 3.73
3259 3511 0.035056 AGCCTAGCTTCGCCAAACAT 60.035 50.000 0.00 0.00 33.89 2.71
3374 3626 0.389948 ACATCCTGCTCGGTTTCGTC 60.390 55.000 0.00 0.00 37.69 4.20
3389 3641 0.179121 TCGTCTTTGTGCACTGTCGT 60.179 50.000 19.41 0.00 0.00 4.34
3437 3689 3.057104 TGCATTTGTGCCATGAAAGAGAG 60.057 43.478 0.00 0.00 0.00 3.20
3452 3704 4.566426 AAGAGAGCTCTATTTGGCAGTT 57.434 40.909 18.25 0.00 39.39 3.16
3458 3710 3.009473 AGCTCTATTTGGCAGTTCTCCAA 59.991 43.478 0.00 0.00 41.47 3.53
3479 3731 2.365617 ACCATCTGTCGTTGAGAAGTGT 59.634 45.455 0.00 0.00 0.00 3.55
3480 3732 2.733552 CCATCTGTCGTTGAGAAGTGTG 59.266 50.000 0.00 0.00 0.00 3.82
3488 3740 1.605710 GTTGAGAAGTGTGTGCTGCAT 59.394 47.619 5.27 0.00 0.00 3.96
3577 3829 2.656069 CCGTGAATCCACCGGTCCT 61.656 63.158 2.59 0.00 40.12 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 8.500753 TTAACATGTACACAGGGATCATTAAC 57.499 34.615 0.00 0.00 30.95 2.01
100 102 7.306013 TCCATCATACTACTTCTTGAGGGTAT 58.694 38.462 2.84 0.00 40.13 2.73
101 103 6.679542 TCCATCATACTACTTCTTGAGGGTA 58.320 40.000 2.84 0.00 40.13 3.69
102 104 5.529289 TCCATCATACTACTTCTTGAGGGT 58.471 41.667 2.84 0.00 40.13 4.34
144 146 3.209410 CACCTCTTCAGCAACTTCACTT 58.791 45.455 0.00 0.00 0.00 3.16
145 147 2.171448 ACACCTCTTCAGCAACTTCACT 59.829 45.455 0.00 0.00 0.00 3.41
237 241 1.123077 TCGCAGCAACATAGATCCCT 58.877 50.000 0.00 0.00 0.00 4.20
238 242 1.802960 CATCGCAGCAACATAGATCCC 59.197 52.381 0.00 0.00 0.00 3.85
254 258 2.279120 GCCTCTGAGCGTCCATCG 60.279 66.667 0.00 0.00 43.12 3.84
265 269 1.654317 GAGTGATCTTGCTGCCTCTG 58.346 55.000 0.00 0.00 0.00 3.35
266 270 0.540923 GGAGTGATCTTGCTGCCTCT 59.459 55.000 0.00 0.00 0.00 3.69
283 289 6.773638 AGAACAGAGAGAAATAAAAGCAGGA 58.226 36.000 0.00 0.00 0.00 3.86
286 292 8.686334 ACAAAAGAACAGAGAGAAATAAAAGCA 58.314 29.630 0.00 0.00 0.00 3.91
287 293 9.521503 AACAAAAGAACAGAGAGAAATAAAAGC 57.478 29.630 0.00 0.00 0.00 3.51
293 299 6.705863 AGCAACAAAAGAACAGAGAGAAAT 57.294 33.333 0.00 0.00 0.00 2.17
298 304 7.391148 ACTTAAAGCAACAAAAGAACAGAGA 57.609 32.000 0.00 0.00 0.00 3.10
313 319 3.261897 CCCTCTCAGGAGAACTTAAAGCA 59.738 47.826 0.08 0.00 41.86 3.91
314 320 3.369997 CCCCTCTCAGGAGAACTTAAAGC 60.370 52.174 0.08 0.00 41.86 3.51
318 324 4.354208 AATCCCCTCTCAGGAGAACTTA 57.646 45.455 0.08 0.00 41.86 2.24
319 325 2.959421 ATCCCCTCTCAGGAGAACTT 57.041 50.000 0.08 0.00 41.86 2.66
320 326 2.959421 AATCCCCTCTCAGGAGAACT 57.041 50.000 0.08 0.00 41.86 3.01
321 327 4.283212 CAGATAATCCCCTCTCAGGAGAAC 59.717 50.000 0.08 0.00 41.86 3.01
348 357 4.084952 CGACCGTTTTTAACATCGAACTCA 60.085 41.667 0.00 0.00 40.26 3.41
349 358 4.380290 CGACCGTTTTTAACATCGAACTC 58.620 43.478 0.00 0.00 40.26 3.01
350 359 3.184986 CCGACCGTTTTTAACATCGAACT 59.815 43.478 12.22 0.00 40.26 3.01
353 362 2.067766 CCCGACCGTTTTTAACATCGA 58.932 47.619 12.22 0.00 40.26 3.59
370 379 0.812412 ACCAAACGAACACAGACCCG 60.812 55.000 0.00 0.00 0.00 5.28
371 380 0.942252 GACCAAACGAACACAGACCC 59.058 55.000 0.00 0.00 0.00 4.46
372 381 0.580104 CGACCAAACGAACACAGACC 59.420 55.000 0.00 0.00 35.09 3.85
373 382 0.042448 GCGACCAAACGAACACAGAC 60.042 55.000 0.00 0.00 35.09 3.51
374 383 1.155424 GGCGACCAAACGAACACAGA 61.155 55.000 0.00 0.00 35.09 3.41
375 384 1.157870 AGGCGACCAAACGAACACAG 61.158 55.000 0.00 0.00 35.09 3.66
415 426 4.952460 AGAACCAGCGTAACAGAGTTTTA 58.048 39.130 0.00 0.00 0.00 1.52
416 427 3.805207 AGAACCAGCGTAACAGAGTTTT 58.195 40.909 0.00 0.00 0.00 2.43
422 433 1.739371 GCCCTAGAACCAGCGTAACAG 60.739 57.143 0.00 0.00 0.00 3.16
428 439 2.187946 CCTGCCCTAGAACCAGCG 59.812 66.667 0.00 0.00 0.00 5.18
441 452 1.597578 GCCTGAGCTATGAGCCTGC 60.598 63.158 0.00 0.00 43.77 4.85
443 454 3.560989 GGCCTGAGCTATGAGCCT 58.439 61.111 8.82 0.00 43.77 4.58
444 455 0.182299 AAAGGCCTGAGCTATGAGCC 59.818 55.000 5.69 8.16 43.77 4.70
449 460 2.158696 GGTGATCAAAGGCCTGAGCTAT 60.159 50.000 5.69 0.00 39.73 2.97
454 466 0.329261 CAGGGTGATCAAAGGCCTGA 59.671 55.000 5.69 0.00 0.00 3.86
477 489 3.903932 GAAAAGCAGTGCCGCCAGC 62.904 63.158 12.58 0.00 44.14 4.85
534 546 2.478370 CGGCAATGCACTAAACAGATGG 60.478 50.000 7.79 0.00 0.00 3.51
538 550 0.171007 CCCGGCAATGCACTAAACAG 59.829 55.000 7.79 0.00 0.00 3.16
542 554 0.546122 ATCTCCCGGCAATGCACTAA 59.454 50.000 7.79 0.00 0.00 2.24
550 562 0.539438 AAAGCAACATCTCCCGGCAA 60.539 50.000 0.00 0.00 0.00 4.52
561 573 8.308207 AGAAAAACTAAAACTACCAAAGCAACA 58.692 29.630 0.00 0.00 0.00 3.33
568 580 7.832769 ACAGCAAGAAAAACTAAAACTACCAA 58.167 30.769 0.00 0.00 0.00 3.67
578 590 6.826741 ACCAAGTCTTACAGCAAGAAAAACTA 59.173 34.615 0.00 0.00 44.89 2.24
579 591 5.652452 ACCAAGTCTTACAGCAAGAAAAACT 59.348 36.000 0.00 0.00 44.89 2.66
586 598 5.471456 AGAAATCACCAAGTCTTACAGCAAG 59.529 40.000 0.00 0.00 35.38 4.01
650 672 6.238703 GGATGCACATTGGTCAAAACATTTTT 60.239 34.615 0.00 0.00 0.00 1.94
651 673 5.239087 GGATGCACATTGGTCAAAACATTTT 59.761 36.000 0.00 0.00 0.00 1.82
652 674 4.756135 GGATGCACATTGGTCAAAACATTT 59.244 37.500 0.00 0.00 0.00 2.32
653 675 4.317488 GGATGCACATTGGTCAAAACATT 58.683 39.130 0.00 0.00 0.00 2.71
654 676 3.614630 CGGATGCACATTGGTCAAAACAT 60.615 43.478 0.00 0.00 0.00 2.71
655 677 2.288091 CGGATGCACATTGGTCAAAACA 60.288 45.455 0.00 0.00 0.00 2.83
656 678 2.030363 TCGGATGCACATTGGTCAAAAC 60.030 45.455 0.00 0.00 0.00 2.43
657 679 2.234143 TCGGATGCACATTGGTCAAAA 58.766 42.857 0.00 0.00 0.00 2.44
658 680 1.902938 TCGGATGCACATTGGTCAAA 58.097 45.000 0.00 0.00 0.00 2.69
659 681 1.902938 TTCGGATGCACATTGGTCAA 58.097 45.000 0.00 0.00 0.00 3.18
660 682 1.539388 GTTTCGGATGCACATTGGTCA 59.461 47.619 0.00 0.00 0.00 4.02
661 683 1.465689 CGTTTCGGATGCACATTGGTC 60.466 52.381 0.00 0.00 0.00 4.02
662 684 0.521291 CGTTTCGGATGCACATTGGT 59.479 50.000 0.00 0.00 0.00 3.67
663 685 0.798009 GCGTTTCGGATGCACATTGG 60.798 55.000 0.00 0.00 40.14 3.16
664 686 0.109827 TGCGTTTCGGATGCACATTG 60.110 50.000 0.00 0.00 45.11 2.82
665 687 2.252556 TGCGTTTCGGATGCACATT 58.747 47.368 0.00 0.00 45.11 2.71
666 688 3.979789 TGCGTTTCGGATGCACAT 58.020 50.000 0.00 0.00 45.11 3.21
670 692 0.517316 AGAACTTGCGTTTCGGATGC 59.483 50.000 0.00 0.00 40.83 3.91
671 693 1.531149 ACAGAACTTGCGTTTCGGATG 59.469 47.619 0.19 0.00 32.39 3.51
672 694 1.531149 CACAGAACTTGCGTTTCGGAT 59.469 47.619 0.19 0.00 32.39 4.18
673 695 0.934496 CACAGAACTTGCGTTTCGGA 59.066 50.000 0.19 0.00 32.39 4.55
674 696 0.934496 TCACAGAACTTGCGTTTCGG 59.066 50.000 0.00 0.00 32.39 4.30
675 697 2.222931 TGTTCACAGAACTTGCGTTTCG 60.223 45.455 10.79 0.00 32.39 3.46
676 698 3.181510 ACTGTTCACAGAACTTGCGTTTC 60.182 43.478 14.00 0.00 46.59 2.78
677 699 2.747446 ACTGTTCACAGAACTTGCGTTT 59.253 40.909 14.00 0.00 46.59 3.60
678 700 2.356135 ACTGTTCACAGAACTTGCGTT 58.644 42.857 14.00 0.00 46.59 4.84
679 701 2.024176 ACTGTTCACAGAACTTGCGT 57.976 45.000 14.00 0.00 46.59 5.24
680 702 3.405170 AAACTGTTCACAGAACTTGCG 57.595 42.857 14.00 0.00 46.59 4.85
681 703 5.287035 CAGAAAAACTGTTCACAGAACTTGC 59.713 40.000 14.00 2.86 46.59 4.01
682 704 5.801947 CCAGAAAAACTGTTCACAGAACTTG 59.198 40.000 14.00 2.88 46.59 3.16
683 705 5.476945 ACCAGAAAAACTGTTCACAGAACTT 59.523 36.000 14.00 3.41 46.59 2.66
684 706 5.010282 ACCAGAAAAACTGTTCACAGAACT 58.990 37.500 14.00 2.99 46.59 3.01
685 707 5.310720 ACCAGAAAAACTGTTCACAGAAC 57.689 39.130 14.00 2.59 46.59 3.01
686 708 5.975693 AACCAGAAAAACTGTTCACAGAA 57.024 34.783 14.00 0.00 46.59 3.02
687 709 5.708948 CAAACCAGAAAAACTGTTCACAGA 58.291 37.500 14.00 0.00 46.59 3.41
689 711 4.241681 GCAAACCAGAAAAACTGTTCACA 58.758 39.130 0.00 0.00 44.40 3.58
690 712 3.303229 CGCAAACCAGAAAAACTGTTCAC 59.697 43.478 0.00 0.00 44.40 3.18
691 713 3.191581 TCGCAAACCAGAAAAACTGTTCA 59.808 39.130 0.00 0.00 44.40 3.18
692 714 3.765026 TCGCAAACCAGAAAAACTGTTC 58.235 40.909 0.00 0.00 44.40 3.18
693 715 3.192633 ACTCGCAAACCAGAAAAACTGTT 59.807 39.130 0.00 0.00 44.40 3.16
694 716 2.752903 ACTCGCAAACCAGAAAAACTGT 59.247 40.909 0.00 0.00 44.40 3.55
695 717 3.420839 ACTCGCAAACCAGAAAAACTG 57.579 42.857 0.00 0.00 45.36 3.16
696 718 3.564225 CCTACTCGCAAACCAGAAAAACT 59.436 43.478 0.00 0.00 0.00 2.66
697 719 3.304458 CCCTACTCGCAAACCAGAAAAAC 60.304 47.826 0.00 0.00 0.00 2.43
698 720 2.882137 CCCTACTCGCAAACCAGAAAAA 59.118 45.455 0.00 0.00 0.00 1.94
699 721 2.158726 ACCCTACTCGCAAACCAGAAAA 60.159 45.455 0.00 0.00 0.00 2.29
700 722 1.418637 ACCCTACTCGCAAACCAGAAA 59.581 47.619 0.00 0.00 0.00 2.52
701 723 1.053424 ACCCTACTCGCAAACCAGAA 58.947 50.000 0.00 0.00 0.00 3.02
702 724 0.320374 CACCCTACTCGCAAACCAGA 59.680 55.000 0.00 0.00 0.00 3.86
703 725 0.320374 TCACCCTACTCGCAAACCAG 59.680 55.000 0.00 0.00 0.00 4.00
704 726 0.034337 GTCACCCTACTCGCAAACCA 59.966 55.000 0.00 0.00 0.00 3.67
705 727 0.320697 AGTCACCCTACTCGCAAACC 59.679 55.000 0.00 0.00 0.00 3.27
706 728 3.308438 TTAGTCACCCTACTCGCAAAC 57.692 47.619 0.00 0.00 0.00 2.93
707 729 3.322828 ACTTTAGTCACCCTACTCGCAAA 59.677 43.478 0.00 0.00 0.00 3.68
708 730 2.895404 ACTTTAGTCACCCTACTCGCAA 59.105 45.455 0.00 0.00 0.00 4.85
709 731 2.230508 CACTTTAGTCACCCTACTCGCA 59.769 50.000 0.00 0.00 0.00 5.10
710 732 2.230750 ACACTTTAGTCACCCTACTCGC 59.769 50.000 0.00 0.00 0.00 5.03
711 733 4.142513 GGTACACTTTAGTCACCCTACTCG 60.143 50.000 0.00 0.00 0.00 4.18
712 734 4.159321 GGGTACACTTTAGTCACCCTACTC 59.841 50.000 16.74 0.00 42.74 2.59
713 735 4.092279 GGGTACACTTTAGTCACCCTACT 58.908 47.826 16.74 0.00 42.74 2.57
714 736 3.834231 TGGGTACACTTTAGTCACCCTAC 59.166 47.826 21.40 5.15 44.73 3.18
715 737 4.130719 TGGGTACACTTTAGTCACCCTA 57.869 45.455 21.40 11.14 44.73 3.53
716 738 2.980548 TGGGTACACTTTAGTCACCCT 58.019 47.619 21.40 0.00 44.73 4.34
717 739 3.262405 TGATGGGTACACTTTAGTCACCC 59.738 47.826 17.01 17.01 44.71 4.61
718 740 4.251268 GTGATGGGTACACTTTAGTCACC 58.749 47.826 0.00 2.81 35.66 4.02
719 741 4.689345 GTGTGATGGGTACACTTTAGTCAC 59.311 45.833 0.00 4.25 43.79 3.67
720 742 4.345547 TGTGTGATGGGTACACTTTAGTCA 59.654 41.667 9.34 0.00 46.49 3.41
721 743 4.890088 TGTGTGATGGGTACACTTTAGTC 58.110 43.478 9.34 0.00 46.49 2.59
722 744 4.967084 TGTGTGATGGGTACACTTTAGT 57.033 40.909 9.34 0.00 46.49 2.24
723 745 6.817765 ATTTGTGTGATGGGTACACTTTAG 57.182 37.500 9.34 0.00 46.49 1.85
724 746 7.001674 AGAATTTGTGTGATGGGTACACTTTA 58.998 34.615 9.34 0.00 46.49 1.85
725 747 5.833131 AGAATTTGTGTGATGGGTACACTTT 59.167 36.000 9.34 1.94 46.49 2.66
726 748 5.241506 CAGAATTTGTGTGATGGGTACACTT 59.758 40.000 9.34 0.00 46.49 3.16
727 749 4.761739 CAGAATTTGTGTGATGGGTACACT 59.238 41.667 9.34 0.00 46.49 3.55
728 750 4.518970 ACAGAATTTGTGTGATGGGTACAC 59.481 41.667 0.00 0.00 46.52 2.90
729 751 4.724399 ACAGAATTTGTGTGATGGGTACA 58.276 39.130 0.00 0.00 38.99 2.90
741 763 3.067106 CACTAGCGGTCACAGAATTTGT 58.933 45.455 0.00 0.00 41.94 2.83
742 764 2.159653 GCACTAGCGGTCACAGAATTTG 60.160 50.000 0.00 0.00 0.00 2.32
743 765 2.076863 GCACTAGCGGTCACAGAATTT 58.923 47.619 0.00 0.00 0.00 1.82
744 766 1.726853 GCACTAGCGGTCACAGAATT 58.273 50.000 0.00 0.00 0.00 2.17
745 767 3.442996 GCACTAGCGGTCACAGAAT 57.557 52.632 0.00 0.00 0.00 2.40
746 768 4.988065 GCACTAGCGGTCACAGAA 57.012 55.556 0.00 0.00 0.00 3.02
756 778 2.096174 CGATAGGGTAGATCGCACTAGC 59.904 54.545 7.50 7.50 39.71 3.42
772 794 9.852091 GTAGTACAGTTATATTTTCCCCGATAG 57.148 37.037 0.00 0.00 0.00 2.08
773 795 9.365906 TGTAGTACAGTTATATTTTCCCCGATA 57.634 33.333 0.00 0.00 0.00 2.92
774 796 8.253867 TGTAGTACAGTTATATTTTCCCCGAT 57.746 34.615 0.00 0.00 0.00 4.18
775 797 7.658525 TGTAGTACAGTTATATTTTCCCCGA 57.341 36.000 0.00 0.00 0.00 5.14
776 798 8.721019 TTTGTAGTACAGTTATATTTTCCCCG 57.279 34.615 2.68 0.00 0.00 5.73
786 808 9.239551 GGGGAGAAAATTTTGTAGTACAGTTAT 57.760 33.333 8.47 0.00 0.00 1.89
787 809 8.219178 TGGGGAGAAAATTTTGTAGTACAGTTA 58.781 33.333 8.47 0.00 0.00 2.24
788 810 7.013942 GTGGGGAGAAAATTTTGTAGTACAGTT 59.986 37.037 8.47 0.00 0.00 3.16
789 811 6.489022 GTGGGGAGAAAATTTTGTAGTACAGT 59.511 38.462 8.47 0.00 0.00 3.55
790 812 6.488683 TGTGGGGAGAAAATTTTGTAGTACAG 59.511 38.462 8.47 0.00 0.00 2.74
791 813 6.263617 GTGTGGGGAGAAAATTTTGTAGTACA 59.736 38.462 8.47 0.00 0.00 2.90
792 814 6.489022 AGTGTGGGGAGAAAATTTTGTAGTAC 59.511 38.462 8.47 3.25 0.00 2.73
793 815 6.607019 AGTGTGGGGAGAAAATTTTGTAGTA 58.393 36.000 8.47 0.00 0.00 1.82
794 816 5.454966 AGTGTGGGGAGAAAATTTTGTAGT 58.545 37.500 8.47 0.00 0.00 2.73
795 817 5.334879 CGAGTGTGGGGAGAAAATTTTGTAG 60.335 44.000 8.47 0.00 0.00 2.74
796 818 4.517453 CGAGTGTGGGGAGAAAATTTTGTA 59.483 41.667 8.47 0.00 0.00 2.41
797 819 3.317993 CGAGTGTGGGGAGAAAATTTTGT 59.682 43.478 8.47 3.78 0.00 2.83
798 820 3.568007 TCGAGTGTGGGGAGAAAATTTTG 59.432 43.478 8.47 0.00 0.00 2.44
799 821 3.827722 TCGAGTGTGGGGAGAAAATTTT 58.172 40.909 2.28 2.28 0.00 1.82
800 822 3.502123 TCGAGTGTGGGGAGAAAATTT 57.498 42.857 0.00 0.00 0.00 1.82
801 823 3.502123 TTCGAGTGTGGGGAGAAAATT 57.498 42.857 0.00 0.00 0.00 1.82
807 829 0.461961 GGAGATTCGAGTGTGGGGAG 59.538 60.000 0.00 0.00 0.00 4.30
811 833 0.526524 GCGAGGAGATTCGAGTGTGG 60.527 60.000 0.00 0.00 43.03 4.17
813 835 1.107114 ATGCGAGGAGATTCGAGTGT 58.893 50.000 0.00 0.00 43.03 3.55
827 849 1.629345 CGAAACAGCTCTGCATGCGA 61.629 55.000 14.09 12.21 35.28 5.10
829 851 1.136147 CCGAAACAGCTCTGCATGC 59.864 57.895 11.82 11.82 0.00 4.06
832 854 1.550524 AGTATCCGAAACAGCTCTGCA 59.449 47.619 0.00 0.00 0.00 4.41
870 892 1.265905 GTTTGTGTGGATCAACGACCC 59.734 52.381 0.00 0.00 0.00 4.46
893 917 4.527509 ATCTGCCTGGATACGTTATGAG 57.472 45.455 0.00 0.00 42.51 2.90
896 920 5.163301 ACTGAAATCTGCCTGGATACGTTAT 60.163 40.000 0.00 0.00 42.51 1.89
897 921 4.161565 ACTGAAATCTGCCTGGATACGTTA 59.838 41.667 0.00 0.00 42.51 3.18
899 923 2.501723 ACTGAAATCTGCCTGGATACGT 59.498 45.455 0.00 0.00 42.51 3.57
953 980 3.774959 ATAGTCGAGCTTGCGGCCG 62.775 63.158 24.05 24.05 43.05 6.13
954 981 1.491505 GAATAGTCGAGCTTGCGGCC 61.492 60.000 0.00 0.00 43.05 6.13
995 1048 0.827925 CCCGCTCCTAGCCATGAGTA 60.828 60.000 0.00 0.00 38.18 2.59
1597 1718 1.493311 CGAGTTTGAGGCTTCGCAC 59.507 57.895 0.00 0.00 0.00 5.34
1917 2082 2.742372 CAGGGAAACGAGGCGGTG 60.742 66.667 0.00 0.00 0.00 4.94
2052 2226 1.939974 ACCGAATGATCATGTCCGTG 58.060 50.000 9.46 9.70 0.00 4.94
2127 2313 4.101448 AGCAGCCGCCGGAGATTT 62.101 61.111 7.68 0.00 39.83 2.17
2485 2692 2.338984 GTCGGTCCACTGCGAGTT 59.661 61.111 0.00 0.00 0.00 3.01
2505 2715 3.861131 GCTTAAGCGTCTTGTCCTTCTCA 60.861 47.826 12.53 0.00 0.00 3.27
2568 2778 7.092716 CAGCAAATCAGCCAAAAACTATAACT 58.907 34.615 0.00 0.00 34.23 2.24
2591 2801 6.538742 ACGTTATGGATGGACAAAGATTACAG 59.461 38.462 0.00 0.00 0.00 2.74
2598 2808 5.181245 ACTTTCACGTTATGGATGGACAAAG 59.819 40.000 0.00 0.00 0.00 2.77
2624 2834 4.616802 ACAAATTTAACTCGCAAATGCTCG 59.383 37.500 3.63 0.00 39.32 5.03
2625 2835 6.251376 CCTACAAATTTAACTCGCAAATGCTC 59.749 38.462 3.63 0.00 39.32 4.26
2634 2844 4.201783 CCGGAAGCCTACAAATTTAACTCG 60.202 45.833 0.00 0.00 0.00 4.18
2635 2845 4.698780 ACCGGAAGCCTACAAATTTAACTC 59.301 41.667 9.46 0.00 0.00 3.01
2636 2846 4.659115 ACCGGAAGCCTACAAATTTAACT 58.341 39.130 9.46 0.00 0.00 2.24
2637 2847 5.381174 AACCGGAAGCCTACAAATTTAAC 57.619 39.130 9.46 0.00 0.00 2.01
2638 2848 6.040616 TCAAAACCGGAAGCCTACAAATTTAA 59.959 34.615 9.46 0.00 0.00 1.52
2640 2850 4.342665 TCAAAACCGGAAGCCTACAAATTT 59.657 37.500 9.46 0.00 0.00 1.82
2725 2939 4.734854 GCATTCGTGCCACACATTTTATAG 59.265 41.667 0.00 0.00 33.40 1.31
2728 2942 2.666895 CGCATTCGTGCCACACATTTTA 60.667 45.455 0.00 0.00 33.40 1.52
2731 2945 1.209898 CGCATTCGTGCCACACATT 59.790 52.632 0.00 0.00 33.40 2.71
2767 2981 1.777941 GGTGTTGGTGTTGGGGTAAA 58.222 50.000 0.00 0.00 0.00 2.01
2771 2985 1.730451 GAACGGTGTTGGTGTTGGGG 61.730 60.000 0.00 0.00 0.00 4.96
2787 3001 6.072064 TGAGTTAGTCTAGGTGTAGCTTGAAC 60.072 42.308 0.00 0.00 0.00 3.18
2788 3002 6.008331 TGAGTTAGTCTAGGTGTAGCTTGAA 58.992 40.000 0.00 0.00 0.00 2.69
2789 3003 5.567430 TGAGTTAGTCTAGGTGTAGCTTGA 58.433 41.667 0.00 0.00 0.00 3.02
2804 3018 7.956420 TTACAACGATTTGTGATGAGTTAGT 57.044 32.000 1.90 0.00 45.91 2.24
2812 3026 5.007034 TGGTGGATTACAACGATTTGTGAT 58.993 37.500 1.90 0.00 45.91 3.06
2829 3043 4.947147 GCAGGCGGTGTTGGTGGA 62.947 66.667 0.00 0.00 0.00 4.02
2966 3217 1.623811 CGAGGAGGAGTTTTCAAGGGA 59.376 52.381 0.00 0.00 0.00 4.20
3080 3331 1.078848 CTCCTGCAGTGCCTGTACC 60.079 63.158 13.72 0.00 33.43 3.34
3186 3437 3.550030 CGATGCAGTACACGATATGGACA 60.550 47.826 0.00 0.00 45.86 4.02
3196 3447 0.389817 TGGCTGACGATGCAGTACAC 60.390 55.000 0.00 0.00 38.17 2.90
3209 3460 3.315191 GTGTAAGCTCTTTGTTTGGCTGA 59.685 43.478 0.00 0.00 35.08 4.26
3281 3533 2.425143 CAGTCTATGCAATGGGTGGT 57.575 50.000 0.00 0.00 0.00 4.16
3374 3626 0.304705 GGTGACGACAGTGCACAAAG 59.695 55.000 21.04 10.96 33.28 2.77
3389 3641 1.936436 GCATCTTTGCCATGCGGTGA 61.936 55.000 0.00 0.00 43.38 4.02
3437 3689 2.991250 TGGAGAACTGCCAAATAGAGC 58.009 47.619 0.00 0.00 31.13 4.09
3452 3704 1.967779 TCAACGACAGATGGTTGGAGA 59.032 47.619 4.32 0.00 42.89 3.71
3458 3710 2.365617 ACACTTCTCAACGACAGATGGT 59.634 45.455 0.00 0.00 0.00 3.55
3479 3731 3.801114 ATACTAGAACGATGCAGCACA 57.199 42.857 1.53 0.00 0.00 4.57
3480 3732 4.112634 TCAATACTAGAACGATGCAGCAC 58.887 43.478 1.53 0.00 0.00 4.40
3488 3740 4.275196 CGAGGGTGATCAATACTAGAACGA 59.725 45.833 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.