Multiple sequence alignment - TraesCS5A01G371000

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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 TraesCS5A01G371000 chr5A 100.000 2383 0 0 1 2383 570174190 570176572 0.000000e+00 4401.0
1 TraesCS5A01G371000 chr5A 98.165 109 2 0 487 595 323914616 323914724 8.690000e-45 191.0
2 TraesCS5A01G371000 chr5A 95.455 110 5 0 486 595 535619256 535619147 2.430000e-40 176.0
3 TraesCS5A01G371000 chr5A 93.220 118 7 1 479 595 471713969 471714086 3.150000e-39 172.0
4 TraesCS5A01G371000 chr5A 100.000 50 0 0 838 887 2081515 2081466 2.520000e-15 93.5
5 TraesCS5A01G371000 chr5A 95.652 46 2 0 1505 1550 570175630 570175675 9.140000e-10 75.0
6 TraesCS5A01G371000 chr5A 95.652 46 2 0 1441 1486 570175694 570175739 9.140000e-10 75.0
7 TraesCS5A01G371000 chr5A 80.583 103 13 7 3 101 26439027 26438928 3.290000e-09 73.1
8 TraesCS5A01G371000 chr5B 87.291 598 37 14 932 1509 551141651 551142229 0.000000e+00 647.0
9 TraesCS5A01G371000 chr5B 87.500 296 17 10 635 914 551141308 551141599 8.220000e-85 324.0
10 TraesCS5A01G371000 chr5B 90.213 235 20 2 1 232 551138744 551138978 1.070000e-78 303.0
11 TraesCS5A01G371000 chr5B 92.903 155 9 1 1555 1707 551142459 551142613 8.570000e-55 224.0
12 TraesCS5A01G371000 chr5B 100.000 50 0 0 838 887 473816916 473816867 2.520000e-15 93.5
13 TraesCS5A01G371000 chr5B 100.000 50 0 0 838 887 580378791 580378840 2.520000e-15 93.5
14 TraesCS5A01G371000 chr5D 86.456 539 51 14 1860 2377 450945984 450946521 2.660000e-159 571.0
15 TraesCS5A01G371000 chr5D 87.623 509 34 12 1000 1504 450944432 450944915 4.450000e-157 564.0
16 TraesCS5A01G371000 chr5D 85.423 343 45 5 1961 2300 312383987 312384327 3.770000e-93 351.0
17 TraesCS5A01G371000 chr5D 94.156 154 9 0 1554 1707 450945307 450945460 3.960000e-58 235.0
18 TraesCS5A01G371000 chr5D 87.624 202 16 4 635 827 450944154 450944355 2.380000e-55 226.0
19 TraesCS5A01G371000 chr2B 84.283 579 66 15 1813 2368 109319761 109320337 2.080000e-150 542.0
20 TraesCS5A01G371000 chr2B 100.000 50 0 0 838 887 157368806 157368757 2.520000e-15 93.5
21 TraesCS5A01G371000 chr2B 81.609 87 7 7 280 363 632516582 632516502 1.980000e-06 63.9
22 TraesCS5A01G371000 chr2B 80.233 86 12 4 280 363 632508805 632508723 2.560000e-05 60.2
23 TraesCS5A01G371000 chr6D 81.179 526 78 14 1856 2368 108457015 108457532 1.030000e-108 403.0
24 TraesCS5A01G371000 chr4A 99.091 110 1 0 486 595 599483043 599483152 5.200000e-47 198.0
25 TraesCS5A01G371000 chr4A 96.364 110 4 0 486 595 83567352 83567461 5.230000e-42 182.0
26 TraesCS5A01G371000 chr4A 96.330 109 4 0 487 595 70743156 70743264 1.880000e-41 180.0
27 TraesCS5A01G371000 chr6A 98.182 110 2 0 486 595 216014120 216014011 2.420000e-45 193.0
28 TraesCS5A01G371000 chr6A 96.330 109 4 0 487 595 524858840 524858948 1.880000e-41 180.0
29 TraesCS5A01G371000 chr3A 92.593 108 8 0 486 593 571857350 571857457 3.170000e-34 156.0
30 TraesCS5A01G371000 chr3A 100.000 50 0 0 838 887 508181327 508181278 2.520000e-15 93.5
31 TraesCS5A01G371000 chr3A 100.000 50 0 0 838 887 517103604 517103555 2.520000e-15 93.5
32 TraesCS5A01G371000 chr1A 91.743 109 9 0 487 595 284906984 284907092 4.100000e-33 152.0
33 TraesCS5A01G371000 chr2D 89.062 64 7 0 280 343 532496966 532496903 1.960000e-11 80.5
34 TraesCS5A01G371000 chr2A 83.333 84 12 2 280 363 677034646 677034565 2.540000e-10 76.8
35 TraesCS5A01G371000 chrUn 80.899 89 9 7 280 363 183923619 183923704 1.980000e-06 63.9
36 TraesCS5A01G371000 chrUn 80.899 89 9 7 280 363 271274359 271274274 1.980000e-06 63.9
37 TraesCS5A01G371000 chrUn 80.899 89 9 7 280 363 315020509 315020594 1.980000e-06 63.9
38 TraesCS5A01G371000 chrUn 88.462 52 1 4 314 363 349126863 349126911 9.200000e-05 58.4
39 TraesCS5A01G371000 chrUn 88.462 52 1 4 314 363 370910443 370910491 9.200000e-05 58.4


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 TraesCS5A01G371000 chr5A 570174190 570176572 2382 False 1517.0 4401 97.101333 1 2383 3 chr5A.!!$F3 2382
1 TraesCS5A01G371000 chr5B 551138744 551142613 3869 False 374.5 647 89.476750 1 1707 4 chr5B.!!$F2 1706
2 TraesCS5A01G371000 chr5D 450944154 450946521 2367 False 399.0 571 88.964750 635 2377 4 chr5D.!!$F2 1742
3 TraesCS5A01G371000 chr2B 109319761 109320337 576 False 542.0 542 84.283000 1813 2368 1 chr2B.!!$F1 555
4 TraesCS5A01G371000 chr6D 108457015 108457532 517 False 403.0 403 81.179000 1856 2368 1 chr6D.!!$F1 512

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
554 2598 0.107897 CCCACAACATAGGCAGCGTA 60.108 55.0 0.0 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 5040 0.034863 TGGCCTAAACCCGAATCCAC 60.035 55.0 3.32 0.0 0.0 4.02 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
137 138 9.871238 AGACGTTTACAGAGTATGTATTTTCAT 57.129 29.630 0.00 0.00 43.87 2.57
226 230 2.952245 CAGCAGCACACAGGCTTC 59.048 61.111 0.00 0.00 42.71 3.86
232 236 1.301401 GCACACAGGCTTCGTGGTA 60.301 57.895 13.37 0.00 38.74 3.25
233 237 0.673644 GCACACAGGCTTCGTGGTAT 60.674 55.000 13.37 0.00 38.74 2.73
234 238 1.808411 CACACAGGCTTCGTGGTATT 58.192 50.000 9.48 0.00 38.74 1.89
236 240 2.552315 CACACAGGCTTCGTGGTATTTT 59.448 45.455 9.48 0.00 38.74 1.82
237 241 3.749088 CACACAGGCTTCGTGGTATTTTA 59.251 43.478 9.48 0.00 38.74 1.52
238 242 4.394920 CACACAGGCTTCGTGGTATTTTAT 59.605 41.667 9.48 0.00 38.74 1.40
239 243 5.007682 ACACAGGCTTCGTGGTATTTTATT 58.992 37.500 9.48 0.00 38.74 1.40
240 244 5.475564 ACACAGGCTTCGTGGTATTTTATTT 59.524 36.000 9.48 0.00 38.74 1.40
241 245 6.655848 ACACAGGCTTCGTGGTATTTTATTTA 59.344 34.615 9.48 0.00 38.74 1.40
242 246 7.175293 ACACAGGCTTCGTGGTATTTTATTTAA 59.825 33.333 9.48 0.00 38.74 1.52
243 247 8.188139 CACAGGCTTCGTGGTATTTTATTTAAT 58.812 33.333 0.00 0.00 0.00 1.40
244 248 8.745590 ACAGGCTTCGTGGTATTTTATTTAATT 58.254 29.630 0.00 0.00 0.00 1.40
245 249 9.581099 CAGGCTTCGTGGTATTTTATTTAATTT 57.419 29.630 0.00 0.00 0.00 1.82
246 250 9.797556 AGGCTTCGTGGTATTTTATTTAATTTC 57.202 29.630 0.00 0.00 0.00 2.17
247 251 9.575783 GGCTTCGTGGTATTTTATTTAATTTCA 57.424 29.630 0.00 0.00 0.00 2.69
269 273 9.986833 TTTCATTTAATCTCATCAACATGTACG 57.013 29.630 0.00 0.00 0.00 3.67
272 276 8.611757 CATTTAATCTCATCAACATGTACGGAA 58.388 33.333 0.00 0.00 0.00 4.30
273 277 8.554835 TTTAATCTCATCAACATGTACGGAAA 57.445 30.769 0.00 0.00 0.00 3.13
274 278 8.554835 TTAATCTCATCAACATGTACGGAAAA 57.445 30.769 0.00 0.00 0.00 2.29
275 279 7.630242 AATCTCATCAACATGTACGGAAAAT 57.370 32.000 0.00 0.00 0.00 1.82
276 280 6.421377 TCTCATCAACATGTACGGAAAATG 57.579 37.500 0.00 0.00 0.00 2.32
277 281 6.169800 TCTCATCAACATGTACGGAAAATGA 58.830 36.000 0.00 0.00 0.00 2.57
280 284 7.915508 TCATCAACATGTACGGAAAATGATAC 58.084 34.615 0.00 0.00 0.00 2.24
282 286 7.915293 TCAACATGTACGGAAAATGATACTT 57.085 32.000 0.00 0.00 0.00 2.24
283 287 9.607988 ATCAACATGTACGGAAAATGATACTTA 57.392 29.630 0.00 0.00 0.00 2.24
284 288 9.607988 TCAACATGTACGGAAAATGATACTTAT 57.392 29.630 0.00 0.00 0.00 1.73
324 862 8.214721 TCACAACCGCATAATAATCAAATACA 57.785 30.769 0.00 0.00 0.00 2.29
325 863 8.678199 TCACAACCGCATAATAATCAAATACAA 58.322 29.630 0.00 0.00 0.00 2.41
326 864 9.462174 CACAACCGCATAATAATCAAATACAAT 57.538 29.630 0.00 0.00 0.00 2.71
392 2266 9.685276 ATCTCATTTACAACCTCATCAAATACA 57.315 29.630 0.00 0.00 0.00 2.29
394 2268 9.166173 CTCATTTACAACCTCATCAAATACAGA 57.834 33.333 0.00 0.00 0.00 3.41
401 2275 7.067494 ACAACCTCATCAAATACAGAATTAGCC 59.933 37.037 0.00 0.00 0.00 3.93
403 2277 6.543831 ACCTCATCAAATACAGAATTAGCCAC 59.456 38.462 0.00 0.00 0.00 5.01
405 2279 7.255035 CCTCATCAAATACAGAATTAGCCACAG 60.255 40.741 0.00 0.00 0.00 3.66
474 2518 0.398696 ATTACTGGTTCCACCACGCA 59.601 50.000 0.00 0.00 44.79 5.24
476 2520 1.404479 TACTGGTTCCACCACGCACT 61.404 55.000 0.00 0.00 44.79 4.40
477 2521 2.203139 TGGTTCCACCACGCACTG 60.203 61.111 0.00 0.00 44.79 3.66
478 2522 2.203153 GGTTCCACCACGCACTGT 60.203 61.111 0.00 0.00 38.42 3.55
479 2523 1.070105 GGTTCCACCACGCACTGTA 59.930 57.895 0.00 0.00 38.42 2.74
480 2524 1.226030 GGTTCCACCACGCACTGTAC 61.226 60.000 0.00 0.00 38.42 2.90
481 2525 0.531090 GTTCCACCACGCACTGTACA 60.531 55.000 0.00 0.00 0.00 2.90
482 2526 0.249699 TTCCACCACGCACTGTACAG 60.250 55.000 21.44 21.44 0.00 2.74
483 2527 1.110518 TCCACCACGCACTGTACAGA 61.111 55.000 29.30 0.00 0.00 3.41
484 2528 0.249699 CCACCACGCACTGTACAGAA 60.250 55.000 29.30 0.00 0.00 3.02
485 2529 1.608025 CCACCACGCACTGTACAGAAT 60.608 52.381 29.30 4.89 0.00 2.40
486 2530 2.143122 CACCACGCACTGTACAGAATT 58.857 47.619 29.30 4.07 0.00 2.17
487 2531 2.548057 CACCACGCACTGTACAGAATTT 59.452 45.455 29.30 3.66 0.00 1.82
488 2532 3.003275 CACCACGCACTGTACAGAATTTT 59.997 43.478 29.30 3.25 0.00 1.82
489 2533 3.630312 ACCACGCACTGTACAGAATTTTT 59.370 39.130 29.30 2.44 0.00 1.94
511 2555 5.988310 TTTTAGAACATAGACGTCAGGGA 57.012 39.130 19.50 0.00 0.00 4.20
512 2556 4.978083 TTAGAACATAGACGTCAGGGAC 57.022 45.455 19.50 4.56 0.00 4.46
521 2565 2.739132 GTCAGGGACGTCCGGTTT 59.261 61.111 27.68 10.83 41.52 3.27
522 2566 1.070275 GTCAGGGACGTCCGGTTTT 59.930 57.895 27.68 8.31 41.52 2.43
523 2567 0.318120 GTCAGGGACGTCCGGTTTTA 59.682 55.000 27.68 7.49 41.52 1.52
524 2568 1.047002 TCAGGGACGTCCGGTTTTAA 58.953 50.000 27.68 6.44 41.52 1.52
525 2569 1.415659 TCAGGGACGTCCGGTTTTAAA 59.584 47.619 27.68 4.86 41.52 1.52
526 2570 2.038820 TCAGGGACGTCCGGTTTTAAAT 59.961 45.455 27.68 2.64 41.52 1.40
527 2571 2.815503 CAGGGACGTCCGGTTTTAAATT 59.184 45.455 27.68 0.85 41.52 1.82
528 2572 4.002316 CAGGGACGTCCGGTTTTAAATTA 58.998 43.478 27.68 0.00 41.52 1.40
529 2573 4.455190 CAGGGACGTCCGGTTTTAAATTAA 59.545 41.667 27.68 0.00 41.52 1.40
530 2574 5.124297 CAGGGACGTCCGGTTTTAAATTAAT 59.876 40.000 27.68 0.00 41.52 1.40
531 2575 6.315891 CAGGGACGTCCGGTTTTAAATTAATA 59.684 38.462 27.68 0.00 41.52 0.98
532 2576 6.883756 AGGGACGTCCGGTTTTAAATTAATAA 59.116 34.615 27.68 0.00 41.52 1.40
533 2577 7.392953 AGGGACGTCCGGTTTTAAATTAATAAA 59.607 33.333 27.68 0.00 41.52 1.40
534 2578 7.697710 GGGACGTCCGGTTTTAAATTAATAAAG 59.302 37.037 27.68 0.00 36.71 1.85
535 2579 7.218773 GGACGTCCGGTTTTAAATTAATAAAGC 59.781 37.037 20.85 0.00 0.00 3.51
536 2580 7.028962 ACGTCCGGTTTTAAATTAATAAAGCC 58.971 34.615 0.00 6.54 40.64 4.35
537 2581 6.473131 CGTCCGGTTTTAAATTAATAAAGCCC 59.527 38.462 0.00 2.95 40.84 5.19
538 2582 7.321908 GTCCGGTTTTAAATTAATAAAGCCCA 58.678 34.615 0.00 0.00 40.84 5.36
539 2583 7.276218 GTCCGGTTTTAAATTAATAAAGCCCAC 59.724 37.037 0.00 5.09 40.84 4.61
540 2584 7.039223 TCCGGTTTTAAATTAATAAAGCCCACA 60.039 33.333 0.00 0.00 40.84 4.17
541 2585 7.603024 CCGGTTTTAAATTAATAAAGCCCACAA 59.397 33.333 9.66 0.00 40.84 3.33
542 2586 8.436970 CGGTTTTAAATTAATAAAGCCCACAAC 58.563 33.333 9.66 0.74 40.84 3.32
543 2587 9.274206 GGTTTTAAATTAATAAAGCCCACAACA 57.726 29.630 5.64 0.00 39.11 3.33
551 2595 3.200522 GCCCACAACATAGGCAGC 58.799 61.111 0.00 0.00 46.34 5.25
552 2596 2.764314 GCCCACAACATAGGCAGCG 61.764 63.158 0.00 0.00 46.34 5.18
553 2597 1.377202 CCCACAACATAGGCAGCGT 60.377 57.895 0.00 0.00 0.00 5.07
554 2598 0.107897 CCCACAACATAGGCAGCGTA 60.108 55.000 0.00 0.00 0.00 4.42
555 2599 1.475034 CCCACAACATAGGCAGCGTAT 60.475 52.381 1.54 1.54 0.00 3.06
556 2600 1.599071 CCACAACATAGGCAGCGTATG 59.401 52.381 26.55 26.55 37.95 2.39
557 2601 2.549926 CACAACATAGGCAGCGTATGA 58.450 47.619 32.25 0.33 36.22 2.15
558 2602 2.285220 CACAACATAGGCAGCGTATGAC 59.715 50.000 32.25 0.00 36.22 3.06
559 2603 2.093711 ACAACATAGGCAGCGTATGACA 60.094 45.455 32.25 0.00 40.68 3.58
560 2604 2.935849 CAACATAGGCAGCGTATGACAA 59.064 45.455 32.25 0.00 40.68 3.18
561 2605 2.550978 ACATAGGCAGCGTATGACAAC 58.449 47.619 32.25 0.00 40.68 3.32
562 2606 1.867233 CATAGGCAGCGTATGACAACC 59.133 52.381 24.88 0.00 40.68 3.77
563 2607 0.899019 TAGGCAGCGTATGACAACCA 59.101 50.000 0.00 0.00 40.68 3.67
564 2608 0.673644 AGGCAGCGTATGACAACCAC 60.674 55.000 0.00 0.00 40.68 4.16
565 2609 0.953471 GGCAGCGTATGACAACCACA 60.953 55.000 0.00 0.00 36.67 4.17
566 2610 1.086696 GCAGCGTATGACAACCACAT 58.913 50.000 0.00 0.00 0.00 3.21
567 2611 1.202065 GCAGCGTATGACAACCACATG 60.202 52.381 0.00 0.00 0.00 3.21
568 2612 2.345876 CAGCGTATGACAACCACATGA 58.654 47.619 0.00 0.00 0.00 3.07
569 2613 2.094258 CAGCGTATGACAACCACATGAC 59.906 50.000 0.00 0.00 0.00 3.06
570 2614 1.396996 GCGTATGACAACCACATGACC 59.603 52.381 0.00 0.00 0.00 4.02
571 2615 2.694213 CGTATGACAACCACATGACCA 58.306 47.619 0.00 0.00 0.00 4.02
572 2616 3.070748 CGTATGACAACCACATGACCAA 58.929 45.455 0.00 0.00 0.00 3.67
573 2617 3.120338 CGTATGACAACCACATGACCAAC 60.120 47.826 0.00 0.00 0.00 3.77
574 2618 2.426842 TGACAACCACATGACCAACA 57.573 45.000 0.00 0.00 0.00 3.33
575 2619 2.020720 TGACAACCACATGACCAACAC 58.979 47.619 0.00 0.00 0.00 3.32
576 2620 2.020720 GACAACCACATGACCAACACA 58.979 47.619 0.00 0.00 0.00 3.72
577 2621 1.748493 ACAACCACATGACCAACACAC 59.252 47.619 0.00 0.00 0.00 3.82
578 2622 1.021202 AACCACATGACCAACACACG 58.979 50.000 0.00 0.00 0.00 4.49
579 2623 0.817634 ACCACATGACCAACACACGG 60.818 55.000 0.00 0.00 0.00 4.94
580 2624 0.817634 CCACATGACCAACACACGGT 60.818 55.000 0.00 0.00 40.30 4.83
581 2625 1.541452 CCACATGACCAACACACGGTA 60.541 52.381 0.00 0.00 36.69 4.02
582 2626 1.529438 CACATGACCAACACACGGTAC 59.471 52.381 0.00 0.00 36.69 3.34
583 2627 1.153353 CATGACCAACACACGGTACC 58.847 55.000 0.16 0.16 36.69 3.34
584 2628 0.759959 ATGACCAACACACGGTACCA 59.240 50.000 13.54 0.00 36.69 3.25
585 2629 0.540454 TGACCAACACACGGTACCAA 59.460 50.000 13.54 0.00 36.69 3.67
586 2630 1.065636 TGACCAACACACGGTACCAAA 60.066 47.619 13.54 0.00 36.69 3.28
587 2631 1.331447 GACCAACACACGGTACCAAAC 59.669 52.381 13.54 0.00 36.69 2.93
588 2632 1.339824 ACCAACACACGGTACCAAACA 60.340 47.619 13.54 0.00 34.02 2.83
589 2633 1.743958 CCAACACACGGTACCAAACAA 59.256 47.619 13.54 0.00 0.00 2.83
590 2634 2.163815 CCAACACACGGTACCAAACAAA 59.836 45.455 13.54 0.00 0.00 2.83
591 2635 3.367087 CCAACACACGGTACCAAACAAAA 60.367 43.478 13.54 0.00 0.00 2.44
592 2636 3.768468 ACACACGGTACCAAACAAAAG 57.232 42.857 13.54 0.00 0.00 2.27
593 2637 3.345414 ACACACGGTACCAAACAAAAGA 58.655 40.909 13.54 0.00 0.00 2.52
594 2638 3.127376 ACACACGGTACCAAACAAAAGAC 59.873 43.478 13.54 0.00 0.00 3.01
595 2639 2.684374 ACACGGTACCAAACAAAAGACC 59.316 45.455 13.54 0.00 0.00 3.85
596 2640 2.683867 CACGGTACCAAACAAAAGACCA 59.316 45.455 13.54 0.00 0.00 4.02
597 2641 2.684374 ACGGTACCAAACAAAAGACCAC 59.316 45.455 13.54 0.00 0.00 4.16
598 2642 2.946990 CGGTACCAAACAAAAGACCACT 59.053 45.455 13.54 0.00 0.00 4.00
614 2658 3.933332 GACCACTGTACAGAATTAGCCAC 59.067 47.826 29.30 6.75 0.00 5.01
616 2660 4.019321 ACCACTGTACAGAATTAGCCACAT 60.019 41.667 29.30 0.00 0.00 3.21
651 2704 5.128171 TGCGGGAAGAATTAGTAAGCTAGAA 59.872 40.000 0.00 0.00 0.00 2.10
653 2706 6.570692 CGGGAAGAATTAGTAAGCTAGAACA 58.429 40.000 0.00 0.00 0.00 3.18
673 2726 3.114616 CTCGTTGCCAGCTCACGG 61.115 66.667 12.82 0.00 0.00 4.94
688 2741 0.677731 CACGGATGACACATTGGCCT 60.678 55.000 3.32 0.00 0.00 5.19
747 2800 1.338105 ACATACATGCTGACACGTGCT 60.338 47.619 17.22 2.46 0.00 4.40
749 2802 2.734276 TACATGCTGACACGTGCTTA 57.266 45.000 17.22 0.69 0.00 3.09
794 2851 0.601576 GTGTGTGGTGGCACGTATCA 60.602 55.000 12.17 5.87 41.94 2.15
795 2852 0.320334 TGTGTGGTGGCACGTATCAG 60.320 55.000 12.17 0.00 41.94 2.90
820 2888 1.412710 GGCCTAATTTAAAGCCCAGGC 59.587 52.381 17.49 17.49 46.28 4.85
852 2920 2.602267 TCGTTCCCCTCGCCTTCA 60.602 61.111 0.00 0.00 0.00 3.02
874 2943 4.042560 CACCAGTCCAGATTATCCATCCAT 59.957 45.833 0.00 0.00 31.20 3.41
875 2944 4.288105 ACCAGTCCAGATTATCCATCCATC 59.712 45.833 0.00 0.00 31.20 3.51
877 2946 4.287845 CAGTCCAGATTATCCATCCATCCA 59.712 45.833 0.00 0.00 31.20 3.41
878 2947 5.045066 CAGTCCAGATTATCCATCCATCCAT 60.045 44.000 0.00 0.00 31.20 3.41
879 2948 5.191323 AGTCCAGATTATCCATCCATCCATC 59.809 44.000 0.00 0.00 31.20 3.51
880 2949 4.476113 TCCAGATTATCCATCCATCCATCC 59.524 45.833 0.00 0.00 31.20 3.51
881 2950 4.228895 CCAGATTATCCATCCATCCATCCA 59.771 45.833 0.00 0.00 31.20 3.41
908 2977 4.783764 ATAAAGCCACAGCCAGTTTAAC 57.216 40.909 0.00 0.00 41.25 2.01
914 2983 3.756434 GCCACAGCCAGTTTAACTTCATA 59.244 43.478 0.00 0.00 0.00 2.15
916 2985 5.105756 GCCACAGCCAGTTTAACTTCATATT 60.106 40.000 0.00 0.00 0.00 1.28
918 2987 7.201821 GCCACAGCCAGTTTAACTTCATATTAT 60.202 37.037 0.00 0.00 0.00 1.28
923 2992 9.771534 AGCCAGTTTAACTTCATATTATCTCTC 57.228 33.333 0.00 0.00 0.00 3.20
933 3036 8.620177 ACTTCATATTATCTCTCCTACCTAGCT 58.380 37.037 0.00 0.00 0.00 3.32
980 3089 1.207329 GCTGTTCTACAACGGGGAGAT 59.793 52.381 0.00 0.00 39.09 2.75
981 3090 2.354805 GCTGTTCTACAACGGGGAGATT 60.355 50.000 0.00 0.00 39.09 2.40
1151 3275 0.249868 CAGGAGCACGGTGAGTCAAA 60.250 55.000 13.29 0.00 0.00 2.69
1152 3276 0.249911 AGGAGCACGGTGAGTCAAAC 60.250 55.000 13.29 0.00 0.00 2.93
1153 3277 0.531974 GGAGCACGGTGAGTCAAACA 60.532 55.000 13.29 0.00 0.00 2.83
1154 3278 0.861837 GAGCACGGTGAGTCAAACAG 59.138 55.000 13.29 0.00 0.00 3.16
1155 3279 1.160329 AGCACGGTGAGTCAAACAGC 61.160 55.000 13.29 0.00 0.00 4.40
1156 3280 1.436195 GCACGGTGAGTCAAACAGCA 61.436 55.000 13.29 0.00 35.82 4.41
1157 3281 1.229428 CACGGTGAGTCAAACAGCAT 58.771 50.000 0.74 0.00 35.82 3.79
1158 3282 1.069703 CACGGTGAGTCAAACAGCATG 60.070 52.381 0.74 0.00 46.00 4.06
1159 3283 0.110056 CGGTGAGTCAAACAGCATGC 60.110 55.000 10.51 10.51 42.53 4.06
1160 3284 0.110056 GGTGAGTCAAACAGCATGCG 60.110 55.000 13.01 9.99 42.53 4.73
1161 3285 0.867746 GTGAGTCAAACAGCATGCGA 59.132 50.000 13.01 0.00 42.53 5.10
1162 3286 1.466167 GTGAGTCAAACAGCATGCGAT 59.534 47.619 13.01 0.70 42.53 4.58
1163 3287 2.095567 GTGAGTCAAACAGCATGCGATT 60.096 45.455 13.01 7.89 42.53 3.34
1164 3288 2.095617 TGAGTCAAACAGCATGCGATTG 60.096 45.455 20.25 20.25 42.53 2.67
1165 3289 0.986992 GTCAAACAGCATGCGATTGC 59.013 50.000 21.02 14.97 42.53 3.56
1199 3323 4.731612 CGCGCTCTCCTGTGCTGT 62.732 66.667 5.56 0.00 40.87 4.40
1200 3324 3.117171 GCGCTCTCCTGTGCTGTG 61.117 66.667 0.00 0.00 40.01 3.66
1212 3336 3.072211 CTGTGCTGTGTTGATCTGACAT 58.928 45.455 5.91 0.00 0.00 3.06
1235 3359 3.963383 ACTTGTTTTGCTCGTTCGATT 57.037 38.095 0.00 0.00 0.00 3.34
1247 3375 2.169769 TCGTTCGATTGATTTAGGGGCT 59.830 45.455 0.00 0.00 0.00 5.19
1322 3450 4.736896 GACGTGGTGGAGCCGTCC 62.737 72.222 0.00 0.00 43.77 4.79
1336 3464 1.299620 CGTCCTCCAACAACGACGT 60.300 57.895 0.00 0.00 42.31 4.34
1394 3526 2.441348 TCGTAGCTGGCCGATCCA 60.441 61.111 0.00 0.00 44.18 3.41
1400 3532 4.100084 CTGGCCGATCCACCTGCA 62.100 66.667 0.00 0.00 40.72 4.41
1401 3533 3.410628 TGGCCGATCCACCTGCAT 61.411 61.111 0.00 0.00 40.72 3.96
1402 3534 2.903855 GGCCGATCCACCTGCATG 60.904 66.667 0.00 0.00 34.01 4.06
1403 3535 3.589881 GCCGATCCACCTGCATGC 61.590 66.667 11.82 11.82 0.00 4.06
1438 3570 7.800847 TGCTTAGCTTTTGTTTTTGTTTTTGTC 59.199 29.630 5.60 0.00 0.00 3.18
1443 3575 7.855409 AGCTTTTGTTTTTGTTTTTGTCTTGTC 59.145 29.630 0.00 0.00 0.00 3.18
1444 3576 7.855409 GCTTTTGTTTTTGTTTTTGTCTTGTCT 59.145 29.630 0.00 0.00 0.00 3.41
1499 3631 0.861837 GAGTGCTCGTGAAAGGTGTG 59.138 55.000 0.00 0.00 0.00 3.82
1509 3641 4.998033 TCGTGAAAGGTGTGCATATGTTTA 59.002 37.500 4.29 0.00 0.00 2.01
1512 3644 7.334671 TCGTGAAAGGTGTGCATATGTTTATTA 59.665 33.333 4.29 0.00 0.00 0.98
1513 3645 7.428183 CGTGAAAGGTGTGCATATGTTTATTAC 59.572 37.037 4.29 0.00 0.00 1.89
1514 3646 8.458843 GTGAAAGGTGTGCATATGTTTATTACT 58.541 33.333 4.29 0.00 0.00 2.24
1516 3648 9.289303 GAAAGGTGTGCATATGTTTATTACTTG 57.711 33.333 4.29 0.00 0.00 3.16
1517 3649 7.333528 AGGTGTGCATATGTTTATTACTTGG 57.666 36.000 4.29 0.00 0.00 3.61
1519 3651 7.067008 AGGTGTGCATATGTTTATTACTTGGTC 59.933 37.037 4.29 0.00 0.00 4.02
1520 3652 7.067008 GGTGTGCATATGTTTATTACTTGGTCT 59.933 37.037 4.29 0.00 0.00 3.85
1521 3653 7.910162 GTGTGCATATGTTTATTACTTGGTCTG 59.090 37.037 4.29 0.00 0.00 3.51
1523 3655 8.673711 GTGCATATGTTTATTACTTGGTCTGAA 58.326 33.333 4.29 0.00 0.00 3.02
1524 3656 8.673711 TGCATATGTTTATTACTTGGTCTGAAC 58.326 33.333 4.29 0.00 0.00 3.18
1529 3661 9.959721 ATGTTTATTACTTGGTCTGAACATAGT 57.040 29.630 12.73 12.73 35.44 2.12
1530 3662 9.431887 TGTTTATTACTTGGTCTGAACATAGTC 57.568 33.333 11.86 1.74 0.00 2.59
1531 3663 9.431887 GTTTATTACTTGGTCTGAACATAGTCA 57.568 33.333 11.86 4.78 0.00 3.41
1534 3666 7.905604 TTACTTGGTCTGAACATAGTCAATG 57.094 36.000 11.86 0.00 41.74 2.82
1549 3681 8.832487 CATAGTCAATGTTAGATTTTGAGTGC 57.168 34.615 0.00 0.00 35.32 4.40
1551 3683 7.458409 AGTCAATGTTAGATTTTGAGTGCAT 57.542 32.000 0.00 0.00 33.06 3.96
1552 3684 8.565896 AGTCAATGTTAGATTTTGAGTGCATA 57.434 30.769 0.00 0.00 33.06 3.14
1558 4046 9.630098 ATGTTAGATTTTGAGTGCATAAGTTTG 57.370 29.630 0.00 0.00 0.00 2.93
1597 4087 3.791545 AGGGGATTAGGCATGGAAAGTTA 59.208 43.478 0.00 0.00 0.00 2.24
1632 4122 2.264005 ACTAATGTTTGGTGCGTGGA 57.736 45.000 0.00 0.00 0.00 4.02
1666 4156 6.266786 TCAGGGAAAATTTGGGAGAAAGTAAC 59.733 38.462 0.00 0.00 0.00 2.50
1678 4168 3.674997 AGAAAGTAACGTGCCATGTGAT 58.325 40.909 0.00 0.00 0.00 3.06
1707 4197 2.105649 GGGAAGGGCAGGAAAGAGATAG 59.894 54.545 0.00 0.00 0.00 2.08
1734 4356 3.333980 TCCCTTCTCTCCTCAACTCACTA 59.666 47.826 0.00 0.00 0.00 2.74
1752 4389 2.091555 ACTAGCCCCCAAAACAAGTCAA 60.092 45.455 0.00 0.00 0.00 3.18
1768 4406 0.250234 TCAAGAAGACATCGCCCCAG 59.750 55.000 0.00 0.00 0.00 4.45
1811 4464 0.523968 CATTTGCAGAACATCGGCGG 60.524 55.000 7.21 0.00 40.49 6.13
1862 4723 3.120108 AGGATCCGGTTTTCCTTCCATA 58.880 45.455 14.90 0.00 39.36 2.74
1874 4735 6.509418 TTTCCTTCCATAGTGTTTGCATAC 57.491 37.500 0.00 0.00 0.00 2.39
1882 4743 5.239306 CCATAGTGTTTGCATACATAGGGTG 59.761 44.000 13.22 8.21 0.00 4.61
1908 4769 2.482333 CGTTTGGTGGCACCGGAAA 61.482 57.895 30.14 22.55 42.58 3.13
1920 4784 2.580601 CCGGAAAGGTGAGGACGGT 61.581 63.158 0.00 0.00 36.78 4.83
1943 4807 2.030457 CCGCGTCGAATAAATCTGCTTT 59.970 45.455 4.92 0.00 0.00 3.51
1948 4812 5.005394 GCGTCGAATAAATCTGCTTTGTCTA 59.995 40.000 0.00 0.00 0.00 2.59
1960 4824 2.882324 CTTTGTCTACTTCCTCTCCGC 58.118 52.381 0.00 0.00 0.00 5.54
2008 4890 1.277842 TCTTGCCGGCTATTCAAGACA 59.722 47.619 29.70 4.36 40.63 3.41
2010 4892 0.107703 TGCCGGCTATTCAAGACAGG 60.108 55.000 29.70 0.00 29.38 4.00
2026 4910 7.004086 TCAAGACAGGGATATGTTGTTCTTTT 58.996 34.615 0.00 0.00 32.25 2.27
2044 4928 2.570415 TTTATCGTTGGTGGCTTCCA 57.430 45.000 0.00 0.00 35.49 3.53
2049 4933 1.026718 CGTTGGTGGCTTCCATCTCC 61.027 60.000 3.19 0.00 35.30 3.71
2091 4975 5.239351 CAGGATGAGATGATGATCCAGAAC 58.761 45.833 0.00 0.00 39.69 3.01
2166 5052 1.376812 GAAGCGGTGGATTCGGGTT 60.377 57.895 0.00 0.00 0.00 4.11
2170 5057 1.093496 GCGGTGGATTCGGGTTTAGG 61.093 60.000 0.00 0.00 0.00 2.69
2177 5064 0.039035 ATTCGGGTTTAGGCCAGCAA 59.961 50.000 5.01 0.00 0.00 3.91
2278 5165 0.749091 ATTTGGCGATGCTGCTGCTA 60.749 50.000 17.00 3.79 40.48 3.49
2284 5171 0.796927 CGATGCTGCTGCTATGGATG 59.203 55.000 17.00 0.00 40.48 3.51
2291 5178 3.538591 CTGCTGCTATGGATGTTGAGAA 58.461 45.455 0.00 0.00 0.00 2.87
2296 5183 4.910195 TGCTATGGATGTTGAGAAGTTGT 58.090 39.130 0.00 0.00 0.00 3.32
2309 5196 4.223032 TGAGAAGTTGTAGGATCCACTTCC 59.777 45.833 27.12 21.26 35.51 3.46
2316 5204 5.576563 TGTAGGATCCACTTCCTTTTCAA 57.423 39.130 15.82 0.00 43.88 2.69
2368 5256 0.387239 GGTTGTTGGCTTCGATGTGC 60.387 55.000 0.00 0.00 0.00 4.57
2371 5259 1.154413 GTTGGCTTCGATGTGCGTG 60.154 57.895 0.00 0.00 41.80 5.34
2377 5265 1.645034 CTTCGATGTGCGTGGAGATT 58.355 50.000 0.00 0.00 41.80 2.40
2378 5266 2.002586 CTTCGATGTGCGTGGAGATTT 58.997 47.619 0.00 0.00 41.80 2.17
2379 5267 2.951457 TCGATGTGCGTGGAGATTTA 57.049 45.000 0.00 0.00 41.80 1.40
2380 5268 2.809446 TCGATGTGCGTGGAGATTTAG 58.191 47.619 0.00 0.00 41.80 1.85
2381 5269 1.860950 CGATGTGCGTGGAGATTTAGG 59.139 52.381 0.00 0.00 34.64 2.69
2382 5270 1.599542 GATGTGCGTGGAGATTTAGGC 59.400 52.381 0.00 0.00 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 247 9.986833 CGTACATGTTGATGAGATTAAATGAAA 57.013 29.630 2.30 0.00 33.36 2.69
244 248 8.611757 CCGTACATGTTGATGAGATTAAATGAA 58.388 33.333 2.30 0.00 33.36 2.57
245 249 7.984617 TCCGTACATGTTGATGAGATTAAATGA 59.015 33.333 2.30 0.00 33.36 2.57
246 250 8.141835 TCCGTACATGTTGATGAGATTAAATG 57.858 34.615 2.30 0.00 33.36 2.32
247 251 8.731275 TTCCGTACATGTTGATGAGATTAAAT 57.269 30.769 2.30 0.00 33.36 1.40
248 252 8.554835 TTTCCGTACATGTTGATGAGATTAAA 57.445 30.769 2.30 0.00 33.36 1.52
249 253 8.554835 TTTTCCGTACATGTTGATGAGATTAA 57.445 30.769 2.30 0.00 33.36 1.40
250 254 8.611757 CATTTTCCGTACATGTTGATGAGATTA 58.388 33.333 2.30 0.00 33.36 1.75
253 257 6.169800 TCATTTTCCGTACATGTTGATGAGA 58.830 36.000 2.30 0.00 33.36 3.27
257 261 8.506168 AAGTATCATTTTCCGTACATGTTGAT 57.494 30.769 2.30 7.14 0.00 2.57
258 262 7.915293 AAGTATCATTTTCCGTACATGTTGA 57.085 32.000 2.30 0.00 0.00 3.18
295 299 8.818141 TTTGATTATTATGCGGTTGTGAAAAA 57.182 26.923 0.00 0.00 0.00 1.94
296 300 8.994429 ATTTGATTATTATGCGGTTGTGAAAA 57.006 26.923 0.00 0.00 0.00 2.29
297 301 9.509855 GTATTTGATTATTATGCGGTTGTGAAA 57.490 29.630 0.00 0.00 0.00 2.69
298 302 8.678199 TGTATTTGATTATTATGCGGTTGTGAA 58.322 29.630 0.00 0.00 0.00 3.18
299 303 8.214721 TGTATTTGATTATTATGCGGTTGTGA 57.785 30.769 0.00 0.00 0.00 3.58
300 304 8.848948 TTGTATTTGATTATTATGCGGTTGTG 57.151 30.769 0.00 0.00 0.00 3.33
368 1552 9.166173 TCTGTATTTGATGAGGTTGTAAATGAG 57.834 33.333 0.00 0.00 0.00 2.90
369 1553 9.513906 TTCTGTATTTGATGAGGTTGTAAATGA 57.486 29.630 0.00 0.00 0.00 2.57
374 1558 9.109393 GCTAATTCTGTATTTGATGAGGTTGTA 57.891 33.333 0.00 0.00 0.00 2.41
376 1560 7.067372 TGGCTAATTCTGTATTTGATGAGGTTG 59.933 37.037 0.00 0.00 0.00 3.77
378 1562 6.543831 GTGGCTAATTCTGTATTTGATGAGGT 59.456 38.462 0.00 0.00 0.00 3.85
379 1563 6.543465 TGTGGCTAATTCTGTATTTGATGAGG 59.457 38.462 0.00 0.00 0.00 3.86
380 1564 7.496920 TCTGTGGCTAATTCTGTATTTGATGAG 59.503 37.037 0.00 0.00 0.00 2.90
381 1565 7.337938 TCTGTGGCTAATTCTGTATTTGATGA 58.662 34.615 0.00 0.00 0.00 2.92
383 2257 8.757982 AATCTGTGGCTAATTCTGTATTTGAT 57.242 30.769 0.00 0.00 0.00 2.57
441 2485 0.953471 AGTAATGCTTTCGCCGTGCA 60.953 50.000 4.98 4.98 41.13 4.57
448 2492 3.471495 GTGGAACCAGTAATGCTTTCG 57.529 47.619 0.00 0.00 0.00 3.46
488 2532 6.161381 GTCCCTGACGTCTATGTTCTAAAAA 58.839 40.000 17.92 0.00 0.00 1.94
489 2533 5.717119 GTCCCTGACGTCTATGTTCTAAAA 58.283 41.667 17.92 0.00 0.00 1.52
490 2534 5.320549 GTCCCTGACGTCTATGTTCTAAA 57.679 43.478 17.92 0.00 0.00 1.85
491 2535 4.978083 GTCCCTGACGTCTATGTTCTAA 57.022 45.455 17.92 0.00 0.00 2.10
504 2548 0.318120 TAAAACCGGACGTCCCTGAC 59.682 55.000 28.52 3.71 0.00 3.51
505 2549 1.047002 TTAAAACCGGACGTCCCTGA 58.953 50.000 28.52 5.63 0.00 3.86
506 2550 1.881591 TTTAAAACCGGACGTCCCTG 58.118 50.000 28.52 21.36 0.00 4.45
507 2551 2.865119 ATTTAAAACCGGACGTCCCT 57.135 45.000 28.52 11.38 0.00 4.20
508 2552 5.565592 ATTAATTTAAAACCGGACGTCCC 57.434 39.130 28.52 11.28 0.00 4.46
509 2553 7.218773 GCTTTATTAATTTAAAACCGGACGTCC 59.781 37.037 25.28 25.28 0.00 4.79
510 2554 7.218773 GGCTTTATTAATTTAAAACCGGACGTC 59.781 37.037 9.46 7.13 0.00 4.34
511 2555 7.028962 GGCTTTATTAATTTAAAACCGGACGT 58.971 34.615 9.46 0.00 0.00 4.34
512 2556 6.473131 GGGCTTTATTAATTTAAAACCGGACG 59.527 38.462 9.46 0.00 31.08 4.79
513 2557 7.276218 GTGGGCTTTATTAATTTAAAACCGGAC 59.724 37.037 9.46 0.00 31.08 4.79
514 2558 7.039223 TGTGGGCTTTATTAATTTAAAACCGGA 60.039 33.333 9.46 0.00 31.08 5.14
515 2559 7.097834 TGTGGGCTTTATTAATTTAAAACCGG 58.902 34.615 0.00 0.00 31.08 5.28
516 2560 8.436970 GTTGTGGGCTTTATTAATTTAAAACCG 58.563 33.333 0.00 0.00 31.08 4.44
517 2561 9.274206 TGTTGTGGGCTTTATTAATTTAAAACC 57.726 29.630 0.00 0.00 30.03 3.27
535 2579 0.107897 TACGCTGCCTATGTTGTGGG 60.108 55.000 0.00 0.00 0.00 4.61
536 2580 1.599071 CATACGCTGCCTATGTTGTGG 59.401 52.381 9.58 0.00 0.00 4.17
537 2581 2.285220 GTCATACGCTGCCTATGTTGTG 59.715 50.000 15.15 2.79 0.00 3.33
538 2582 2.093711 TGTCATACGCTGCCTATGTTGT 60.094 45.455 15.15 0.04 0.00 3.32
539 2583 2.549926 TGTCATACGCTGCCTATGTTG 58.450 47.619 15.15 0.00 0.00 3.33
540 2584 2.936498 GTTGTCATACGCTGCCTATGTT 59.064 45.455 15.15 0.00 0.00 2.71
541 2585 2.550978 GTTGTCATACGCTGCCTATGT 58.449 47.619 15.15 1.64 0.00 2.29
542 2586 1.867233 GGTTGTCATACGCTGCCTATG 59.133 52.381 11.04 11.04 0.00 2.23
543 2587 1.484653 TGGTTGTCATACGCTGCCTAT 59.515 47.619 0.00 0.00 0.00 2.57
544 2588 0.899019 TGGTTGTCATACGCTGCCTA 59.101 50.000 0.00 0.00 0.00 3.93
545 2589 0.673644 GTGGTTGTCATACGCTGCCT 60.674 55.000 0.00 0.00 0.00 4.75
546 2590 0.953471 TGTGGTTGTCATACGCTGCC 60.953 55.000 0.00 0.00 0.00 4.85
547 2591 1.086696 ATGTGGTTGTCATACGCTGC 58.913 50.000 0.00 0.00 0.00 5.25
548 2592 2.094258 GTCATGTGGTTGTCATACGCTG 59.906 50.000 0.00 0.00 0.00 5.18
549 2593 2.346803 GTCATGTGGTTGTCATACGCT 58.653 47.619 0.00 0.00 0.00 5.07
550 2594 1.396996 GGTCATGTGGTTGTCATACGC 59.603 52.381 0.00 0.00 0.00 4.42
551 2595 2.694213 TGGTCATGTGGTTGTCATACG 58.306 47.619 0.00 0.00 0.00 3.06
552 2596 3.818210 TGTTGGTCATGTGGTTGTCATAC 59.182 43.478 0.00 0.00 0.00 2.39
553 2597 3.818210 GTGTTGGTCATGTGGTTGTCATA 59.182 43.478 0.00 0.00 0.00 2.15
554 2598 2.622942 GTGTTGGTCATGTGGTTGTCAT 59.377 45.455 0.00 0.00 0.00 3.06
555 2599 2.020720 GTGTTGGTCATGTGGTTGTCA 58.979 47.619 0.00 0.00 0.00 3.58
556 2600 2.020720 TGTGTTGGTCATGTGGTTGTC 58.979 47.619 0.00 0.00 0.00 3.18
557 2601 1.748493 GTGTGTTGGTCATGTGGTTGT 59.252 47.619 0.00 0.00 0.00 3.32
558 2602 1.268488 CGTGTGTTGGTCATGTGGTTG 60.268 52.381 0.00 0.00 0.00 3.77
559 2603 1.021202 CGTGTGTTGGTCATGTGGTT 58.979 50.000 0.00 0.00 0.00 3.67
560 2604 0.817634 CCGTGTGTTGGTCATGTGGT 60.818 55.000 0.00 0.00 0.00 4.16
561 2605 0.817634 ACCGTGTGTTGGTCATGTGG 60.818 55.000 0.00 0.00 33.35 4.17
562 2606 1.529438 GTACCGTGTGTTGGTCATGTG 59.471 52.381 0.00 0.00 40.96 3.21
563 2607 1.541670 GGTACCGTGTGTTGGTCATGT 60.542 52.381 0.00 0.00 40.96 3.21
564 2608 1.153353 GGTACCGTGTGTTGGTCATG 58.847 55.000 0.00 0.00 40.96 3.07
565 2609 0.759959 TGGTACCGTGTGTTGGTCAT 59.240 50.000 7.57 0.00 40.96 3.06
566 2610 0.540454 TTGGTACCGTGTGTTGGTCA 59.460 50.000 7.57 0.00 40.96 4.02
567 2611 1.331447 GTTTGGTACCGTGTGTTGGTC 59.669 52.381 7.57 0.00 40.96 4.02
568 2612 1.339824 TGTTTGGTACCGTGTGTTGGT 60.340 47.619 7.57 0.00 43.62 3.67
569 2613 1.380524 TGTTTGGTACCGTGTGTTGG 58.619 50.000 7.57 0.00 0.00 3.77
570 2614 3.489180 TTTGTTTGGTACCGTGTGTTG 57.511 42.857 7.57 0.00 0.00 3.33
571 2615 3.757493 TCTTTTGTTTGGTACCGTGTGTT 59.243 39.130 7.57 0.00 0.00 3.32
572 2616 3.127376 GTCTTTTGTTTGGTACCGTGTGT 59.873 43.478 7.57 0.00 0.00 3.72
573 2617 3.487879 GGTCTTTTGTTTGGTACCGTGTG 60.488 47.826 7.57 0.00 0.00 3.82
574 2618 2.684374 GGTCTTTTGTTTGGTACCGTGT 59.316 45.455 7.57 0.00 0.00 4.49
575 2619 2.683867 TGGTCTTTTGTTTGGTACCGTG 59.316 45.455 7.57 0.00 0.00 4.94
576 2620 2.684374 GTGGTCTTTTGTTTGGTACCGT 59.316 45.455 7.57 0.00 0.00 4.83
577 2621 2.946990 AGTGGTCTTTTGTTTGGTACCG 59.053 45.455 7.57 0.00 0.00 4.02
578 2622 3.697542 ACAGTGGTCTTTTGTTTGGTACC 59.302 43.478 4.43 4.43 0.00 3.34
579 2623 4.976224 ACAGTGGTCTTTTGTTTGGTAC 57.024 40.909 0.00 0.00 0.00 3.34
580 2624 5.498393 TGTACAGTGGTCTTTTGTTTGGTA 58.502 37.500 0.00 0.00 0.00 3.25
581 2625 4.337145 TGTACAGTGGTCTTTTGTTTGGT 58.663 39.130 0.00 0.00 0.00 3.67
582 2626 4.638421 TCTGTACAGTGGTCTTTTGTTTGG 59.362 41.667 21.99 0.00 0.00 3.28
583 2627 5.811399 TCTGTACAGTGGTCTTTTGTTTG 57.189 39.130 21.99 0.00 0.00 2.93
584 2628 7.404671 AATTCTGTACAGTGGTCTTTTGTTT 57.595 32.000 21.99 0.00 0.00 2.83
585 2629 7.255139 GCTAATTCTGTACAGTGGTCTTTTGTT 60.255 37.037 21.99 6.50 0.00 2.83
586 2630 6.204882 GCTAATTCTGTACAGTGGTCTTTTGT 59.795 38.462 21.99 1.12 0.00 2.83
587 2631 6.348540 GGCTAATTCTGTACAGTGGTCTTTTG 60.349 42.308 21.99 9.80 0.00 2.44
588 2632 5.705905 GGCTAATTCTGTACAGTGGTCTTTT 59.294 40.000 21.99 9.07 0.00 2.27
589 2633 5.221843 TGGCTAATTCTGTACAGTGGTCTTT 60.222 40.000 21.99 10.25 0.00 2.52
590 2634 4.286032 TGGCTAATTCTGTACAGTGGTCTT 59.714 41.667 21.99 11.60 0.00 3.01
591 2635 3.838317 TGGCTAATTCTGTACAGTGGTCT 59.162 43.478 21.99 6.82 0.00 3.85
592 2636 3.933332 GTGGCTAATTCTGTACAGTGGTC 59.067 47.826 21.99 7.78 0.00 4.02
593 2637 3.326588 TGTGGCTAATTCTGTACAGTGGT 59.673 43.478 21.99 10.75 0.00 4.16
594 2638 3.937814 TGTGGCTAATTCTGTACAGTGG 58.062 45.455 21.99 6.85 0.00 4.00
595 2639 7.792374 AATATGTGGCTAATTCTGTACAGTG 57.208 36.000 21.99 9.72 0.00 3.66
596 2640 8.807948 AAAATATGTGGCTAATTCTGTACAGT 57.192 30.769 21.99 6.25 0.00 3.55
627 2671 3.906720 AGCTTACTAATTCTTCCCGCA 57.093 42.857 0.00 0.00 0.00 5.69
629 2673 6.570692 TGTTCTAGCTTACTAATTCTTCCCG 58.429 40.000 0.00 0.00 0.00 5.14
651 2704 3.890936 GAGCTGGCAACGAGGCTGT 62.891 63.158 2.64 0.00 44.55 4.40
653 2706 3.630013 TGAGCTGGCAACGAGGCT 61.630 61.111 0.00 0.00 44.55 4.58
656 2709 2.842394 ATCCGTGAGCTGGCAACGAG 62.842 60.000 17.79 10.58 42.51 4.18
658 2711 2.434884 ATCCGTGAGCTGGCAACG 60.435 61.111 0.00 11.86 42.51 4.10
695 2748 0.532115 ATGGGTCATTTTTGGCGAGC 59.468 50.000 0.00 0.00 0.00 5.03
701 2754 4.559153 GTCAGGTCAATGGGTCATTTTTG 58.441 43.478 0.00 0.00 31.05 2.44
778 2831 0.246360 CTCTGATACGTGCCACCACA 59.754 55.000 0.00 0.00 42.17 4.17
794 2851 2.298610 GCTTTAAATTAGGCCGGCTCT 58.701 47.619 28.56 23.19 0.00 4.09
795 2852 1.337071 GGCTTTAAATTAGGCCGGCTC 59.663 52.381 28.56 16.85 35.08 4.70
852 2920 3.668821 TGGATGGATAATCTGGACTGGT 58.331 45.455 0.00 0.00 35.43 4.00
874 2943 6.012337 TGTGGCTTTATTTATCTGGATGGA 57.988 37.500 0.00 0.00 0.00 3.41
875 2944 5.278660 GCTGTGGCTTTATTTATCTGGATGG 60.279 44.000 0.00 0.00 35.22 3.51
877 2946 4.829492 GGCTGTGGCTTTATTTATCTGGAT 59.171 41.667 0.00 0.00 38.73 3.41
878 2947 4.207165 GGCTGTGGCTTTATTTATCTGGA 58.793 43.478 0.00 0.00 38.73 3.86
879 2948 3.953612 TGGCTGTGGCTTTATTTATCTGG 59.046 43.478 0.00 0.00 38.73 3.86
880 2949 4.641989 ACTGGCTGTGGCTTTATTTATCTG 59.358 41.667 0.00 0.00 38.73 2.90
881 2950 4.860022 ACTGGCTGTGGCTTTATTTATCT 58.140 39.130 0.00 0.00 38.73 1.98
908 2977 8.902806 CAGCTAGGTAGGAGAGATAATATGAAG 58.097 40.741 0.00 0.00 0.00 3.02
929 2998 2.782222 GCGATGACCCGACCAGCTA 61.782 63.158 0.00 0.00 0.00 3.32
930 2999 4.148825 GCGATGACCCGACCAGCT 62.149 66.667 0.00 0.00 0.00 4.24
1191 3315 2.486918 TGTCAGATCAACACAGCACAG 58.513 47.619 0.00 0.00 0.00 3.66
1196 3320 5.237996 ACAAGTTCATGTCAGATCAACACAG 59.762 40.000 3.35 1.04 0.00 3.66
1197 3321 5.125356 ACAAGTTCATGTCAGATCAACACA 58.875 37.500 3.35 0.00 0.00 3.72
1198 3322 5.679734 ACAAGTTCATGTCAGATCAACAC 57.320 39.130 3.35 0.00 0.00 3.32
1199 3323 6.698008 AAACAAGTTCATGTCAGATCAACA 57.302 33.333 3.73 3.73 31.81 3.33
1200 3324 6.074676 GCAAAACAAGTTCATGTCAGATCAAC 60.075 38.462 0.00 0.00 31.81 3.18
1212 3336 2.673862 TCGAACGAGCAAAACAAGTTCA 59.326 40.909 7.29 0.00 40.63 3.18
1235 3359 1.143684 GCCATCTGAGCCCCTAAATCA 59.856 52.381 0.00 0.00 0.00 2.57
1322 3450 1.134226 GGTACACGTCGTTGTTGGAG 58.866 55.000 0.00 0.00 0.00 3.86
1336 3464 0.895530 CTGCCTTCTTCTCCGGTACA 59.104 55.000 0.00 0.00 0.00 2.90
1403 3535 1.739067 AAAGCTAAGCAAGGCGTAGG 58.261 50.000 11.95 0.00 40.08 3.18
1438 3570 9.307121 CTATGTTCAGACCAAGTAATAGACAAG 57.693 37.037 0.00 0.00 0.00 3.16
1443 3575 9.823647 ATTGACTATGTTCAGACCAAGTAATAG 57.176 33.333 0.00 0.00 0.00 1.73
1444 3576 9.599866 CATTGACTATGTTCAGACCAAGTAATA 57.400 33.333 0.00 0.00 0.00 0.98
1445 3577 8.103305 ACATTGACTATGTTCAGACCAAGTAAT 58.897 33.333 0.00 0.00 45.19 1.89
1499 3631 8.673711 TGTTCAGACCAAGTAATAAACATATGC 58.326 33.333 1.58 0.00 0.00 3.14
1509 3641 8.103305 ACATTGACTATGTTCAGACCAAGTAAT 58.897 33.333 0.00 0.00 45.19 1.89
1512 3644 5.869579 ACATTGACTATGTTCAGACCAAGT 58.130 37.500 0.00 0.00 45.19 3.16
1524 3656 8.453320 TGCACTCAAAATCTAACATTGACTATG 58.547 33.333 0.00 0.00 40.26 2.23
1526 3658 7.977789 TGCACTCAAAATCTAACATTGACTA 57.022 32.000 0.00 0.00 0.00 2.59
1528 3660 9.282247 CTTATGCACTCAAAATCTAACATTGAC 57.718 33.333 0.00 0.00 0.00 3.18
1529 3661 9.013229 ACTTATGCACTCAAAATCTAACATTGA 57.987 29.630 0.00 0.00 0.00 2.57
1530 3662 9.630098 AACTTATGCACTCAAAATCTAACATTG 57.370 29.630 0.00 0.00 0.00 2.82
1533 3665 7.594758 GCAAACTTATGCACTCAAAATCTAACA 59.405 33.333 0.00 0.00 45.70 2.41
1534 3666 7.942908 GCAAACTTATGCACTCAAAATCTAAC 58.057 34.615 0.00 0.00 45.70 2.34
1549 3681 4.494350 AGCACTCACTTGCAAACTTATG 57.506 40.909 0.00 0.00 45.62 1.90
1551 3683 5.123227 ACTAAGCACTCACTTGCAAACTTA 58.877 37.500 0.00 0.15 45.62 2.24
1552 3684 3.947834 ACTAAGCACTCACTTGCAAACTT 59.052 39.130 0.00 0.00 45.62 2.66
1558 4046 2.622436 CCCTACTAAGCACTCACTTGC 58.378 52.381 0.00 0.00 43.34 4.01
1609 4099 4.579340 TCCACGCACCAAACATTAGTTTTA 59.421 37.500 0.00 0.00 45.32 1.52
1632 4122 5.667172 CCCAAATTTTCCCTGATAATTCCCT 59.333 40.000 0.00 0.00 0.00 4.20
1666 4156 2.159393 CCCTGTTAAATCACATGGCACG 60.159 50.000 0.00 0.00 0.00 5.34
1678 4168 0.407918 CCTGCCCTTCCCCTGTTAAA 59.592 55.000 0.00 0.00 0.00 1.52
1707 4197 5.172687 AGTTGAGGAGAGAAGGGAAAATC 57.827 43.478 0.00 0.00 0.00 2.17
1734 4356 1.063266 TCTTGACTTGTTTTGGGGGCT 60.063 47.619 0.00 0.00 0.00 5.19
1752 4389 2.586792 GCTGGGGCGATGTCTTCT 59.413 61.111 0.00 0.00 0.00 2.85
1785 4438 3.609175 CGATGTTCTGCAAATGAACCGTT 60.609 43.478 13.07 1.11 42.04 4.44
1793 4446 0.676466 TCCGCCGATGTTCTGCAAAT 60.676 50.000 0.00 0.00 0.00 2.32
1825 4500 2.923035 CTCCCCTCCACACACCGT 60.923 66.667 0.00 0.00 0.00 4.83
1826 4501 3.706373 CCTCCCCTCCACACACCG 61.706 72.222 0.00 0.00 0.00 4.94
1828 4503 1.627297 GGATCCTCCCCTCCACACAC 61.627 65.000 3.84 0.00 0.00 3.82
1829 4504 1.306997 GGATCCTCCCCTCCACACA 60.307 63.158 3.84 0.00 0.00 3.72
1830 4505 2.435693 CGGATCCTCCCCTCCACAC 61.436 68.421 10.75 0.00 31.13 3.82
1831 4506 2.041922 CGGATCCTCCCCTCCACA 60.042 66.667 10.75 0.00 31.13 4.17
1832 4507 2.844839 CCGGATCCTCCCCTCCAC 60.845 72.222 10.75 0.00 31.13 4.02
1833 4508 2.486410 AAACCGGATCCTCCCCTCCA 62.486 60.000 9.46 0.00 31.13 3.86
1835 4510 0.180642 GAAAACCGGATCCTCCCCTC 59.819 60.000 9.46 0.00 31.13 4.30
1836 4511 1.279749 GGAAAACCGGATCCTCCCCT 61.280 60.000 9.46 0.00 31.13 4.79
1848 4523 4.038642 TGCAAACACTATGGAAGGAAAACC 59.961 41.667 0.00 0.00 0.00 3.27
1862 4723 4.301072 ACACCCTATGTATGCAAACACT 57.699 40.909 0.00 0.00 40.88 3.55
1874 4735 4.698304 ACCAAACGAAACATACACCCTATG 59.302 41.667 0.00 0.00 0.00 2.23
1882 4743 2.606065 GGTGCCACCAAACGAAACATAC 60.606 50.000 9.55 0.00 38.42 2.39
1920 4784 0.927537 CAGATTTATTCGACGCGGCA 59.072 50.000 14.85 0.00 0.00 5.69
1943 4807 0.035725 TCGCGGAGAGGAAGTAGACA 60.036 55.000 6.13 0.00 0.00 3.41
1948 4812 2.672307 ACGTCGCGGAGAGGAAGT 60.672 61.111 6.13 0.00 38.08 3.01
1960 4824 0.042361 CTACCGGATTCTCGACGTCG 60.042 60.000 31.30 31.30 41.45 5.12
2008 4890 8.458843 CAACGATAAAAAGAACAACATATCCCT 58.541 33.333 0.00 0.00 0.00 4.20
2010 4892 8.241367 ACCAACGATAAAAAGAACAACATATCC 58.759 33.333 0.00 0.00 0.00 2.59
2026 4910 2.238646 AGATGGAAGCCACCAACGATAA 59.761 45.455 3.61 0.00 43.47 1.75
2073 4957 2.366590 CCGGTTCTGGATCATCATCTCA 59.633 50.000 0.00 0.00 0.00 3.27
2074 4958 2.289320 CCCGGTTCTGGATCATCATCTC 60.289 54.545 0.00 0.00 0.00 2.75
2091 4975 0.881118 CATCTGACCACAAAACCCGG 59.119 55.000 0.00 0.00 0.00 5.73
2145 5031 2.890474 CGAATCCACCGCTTCCCG 60.890 66.667 0.00 0.00 0.00 5.14
2154 5040 0.034863 TGGCCTAAACCCGAATCCAC 60.035 55.000 3.32 0.00 0.00 4.02
2166 5052 1.214305 ACATCCCCTTGCTGGCCTAA 61.214 55.000 3.32 0.00 0.00 2.69
2170 5057 2.054453 GGAACATCCCCTTGCTGGC 61.054 63.158 0.00 0.00 0.00 4.85
2191 5078 3.049674 CGTTGTGGCATGTCGGCT 61.050 61.111 0.00 0.00 41.89 5.52
2230 5117 0.620556 AAGCCGATGAACAGACCCAT 59.379 50.000 0.00 0.00 0.00 4.00
2231 5118 0.400213 AAAGCCGATGAACAGACCCA 59.600 50.000 0.00 0.00 0.00 4.51
2278 5165 5.762179 TCCTACAACTTCTCAACATCCAT 57.238 39.130 0.00 0.00 0.00 3.41
2284 5171 5.153950 AGTGGATCCTACAACTTCTCAAC 57.846 43.478 14.23 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.