Multiple sequence alignment - TraesCS1B01G221700

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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 TraesCS1B01G221700 chr1B 100.000 2678 0 0 1 2678 398961084 398963761 0.000000e+00 4946.0
1 TraesCS1B01G221700 chr1B 97.241 906 22 3 1773 2678 563315280 563314378 0.000000e+00 1531.0
2 TraesCS1B01G221700 chr1B 90.769 585 51 2 1 584 589907302 589906720 0.000000e+00 778.0
3 TraesCS1B01G221700 chr1B 88.946 389 40 3 196 582 658947240 658946853 6.710000e-131 477.0
4 TraesCS1B01G221700 chr1B 83.407 452 70 5 134 580 77616813 77617264 5.330000e-112 414.0
5 TraesCS1B01G221700 chr1B 96.429 84 3 0 588 671 426482317 426482234 3.590000e-29 139.0
6 TraesCS1B01G221700 chr1B 97.222 36 1 0 636 671 133111674 133111639 8.010000e-06 62.1
7 TraesCS1B01G221700 chr5B 97.585 911 21 1 1768 2678 611856640 611855731 0.000000e+00 1559.0
8 TraesCS1B01G221700 chr3B 97.585 911 21 1 1768 2678 448571176 448572085 0.000000e+00 1559.0
9 TraesCS1B01G221700 chr4A 97.475 911 22 1 1768 2678 642118072 642117163 0.000000e+00 1554.0
10 TraesCS1B01G221700 chr4A 83.368 481 66 8 116 584 162802701 162802223 1.470000e-117 433.0
11 TraesCS1B01G221700 chr1D 97.149 912 23 3 1768 2678 203287432 203288341 0.000000e+00 1537.0
12 TraesCS1B01G221700 chr6B 97.036 911 26 1 1768 2678 227260460 227259551 0.000000e+00 1531.0
13 TraesCS1B01G221700 chr6B 97.036 911 23 3 1768 2678 487475825 487476731 0.000000e+00 1530.0
14 TraesCS1B01G221700 chr4B 96.817 911 28 1 1768 2678 393404928 393404019 0.000000e+00 1520.0
15 TraesCS1B01G221700 chrUn 96.711 912 27 3 1768 2678 270055186 270054277 0.000000e+00 1515.0
16 TraesCS1B01G221700 chr7A 90.956 973 78 5 748 1720 626992743 626991781 0.000000e+00 1301.0
17 TraesCS1B01G221700 chr7A 86.644 876 91 14 805 1672 594434438 594435295 0.000000e+00 946.0
18 TraesCS1B01G221700 chr7A 83.932 585 75 7 1 584 648866304 648866870 2.350000e-150 542.0
19 TraesCS1B01G221700 chr7A 87.692 325 37 3 262 584 134995514 134995191 2.520000e-100 375.0
20 TraesCS1B01G221700 chr7A 79.800 500 45 28 590 1057 627045496 627045021 2.000000e-81 313.0
21 TraesCS1B01G221700 chr7A 80.663 362 33 19 726 1057 627113620 627113266 2.060000e-61 246.0
22 TraesCS1B01G221700 chr7B 86.931 1209 74 34 588 1769 589696513 589695362 0.000000e+00 1280.0
23 TraesCS1B01G221700 chr7B 89.988 809 39 10 970 1766 588823345 588822567 0.000000e+00 1007.0
24 TraesCS1B01G221700 chr7B 88.529 741 72 6 969 1709 589935079 589935806 0.000000e+00 885.0
25 TraesCS1B01G221700 chr7B 97.561 82 2 0 631 712 588823631 588823550 1.000000e-29 141.0
26 TraesCS1B01G221700 chr7B 88.776 98 8 2 806 902 589915667 589915762 1.680000e-22 117.0
27 TraesCS1B01G221700 chr7B 92.308 78 4 1 588 663 589735021 589735098 2.820000e-20 110.0
28 TraesCS1B01G221700 chr7B 89.091 55 2 2 688 741 589735092 589735143 6.190000e-07 65.8
29 TraesCS1B01G221700 chr7D 94.363 816 39 5 855 1667 545266994 545266183 0.000000e+00 1245.0
30 TraesCS1B01G221700 chr7D 84.886 1138 100 34 590 1709 545650238 545651321 0.000000e+00 1083.0
31 TraesCS1B01G221700 chr7D 86.576 879 86 18 806 1677 518768853 518769706 0.000000e+00 941.0
32 TraesCS1B01G221700 chr7D 91.748 206 6 5 588 788 545267302 545267103 2.630000e-70 276.0
33 TraesCS1B01G221700 chr7D 100.000 42 0 0 1726 1767 545266175 545266134 7.950000e-11 78.7
34 TraesCS1B01G221700 chr7D 100.000 28 0 0 1709 1736 545266201 545266174 5.000000e-03 52.8
35 TraesCS1B01G221700 chr6A 91.200 750 58 4 968 1717 107264501 107265242 0.000000e+00 1013.0
36 TraesCS1B01G221700 chr6A 90.716 517 43 3 1 516 27655010 27655522 0.000000e+00 684.0
37 TraesCS1B01G221700 chr6A 100.000 41 0 0 1726 1766 107265294 107265334 2.860000e-10 76.8
38 TraesCS1B01G221700 chr6A 100.000 28 0 0 1709 1736 107265268 107265295 5.000000e-03 52.8
39 TraesCS1B01G221700 chr2B 87.903 868 80 19 806 1663 182133833 182132981 0.000000e+00 998.0
40 TraesCS1B01G221700 chr2B 89.157 83 2 4 707 788 182133986 182133910 2.190000e-16 97.1
41 TraesCS1B01G221700 chr6D 88.814 742 77 2 968 1709 124609299 124608564 0.000000e+00 905.0
42 TraesCS1B01G221700 chr6D 87.353 767 80 9 968 1731 122979674 122980426 0.000000e+00 863.0
43 TraesCS1B01G221700 chr1A 89.744 585 55 3 1 584 31807425 31806845 0.000000e+00 743.0
44 TraesCS1B01G221700 chr3D 85.634 355 44 7 236 584 160898404 160898757 1.510000e-97 366.0
45 TraesCS1B01G221700 chr5D 98.246 57 1 0 644 700 289421242 289421186 1.700000e-17 100.0
46 TraesCS1B01G221700 chr5D 98.246 57 1 0 644 700 289727292 289727236 1.700000e-17 100.0
47 TraesCS1B01G221700 chr5D 100.000 42 0 0 1726 1767 289354394 289354353 7.950000e-11 78.7
48 TraesCS1B01G221700 chr5D 100.000 42 0 0 1726 1767 289420201 289420160 7.950000e-11 78.7
49 TraesCS1B01G221700 chr5D 100.000 42 0 0 1726 1767 289726470 289726429 7.950000e-11 78.7
50 TraesCS1B01G221700 chr5D 100.000 28 0 0 1709 1736 289354420 289354393 5.000000e-03 52.8
51 TraesCS1B01G221700 chr5D 100.000 28 0 0 1709 1736 289420227 289420200 5.000000e-03 52.8
52 TraesCS1B01G221700 chr5D 100.000 28 0 0 1709 1736 289726496 289726469 5.000000e-03 52.8


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 TraesCS1B01G221700 chr1B 398961084 398963761 2677 False 4946.000000 4946 100.000000 1 2678 1 chr1B.!!$F2 2677
1 TraesCS1B01G221700 chr1B 563314378 563315280 902 True 1531.000000 1531 97.241000 1773 2678 1 chr1B.!!$R3 905
2 TraesCS1B01G221700 chr1B 589906720 589907302 582 True 778.000000 778 90.769000 1 584 1 chr1B.!!$R4 583
3 TraesCS1B01G221700 chr5B 611855731 611856640 909 True 1559.000000 1559 97.585000 1768 2678 1 chr5B.!!$R1 910
4 TraesCS1B01G221700 chr3B 448571176 448572085 909 False 1559.000000 1559 97.585000 1768 2678 1 chr3B.!!$F1 910
5 TraesCS1B01G221700 chr4A 642117163 642118072 909 True 1554.000000 1554 97.475000 1768 2678 1 chr4A.!!$R2 910
6 TraesCS1B01G221700 chr1D 203287432 203288341 909 False 1537.000000 1537 97.149000 1768 2678 1 chr1D.!!$F1 910
7 TraesCS1B01G221700 chr6B 227259551 227260460 909 True 1531.000000 1531 97.036000 1768 2678 1 chr6B.!!$R1 910
8 TraesCS1B01G221700 chr6B 487475825 487476731 906 False 1530.000000 1530 97.036000 1768 2678 1 chr6B.!!$F1 910
9 TraesCS1B01G221700 chr4B 393404019 393404928 909 True 1520.000000 1520 96.817000 1768 2678 1 chr4B.!!$R1 910
10 TraesCS1B01G221700 chrUn 270054277 270055186 909 True 1515.000000 1515 96.711000 1768 2678 1 chrUn.!!$R1 910
11 TraesCS1B01G221700 chr7A 626991781 626992743 962 True 1301.000000 1301 90.956000 748 1720 1 chr7A.!!$R2 972
12 TraesCS1B01G221700 chr7A 594434438 594435295 857 False 946.000000 946 86.644000 805 1672 1 chr7A.!!$F1 867
13 TraesCS1B01G221700 chr7A 648866304 648866870 566 False 542.000000 542 83.932000 1 584 1 chr7A.!!$F2 583
14 TraesCS1B01G221700 chr7B 589695362 589696513 1151 True 1280.000000 1280 86.931000 588 1769 1 chr7B.!!$R1 1181
15 TraesCS1B01G221700 chr7B 589935079 589935806 727 False 885.000000 885 88.529000 969 1709 1 chr7B.!!$F2 740
16 TraesCS1B01G221700 chr7B 588822567 588823631 1064 True 574.000000 1007 93.774500 631 1766 2 chr7B.!!$R2 1135
17 TraesCS1B01G221700 chr7D 545650238 545651321 1083 False 1083.000000 1083 84.886000 590 1709 1 chr7D.!!$F2 1119
18 TraesCS1B01G221700 chr7D 518768853 518769706 853 False 941.000000 941 86.576000 806 1677 1 chr7D.!!$F1 871
19 TraesCS1B01G221700 chr7D 545266134 545267302 1168 True 413.125000 1245 96.527750 588 1767 4 chr7D.!!$R1 1179
20 TraesCS1B01G221700 chr6A 27655010 27655522 512 False 684.000000 684 90.716000 1 516 1 chr6A.!!$F1 515
21 TraesCS1B01G221700 chr6A 107264501 107265334 833 False 380.866667 1013 97.066667 968 1766 3 chr6A.!!$F2 798
22 TraesCS1B01G221700 chr2B 182132981 182133986 1005 True 547.550000 998 88.530000 707 1663 2 chr2B.!!$R1 956
23 TraesCS1B01G221700 chr6D 124608564 124609299 735 True 905.000000 905 88.814000 968 1709 1 chr6D.!!$R1 741
24 TraesCS1B01G221700 chr6D 122979674 122980426 752 False 863.000000 863 87.353000 968 1731 1 chr6D.!!$F1 763
25 TraesCS1B01G221700 chr1A 31806845 31807425 580 True 743.000000 743 89.744000 1 584 1 chr1A.!!$R1 583

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
388 390 0.032678 CAGACGAGACAGCACAAGGT 59.967 55.0 0.0 0.0 0.0 3.50 F
391 393 0.038159 ACGAGACAGCACAAGGTAGC 60.038 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1394 0.103208 CGGACTCTTCGGATCCTTGG 59.897 60.0 10.75 0.0 0.0 3.61 R
1680 1806 0.965866 TCTGCTTCGATCACCCGAGT 60.966 55.0 0.00 0.0 39.9 4.18 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
273 275 0.606401 CCAAGTCAATGGCTCACGGT 60.606 55.000 0.00 0.00 32.78 4.83
289 291 4.966787 GTCGGTTGCCCAGGCCAA 62.967 66.667 5.01 0.00 41.09 4.52
356 358 4.980805 AGGCCGACGCAAAAGCGA 62.981 61.111 17.27 0.00 36.38 4.93
357 359 3.799755 GGCCGACGCAAAAGCGAT 61.800 61.111 17.27 0.79 36.38 4.58
358 360 2.276680 GCCGACGCAAAAGCGATC 60.277 61.111 17.27 9.18 36.94 3.69
359 361 2.020016 CCGACGCAAAAGCGATCG 59.980 61.111 17.27 11.69 36.91 3.69
360 362 2.020016 CGACGCAAAAGCGATCGG 59.980 61.111 18.30 0.01 35.19 4.18
361 363 2.399611 GACGCAAAAGCGATCGGG 59.600 61.111 18.30 0.00 36.94 5.14
362 364 2.047655 ACGCAAAAGCGATCGGGA 60.048 55.556 18.30 0.00 36.94 5.14
363 365 2.292802 GACGCAAAAGCGATCGGGAC 62.293 60.000 18.30 0.00 36.94 4.46
364 366 2.791927 GCAAAAGCGATCGGGACC 59.208 61.111 18.30 0.00 0.00 4.46
365 367 1.745489 GCAAAAGCGATCGGGACCT 60.745 57.895 18.30 1.77 0.00 3.85
366 368 0.461339 GCAAAAGCGATCGGGACCTA 60.461 55.000 18.30 0.00 0.00 3.08
367 369 1.810412 GCAAAAGCGATCGGGACCTAT 60.810 52.381 18.30 0.00 0.00 2.57
368 370 1.867233 CAAAAGCGATCGGGACCTATG 59.133 52.381 18.30 4.79 0.00 2.23
369 371 0.249911 AAAGCGATCGGGACCTATGC 60.250 55.000 18.30 0.00 0.00 3.14
370 372 1.399744 AAGCGATCGGGACCTATGCA 61.400 55.000 18.30 0.00 0.00 3.96
371 373 1.373497 GCGATCGGGACCTATGCAG 60.373 63.158 18.30 0.00 0.00 4.41
372 374 1.806461 GCGATCGGGACCTATGCAGA 61.806 60.000 18.30 0.00 0.00 4.26
373 375 0.039074 CGATCGGGACCTATGCAGAC 60.039 60.000 7.38 0.00 0.00 3.51
374 376 0.039074 GATCGGGACCTATGCAGACG 60.039 60.000 0.00 0.00 0.00 4.18
375 377 0.467474 ATCGGGACCTATGCAGACGA 60.467 55.000 0.00 0.00 0.00 4.20
376 378 1.101635 TCGGGACCTATGCAGACGAG 61.102 60.000 0.00 0.00 0.00 4.18
377 379 1.101635 CGGGACCTATGCAGACGAGA 61.102 60.000 0.00 0.00 0.00 4.04
378 380 0.386113 GGGACCTATGCAGACGAGAC 59.614 60.000 0.00 0.00 0.00 3.36
379 381 1.103803 GGACCTATGCAGACGAGACA 58.896 55.000 0.00 0.00 0.00 3.41
380 382 1.066303 GGACCTATGCAGACGAGACAG 59.934 57.143 0.00 0.00 0.00 3.51
381 383 0.457851 ACCTATGCAGACGAGACAGC 59.542 55.000 0.00 0.00 0.00 4.40
382 384 0.457443 CCTATGCAGACGAGACAGCA 59.543 55.000 0.00 0.00 41.73 4.41
383 385 1.554392 CTATGCAGACGAGACAGCAC 58.446 55.000 0.00 0.00 40.14 4.40
384 386 0.887933 TATGCAGACGAGACAGCACA 59.112 50.000 0.00 0.00 40.14 4.57
385 387 0.033920 ATGCAGACGAGACAGCACAA 59.966 50.000 0.00 0.00 40.14 3.33
386 388 0.598419 TGCAGACGAGACAGCACAAG 60.598 55.000 0.00 0.00 31.05 3.16
387 389 1.287730 GCAGACGAGACAGCACAAGG 61.288 60.000 0.00 0.00 0.00 3.61
388 390 0.032678 CAGACGAGACAGCACAAGGT 59.967 55.000 0.00 0.00 0.00 3.50
389 391 1.269723 CAGACGAGACAGCACAAGGTA 59.730 52.381 0.00 0.00 0.00 3.08
390 392 1.542030 AGACGAGACAGCACAAGGTAG 59.458 52.381 0.00 0.00 0.00 3.18
391 393 0.038159 ACGAGACAGCACAAGGTAGC 60.038 55.000 0.00 0.00 0.00 3.58
392 394 0.244994 CGAGACAGCACAAGGTAGCT 59.755 55.000 0.00 0.00 42.94 3.32
397 399 3.073228 AGCACAAGGTAGCTGGAGA 57.927 52.632 2.57 0.00 40.13 3.71
398 400 0.901124 AGCACAAGGTAGCTGGAGAG 59.099 55.000 2.57 0.00 40.13 3.20
399 401 0.610687 GCACAAGGTAGCTGGAGAGT 59.389 55.000 2.57 0.00 0.00 3.24
400 402 1.404851 GCACAAGGTAGCTGGAGAGTC 60.405 57.143 2.57 0.00 0.00 3.36
401 403 2.175202 CACAAGGTAGCTGGAGAGTCT 58.825 52.381 2.57 0.00 0.00 3.24
402 404 2.564947 CACAAGGTAGCTGGAGAGTCTT 59.435 50.000 2.57 0.00 0.00 3.01
403 405 2.829120 ACAAGGTAGCTGGAGAGTCTTC 59.171 50.000 2.57 0.00 0.00 2.87
404 406 3.096092 CAAGGTAGCTGGAGAGTCTTCT 58.904 50.000 0.00 0.00 36.01 2.85
405 407 2.733956 AGGTAGCTGGAGAGTCTTCTG 58.266 52.381 0.00 0.00 32.53 3.02
406 408 2.310349 AGGTAGCTGGAGAGTCTTCTGA 59.690 50.000 9.43 0.00 32.53 3.27
407 409 3.052944 AGGTAGCTGGAGAGTCTTCTGAT 60.053 47.826 9.43 5.44 32.53 2.90
408 410 3.317993 GGTAGCTGGAGAGTCTTCTGATC 59.682 52.174 9.43 0.00 32.53 2.92
409 411 2.387757 AGCTGGAGAGTCTTCTGATCC 58.612 52.381 9.43 0.00 32.53 3.36
410 412 1.066908 GCTGGAGAGTCTTCTGATCCG 59.933 57.143 9.43 0.00 32.53 4.18
411 413 1.066908 CTGGAGAGTCTTCTGATCCGC 59.933 57.143 0.00 0.00 32.53 5.54
412 414 0.387565 GGAGAGTCTTCTGATCCGCC 59.612 60.000 0.00 0.00 32.53 6.13
413 415 0.387565 GAGAGTCTTCTGATCCGCCC 59.612 60.000 0.00 0.00 32.53 6.13
414 416 1.045911 AGAGTCTTCTGATCCGCCCC 61.046 60.000 0.00 0.00 30.72 5.80
415 417 2.107141 GTCTTCTGATCCGCCCCG 59.893 66.667 0.00 0.00 0.00 5.73
416 418 2.043349 TCTTCTGATCCGCCCCGA 60.043 61.111 0.00 0.00 0.00 5.14
417 419 2.127869 TCTTCTGATCCGCCCCGAG 61.128 63.158 0.00 0.00 0.00 4.63
418 420 3.798954 CTTCTGATCCGCCCCGAGC 62.799 68.421 0.00 0.00 38.52 5.03
420 422 3.933722 CTGATCCGCCCCGAGCAT 61.934 66.667 0.00 0.00 44.04 3.79
421 423 2.523168 TGATCCGCCCCGAGCATA 60.523 61.111 0.00 0.00 44.04 3.14
422 424 2.262915 GATCCGCCCCGAGCATAG 59.737 66.667 0.00 0.00 44.04 2.23
423 425 2.524394 ATCCGCCCCGAGCATAGT 60.524 61.111 0.00 0.00 44.04 2.12
424 426 2.771763 GATCCGCCCCGAGCATAGTG 62.772 65.000 0.00 0.00 44.04 2.74
425 427 4.609018 CCGCCCCGAGCATAGTGG 62.609 72.222 0.00 0.00 44.04 4.00
426 428 4.609018 CGCCCCGAGCATAGTGGG 62.609 72.222 0.00 0.00 44.04 4.61
444 446 2.185004 GGGGGACGATGGTTATGATG 57.815 55.000 0.00 0.00 0.00 3.07
445 447 1.523758 GGGGACGATGGTTATGATGC 58.476 55.000 0.00 0.00 0.00 3.91
446 448 1.072331 GGGGACGATGGTTATGATGCT 59.928 52.381 0.00 0.00 0.00 3.79
447 449 2.487265 GGGGACGATGGTTATGATGCTT 60.487 50.000 0.00 0.00 0.00 3.91
448 450 3.244422 GGGGACGATGGTTATGATGCTTA 60.244 47.826 0.00 0.00 0.00 3.09
449 451 4.565652 GGGGACGATGGTTATGATGCTTAT 60.566 45.833 0.00 0.00 0.00 1.73
450 452 4.393062 GGGACGATGGTTATGATGCTTATG 59.607 45.833 0.00 0.00 0.00 1.90
451 453 4.393062 GGACGATGGTTATGATGCTTATGG 59.607 45.833 0.00 0.00 0.00 2.74
452 454 4.326826 ACGATGGTTATGATGCTTATGGG 58.673 43.478 0.00 0.00 0.00 4.00
453 455 3.691118 CGATGGTTATGATGCTTATGGGG 59.309 47.826 0.00 0.00 0.00 4.96
454 456 4.565444 CGATGGTTATGATGCTTATGGGGA 60.565 45.833 0.00 0.00 0.00 4.81
455 457 5.513233 GATGGTTATGATGCTTATGGGGAT 58.487 41.667 0.00 0.00 0.00 3.85
456 458 4.665451 TGGTTATGATGCTTATGGGGATG 58.335 43.478 0.00 0.00 0.00 3.51
457 459 4.019174 GGTTATGATGCTTATGGGGATGG 58.981 47.826 0.00 0.00 0.00 3.51
458 460 4.509122 GGTTATGATGCTTATGGGGATGGT 60.509 45.833 0.00 0.00 0.00 3.55
459 461 2.957402 TGATGCTTATGGGGATGGTC 57.043 50.000 0.00 0.00 0.00 4.02
460 462 2.134354 TGATGCTTATGGGGATGGTCA 58.866 47.619 0.00 0.00 0.00 4.02
461 463 2.107031 TGATGCTTATGGGGATGGTCAG 59.893 50.000 0.00 0.00 0.00 3.51
462 464 0.183492 TGCTTATGGGGATGGTCAGC 59.817 55.000 0.00 0.00 0.00 4.26
463 465 0.183492 GCTTATGGGGATGGTCAGCA 59.817 55.000 0.00 0.00 0.00 4.41
464 466 1.972872 CTTATGGGGATGGTCAGCAC 58.027 55.000 0.00 0.00 0.00 4.40
465 467 0.550914 TTATGGGGATGGTCAGCACC 59.449 55.000 0.00 0.00 41.61 5.01
466 468 1.695114 TATGGGGATGGTCAGCACCG 61.695 60.000 2.92 0.00 44.93 4.94
473 475 2.509336 GGTCAGCACCGTGGATCG 60.509 66.667 0.00 0.00 39.52 3.69
474 476 2.261671 GTCAGCACCGTGGATCGT 59.738 61.111 0.00 0.00 37.94 3.73
475 477 1.805945 GTCAGCACCGTGGATCGTC 60.806 63.158 0.00 0.00 37.94 4.20
476 478 2.261361 CAGCACCGTGGATCGTCA 59.739 61.111 0.00 0.00 37.94 4.35
477 479 1.153568 CAGCACCGTGGATCGTCAT 60.154 57.895 0.00 0.00 37.94 3.06
478 480 1.141881 AGCACCGTGGATCGTCATC 59.858 57.895 0.00 0.00 37.94 2.92
479 481 1.141881 GCACCGTGGATCGTCATCT 59.858 57.895 0.00 0.00 37.94 2.90
480 482 0.384309 GCACCGTGGATCGTCATCTA 59.616 55.000 0.00 0.00 37.94 1.98
481 483 1.202371 GCACCGTGGATCGTCATCTAA 60.202 52.381 0.00 0.00 37.94 2.10
482 484 2.732366 CACCGTGGATCGTCATCTAAG 58.268 52.381 0.00 0.00 37.94 2.18
483 485 1.681793 ACCGTGGATCGTCATCTAAGG 59.318 52.381 0.00 1.99 42.57 2.69
484 486 1.954382 CCGTGGATCGTCATCTAAGGA 59.046 52.381 0.00 0.00 40.31 3.36
485 487 2.361119 CCGTGGATCGTCATCTAAGGAA 59.639 50.000 0.00 0.00 40.31 3.36
486 488 3.551046 CCGTGGATCGTCATCTAAGGAAG 60.551 52.174 0.00 0.00 40.31 3.46
487 489 3.551046 CGTGGATCGTCATCTAAGGAAGG 60.551 52.174 0.00 0.00 34.52 3.46
488 490 3.385111 GTGGATCGTCATCTAAGGAAGGT 59.615 47.826 0.00 0.00 0.00 3.50
489 491 3.384789 TGGATCGTCATCTAAGGAAGGTG 59.615 47.826 0.00 0.00 37.71 4.00
490 492 3.243907 GGATCGTCATCTAAGGAAGGTGG 60.244 52.174 0.00 0.00 36.91 4.61
491 493 2.816411 TCGTCATCTAAGGAAGGTGGT 58.184 47.619 0.00 0.00 36.91 4.16
492 494 2.758979 TCGTCATCTAAGGAAGGTGGTC 59.241 50.000 0.00 0.00 36.91 4.02
493 495 2.479730 CGTCATCTAAGGAAGGTGGTCG 60.480 54.545 0.00 0.00 36.91 4.79
494 496 2.496470 GTCATCTAAGGAAGGTGGTCGT 59.504 50.000 0.00 0.00 36.91 4.34
495 497 2.496070 TCATCTAAGGAAGGTGGTCGTG 59.504 50.000 0.00 0.00 36.91 4.35
496 498 1.263356 TCTAAGGAAGGTGGTCGTGG 58.737 55.000 0.00 0.00 0.00 4.94
497 499 0.974383 CTAAGGAAGGTGGTCGTGGT 59.026 55.000 0.00 0.00 0.00 4.16
498 500 1.346722 CTAAGGAAGGTGGTCGTGGTT 59.653 52.381 0.00 0.00 0.00 3.67
499 501 1.426751 AAGGAAGGTGGTCGTGGTTA 58.573 50.000 0.00 0.00 0.00 2.85
500 502 1.652947 AGGAAGGTGGTCGTGGTTAT 58.347 50.000 0.00 0.00 0.00 1.89
501 503 1.278127 AGGAAGGTGGTCGTGGTTATG 59.722 52.381 0.00 0.00 0.00 1.90
502 504 1.084289 GAAGGTGGTCGTGGTTATGC 58.916 55.000 0.00 0.00 0.00 3.14
503 505 0.690762 AAGGTGGTCGTGGTTATGCT 59.309 50.000 0.00 0.00 0.00 3.79
504 506 0.690762 AGGTGGTCGTGGTTATGCTT 59.309 50.000 0.00 0.00 0.00 3.91
505 507 0.802494 GGTGGTCGTGGTTATGCTTG 59.198 55.000 0.00 0.00 0.00 4.01
506 508 0.802494 GTGGTCGTGGTTATGCTTGG 59.198 55.000 0.00 0.00 0.00 3.61
507 509 0.958382 TGGTCGTGGTTATGCTTGGC 60.958 55.000 0.00 0.00 0.00 4.52
508 510 0.958382 GGTCGTGGTTATGCTTGGCA 60.958 55.000 0.00 0.00 44.86 4.92
509 511 0.447801 GTCGTGGTTATGCTTGGCAG 59.552 55.000 0.00 0.00 43.65 4.85
510 512 0.323302 TCGTGGTTATGCTTGGCAGA 59.677 50.000 0.00 0.00 43.65 4.26
511 513 0.729116 CGTGGTTATGCTTGGCAGAG 59.271 55.000 0.00 0.00 43.65 3.35
512 514 1.826385 GTGGTTATGCTTGGCAGAGT 58.174 50.000 0.00 0.00 43.65 3.24
513 515 1.470098 GTGGTTATGCTTGGCAGAGTG 59.530 52.381 0.00 0.00 43.65 3.51
514 516 1.350684 TGGTTATGCTTGGCAGAGTGA 59.649 47.619 0.00 0.00 43.65 3.41
515 517 2.025981 TGGTTATGCTTGGCAGAGTGAT 60.026 45.455 0.00 0.00 43.65 3.06
516 518 2.357009 GGTTATGCTTGGCAGAGTGATG 59.643 50.000 0.00 0.00 43.65 3.07
517 519 2.336945 TATGCTTGGCAGAGTGATGG 57.663 50.000 0.00 0.00 43.65 3.51
518 520 0.330604 ATGCTTGGCAGAGTGATGGT 59.669 50.000 0.00 0.00 43.65 3.55
519 521 0.111061 TGCTTGGCAGAGTGATGGTT 59.889 50.000 0.00 0.00 33.32 3.67
520 522 0.807496 GCTTGGCAGAGTGATGGTTC 59.193 55.000 0.00 0.00 0.00 3.62
521 523 1.457346 CTTGGCAGAGTGATGGTTCC 58.543 55.000 0.00 0.00 0.00 3.62
522 524 0.321564 TTGGCAGAGTGATGGTTCCG 60.322 55.000 0.00 0.00 0.00 4.30
523 525 2.109126 GGCAGAGTGATGGTTCCGC 61.109 63.158 0.00 0.00 0.00 5.54
524 526 1.078848 GCAGAGTGATGGTTCCGCT 60.079 57.895 0.00 0.00 0.00 5.52
525 527 1.364626 GCAGAGTGATGGTTCCGCTG 61.365 60.000 0.00 0.00 0.00 5.18
526 528 0.247460 CAGAGTGATGGTTCCGCTGA 59.753 55.000 0.00 0.00 0.00 4.26
527 529 0.976641 AGAGTGATGGTTCCGCTGAA 59.023 50.000 0.00 0.00 0.00 3.02
528 530 1.347707 AGAGTGATGGTTCCGCTGAAA 59.652 47.619 0.00 0.00 30.79 2.69
529 531 1.734465 GAGTGATGGTTCCGCTGAAAG 59.266 52.381 0.00 0.00 30.79 2.62
530 532 0.804989 GTGATGGTTCCGCTGAAAGG 59.195 55.000 0.00 0.00 30.79 3.11
531 533 0.690192 TGATGGTTCCGCTGAAAGGA 59.310 50.000 0.00 0.00 35.69 3.36
532 534 1.087501 GATGGTTCCGCTGAAAGGAC 58.912 55.000 0.00 0.00 37.53 3.85
533 535 0.673644 ATGGTTCCGCTGAAAGGACG 60.674 55.000 0.00 0.00 37.53 4.79
534 536 1.301479 GGTTCCGCTGAAAGGACGT 60.301 57.895 0.00 0.00 37.53 4.34
535 537 0.883370 GGTTCCGCTGAAAGGACGTT 60.883 55.000 0.00 0.00 37.53 3.99
536 538 0.511653 GTTCCGCTGAAAGGACGTTC 59.488 55.000 0.00 0.00 37.53 3.95
537 539 0.601841 TTCCGCTGAAAGGACGTTCC 60.602 55.000 0.00 0.00 37.53 3.62
546 548 4.097361 GGACGTTCCTGGCCCTCC 62.097 72.222 0.00 0.00 32.53 4.30
547 549 4.452733 GACGTTCCTGGCCCTCCG 62.453 72.222 0.00 0.00 34.14 4.63
558 560 4.653888 CCCTCCGGGCGGTTTTGT 62.654 66.667 0.00 0.00 35.35 2.83
559 561 3.053896 CCTCCGGGCGGTTTTGTC 61.054 66.667 0.00 0.00 36.47 3.18
560 562 3.419759 CTCCGGGCGGTTTTGTCG 61.420 66.667 0.00 0.00 36.47 4.35
561 563 3.869473 CTCCGGGCGGTTTTGTCGA 62.869 63.158 0.00 0.00 36.47 4.20
562 564 3.419759 CCGGGCGGTTTTGTCGAG 61.420 66.667 0.00 0.00 0.00 4.04
563 565 3.419759 CGGGCGGTTTTGTCGAGG 61.420 66.667 0.00 0.00 0.00 4.63
564 566 3.053896 GGGCGGTTTTGTCGAGGG 61.054 66.667 0.00 0.00 0.00 4.30
565 567 2.281276 GGCGGTTTTGTCGAGGGT 60.281 61.111 0.00 0.00 0.00 4.34
566 568 2.613506 GGCGGTTTTGTCGAGGGTG 61.614 63.158 0.00 0.00 0.00 4.61
567 569 2.943653 CGGTTTTGTCGAGGGTGC 59.056 61.111 0.00 0.00 0.00 5.01
568 570 1.597027 CGGTTTTGTCGAGGGTGCT 60.597 57.895 0.00 0.00 0.00 4.40
569 571 1.164041 CGGTTTTGTCGAGGGTGCTT 61.164 55.000 0.00 0.00 0.00 3.91
570 572 0.591659 GGTTTTGTCGAGGGTGCTTC 59.408 55.000 0.00 0.00 0.00 3.86
571 573 1.594331 GTTTTGTCGAGGGTGCTTCT 58.406 50.000 0.00 0.00 0.00 2.85
572 574 2.549349 GGTTTTGTCGAGGGTGCTTCTA 60.549 50.000 0.00 0.00 0.00 2.10
573 575 2.737252 GTTTTGTCGAGGGTGCTTCTAG 59.263 50.000 0.00 0.00 0.00 2.43
574 576 0.895530 TTGTCGAGGGTGCTTCTAGG 59.104 55.000 0.00 0.00 0.00 3.02
575 577 1.142097 GTCGAGGGTGCTTCTAGGC 59.858 63.158 0.00 0.00 0.00 3.93
576 578 2.058595 TCGAGGGTGCTTCTAGGCC 61.059 63.158 0.00 0.00 0.00 5.19
577 579 2.501610 GAGGGTGCTTCTAGGCCG 59.498 66.667 0.00 0.00 0.00 6.13
578 580 3.083997 AGGGTGCTTCTAGGCCGG 61.084 66.667 0.00 0.00 0.00 6.13
579 581 3.081409 GGGTGCTTCTAGGCCGGA 61.081 66.667 5.05 0.00 0.00 5.14
580 582 2.444256 GGGTGCTTCTAGGCCGGAT 61.444 63.158 5.05 0.00 0.00 4.18
581 583 1.527370 GGTGCTTCTAGGCCGGATT 59.473 57.895 5.05 0.00 0.00 3.01
582 584 0.756903 GGTGCTTCTAGGCCGGATTA 59.243 55.000 5.05 0.00 0.00 1.75
583 585 1.540580 GGTGCTTCTAGGCCGGATTAC 60.541 57.143 5.05 0.00 0.00 1.89
584 586 1.138266 GTGCTTCTAGGCCGGATTACA 59.862 52.381 5.05 0.00 0.00 2.41
585 587 1.412710 TGCTTCTAGGCCGGATTACAG 59.587 52.381 5.05 0.00 0.00 2.74
586 588 1.413077 GCTTCTAGGCCGGATTACAGT 59.587 52.381 5.05 0.00 0.00 3.55
627 629 1.064060 GTCCTCTTTGTGTGTGTGTGC 59.936 52.381 0.00 0.00 0.00 4.57
676 689 3.056536 TGAAGCAGAGAGACGTAAGCAAT 60.057 43.478 0.00 0.00 45.62 3.56
723 738 5.143916 AGTGCGCGTTTAGATTTCTTATG 57.856 39.130 8.43 0.00 0.00 1.90
823 907 4.868734 ACTTCGACTCGGATTCAAATTACC 59.131 41.667 0.00 0.00 0.00 2.85
891 980 1.571773 CCCCCGTCTCCCAAATTCCT 61.572 60.000 0.00 0.00 0.00 3.36
1222 1333 3.785859 GGGGCGAGCTCCATGTCA 61.786 66.667 9.48 0.00 36.36 3.58
1302 1422 0.108615 CGAAGAGTCCGATGTGCCTT 60.109 55.000 0.00 0.00 0.00 4.35
1419 1539 2.270205 CTCACCATGGCTCGCCTT 59.730 61.111 13.04 0.00 36.94 4.35
1572 1693 2.346365 GACGTGACCAAGTCCCCC 59.654 66.667 0.00 0.00 34.46 5.40
1680 1806 0.322366 TGCAAATCCACGGATGAGCA 60.322 50.000 17.15 17.15 40.43 4.26
1934 2102 4.603171 ACCCATATGATGAAGGGATGCTAA 59.397 41.667 3.65 0.00 44.30 3.09
2063 2231 2.125552 TCGCAGCCATCTTCCACG 60.126 61.111 0.00 0.00 0.00 4.94
2403 2572 2.672651 CTCGCCATGCACACCCAA 60.673 61.111 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 25 2.436115 GTAGACAAGGGCGGCACC 60.436 66.667 12.47 0.00 37.93 5.01
24 26 2.813908 CGTAGACAAGGGCGGCAC 60.814 66.667 12.47 0.00 0.00 5.01
51 53 4.265056 ACCACCAGGAACACCGGC 62.265 66.667 0.00 0.00 38.69 6.13
289 291 0.179009 AGACTGCATGCCGGCATTAT 60.179 50.000 38.86 23.44 43.97 1.28
356 358 0.467474 TCGTCTGCATAGGTCCCGAT 60.467 55.000 0.00 0.00 0.00 4.18
357 359 1.077285 TCGTCTGCATAGGTCCCGA 60.077 57.895 0.00 0.00 0.00 5.14
358 360 1.101635 TCTCGTCTGCATAGGTCCCG 61.102 60.000 0.00 0.00 0.00 5.14
359 361 0.386113 GTCTCGTCTGCATAGGTCCC 59.614 60.000 0.00 0.00 0.00 4.46
360 362 1.066303 CTGTCTCGTCTGCATAGGTCC 59.934 57.143 0.00 0.00 0.00 4.46
361 363 1.535015 GCTGTCTCGTCTGCATAGGTC 60.535 57.143 0.00 0.00 33.55 3.85
362 364 0.457851 GCTGTCTCGTCTGCATAGGT 59.542 55.000 0.00 0.00 33.55 3.08
363 365 0.457443 TGCTGTCTCGTCTGCATAGG 59.543 55.000 0.00 0.00 37.36 2.57
364 366 1.135286 TGTGCTGTCTCGTCTGCATAG 60.135 52.381 10.83 0.00 42.32 2.23
365 367 0.887933 TGTGCTGTCTCGTCTGCATA 59.112 50.000 10.83 7.24 42.32 3.14
366 368 0.033920 TTGTGCTGTCTCGTCTGCAT 59.966 50.000 10.83 0.00 42.32 3.96
367 369 0.598419 CTTGTGCTGTCTCGTCTGCA 60.598 55.000 0.00 0.00 39.29 4.41
368 370 1.287730 CCTTGTGCTGTCTCGTCTGC 61.288 60.000 0.00 0.00 0.00 4.26
369 371 0.032678 ACCTTGTGCTGTCTCGTCTG 59.967 55.000 0.00 0.00 0.00 3.51
370 372 1.542030 CTACCTTGTGCTGTCTCGTCT 59.458 52.381 0.00 0.00 0.00 4.18
371 373 1.983972 CTACCTTGTGCTGTCTCGTC 58.016 55.000 0.00 0.00 0.00 4.20
372 374 0.038159 GCTACCTTGTGCTGTCTCGT 60.038 55.000 0.00 0.00 0.00 4.18
373 375 0.244994 AGCTACCTTGTGCTGTCTCG 59.755 55.000 0.00 0.00 38.21 4.04
379 381 0.901124 CTCTCCAGCTACCTTGTGCT 59.099 55.000 0.00 0.00 40.54 4.40
380 382 0.610687 ACTCTCCAGCTACCTTGTGC 59.389 55.000 0.00 0.00 0.00 4.57
381 383 2.175202 AGACTCTCCAGCTACCTTGTG 58.825 52.381 0.00 0.00 0.00 3.33
382 384 2.614134 AGACTCTCCAGCTACCTTGT 57.386 50.000 0.00 0.00 0.00 3.16
383 385 3.096092 AGAAGACTCTCCAGCTACCTTG 58.904 50.000 0.00 0.00 0.00 3.61
384 386 3.096092 CAGAAGACTCTCCAGCTACCTT 58.904 50.000 0.00 0.00 0.00 3.50
385 387 2.310349 TCAGAAGACTCTCCAGCTACCT 59.690 50.000 0.00 0.00 0.00 3.08
386 388 2.729194 TCAGAAGACTCTCCAGCTACC 58.271 52.381 0.00 0.00 0.00 3.18
387 389 3.317993 GGATCAGAAGACTCTCCAGCTAC 59.682 52.174 0.00 0.00 0.00 3.58
388 390 3.561143 GGATCAGAAGACTCTCCAGCTA 58.439 50.000 0.00 0.00 0.00 3.32
389 391 2.387757 GGATCAGAAGACTCTCCAGCT 58.612 52.381 0.00 0.00 0.00 4.24
390 392 1.066908 CGGATCAGAAGACTCTCCAGC 59.933 57.143 0.00 0.00 0.00 4.85
391 393 1.066908 GCGGATCAGAAGACTCTCCAG 59.933 57.143 0.00 0.00 0.00 3.86
392 394 1.107114 GCGGATCAGAAGACTCTCCA 58.893 55.000 0.00 0.00 0.00 3.86
393 395 0.387565 GGCGGATCAGAAGACTCTCC 59.612 60.000 0.00 0.00 0.00 3.71
394 396 0.387565 GGGCGGATCAGAAGACTCTC 59.612 60.000 0.00 0.00 0.00 3.20
395 397 1.045911 GGGGCGGATCAGAAGACTCT 61.046 60.000 0.00 0.00 0.00 3.24
396 398 1.443828 GGGGCGGATCAGAAGACTC 59.556 63.158 0.00 0.00 0.00 3.36
397 399 2.427245 CGGGGCGGATCAGAAGACT 61.427 63.158 0.00 0.00 0.00 3.24
398 400 2.107141 CGGGGCGGATCAGAAGAC 59.893 66.667 0.00 0.00 0.00 3.01
399 401 2.043349 TCGGGGCGGATCAGAAGA 60.043 61.111 0.00 0.00 0.00 2.87
400 402 2.419198 CTCGGGGCGGATCAGAAG 59.581 66.667 0.00 0.00 0.00 2.85
401 403 3.849951 GCTCGGGGCGGATCAGAA 61.850 66.667 0.00 0.00 0.00 3.02
402 404 2.994643 TATGCTCGGGGCGGATCAGA 62.995 60.000 0.00 0.00 45.43 3.27
403 405 2.498291 CTATGCTCGGGGCGGATCAG 62.498 65.000 0.00 0.00 45.43 2.90
404 406 2.523168 TATGCTCGGGGCGGATCA 60.523 61.111 0.00 0.00 45.43 2.92
405 407 2.262915 CTATGCTCGGGGCGGATC 59.737 66.667 0.00 0.00 45.43 3.36
406 408 2.524394 ACTATGCTCGGGGCGGAT 60.524 61.111 0.00 0.00 45.43 4.18
407 409 3.536917 CACTATGCTCGGGGCGGA 61.537 66.667 0.00 0.00 45.43 5.54
408 410 4.609018 CCACTATGCTCGGGGCGG 62.609 72.222 0.00 0.00 45.43 6.13
409 411 4.609018 CCCACTATGCTCGGGGCG 62.609 72.222 0.00 0.00 45.43 6.13
425 427 1.882352 GCATCATAACCATCGTCCCCC 60.882 57.143 0.00 0.00 0.00 5.40
426 428 1.072331 AGCATCATAACCATCGTCCCC 59.928 52.381 0.00 0.00 0.00 4.81
427 429 2.550830 AGCATCATAACCATCGTCCC 57.449 50.000 0.00 0.00 0.00 4.46
428 430 4.393062 CCATAAGCATCATAACCATCGTCC 59.607 45.833 0.00 0.00 0.00 4.79
429 431 4.393062 CCCATAAGCATCATAACCATCGTC 59.607 45.833 0.00 0.00 0.00 4.20
430 432 4.326826 CCCATAAGCATCATAACCATCGT 58.673 43.478 0.00 0.00 0.00 3.73
431 433 3.691118 CCCCATAAGCATCATAACCATCG 59.309 47.826 0.00 0.00 0.00 3.84
432 434 4.922206 TCCCCATAAGCATCATAACCATC 58.078 43.478 0.00 0.00 0.00 3.51
433 435 5.266788 CATCCCCATAAGCATCATAACCAT 58.733 41.667 0.00 0.00 0.00 3.55
434 436 4.508943 CCATCCCCATAAGCATCATAACCA 60.509 45.833 0.00 0.00 0.00 3.67
435 437 4.019174 CCATCCCCATAAGCATCATAACC 58.981 47.826 0.00 0.00 0.00 2.85
436 438 4.666512 ACCATCCCCATAAGCATCATAAC 58.333 43.478 0.00 0.00 0.00 1.89
437 439 4.353489 TGACCATCCCCATAAGCATCATAA 59.647 41.667 0.00 0.00 0.00 1.90
438 440 3.915711 TGACCATCCCCATAAGCATCATA 59.084 43.478 0.00 0.00 0.00 2.15
439 441 2.718062 TGACCATCCCCATAAGCATCAT 59.282 45.455 0.00 0.00 0.00 2.45
440 442 2.107031 CTGACCATCCCCATAAGCATCA 59.893 50.000 0.00 0.00 0.00 3.07
441 443 2.787994 CTGACCATCCCCATAAGCATC 58.212 52.381 0.00 0.00 0.00 3.91
442 444 1.202976 GCTGACCATCCCCATAAGCAT 60.203 52.381 0.00 0.00 0.00 3.79
443 445 0.183492 GCTGACCATCCCCATAAGCA 59.817 55.000 0.00 0.00 0.00 3.91
444 446 0.183492 TGCTGACCATCCCCATAAGC 59.817 55.000 0.00 0.00 0.00 3.09
445 447 1.477558 GGTGCTGACCATCCCCATAAG 60.478 57.143 0.00 0.00 42.59 1.73
446 448 0.550914 GGTGCTGACCATCCCCATAA 59.449 55.000 0.00 0.00 42.59 1.90
447 449 1.695114 CGGTGCTGACCATCCCCATA 61.695 60.000 0.00 0.00 43.33 2.74
448 450 3.010144 GGTGCTGACCATCCCCAT 58.990 61.111 0.00 0.00 42.59 4.00
449 451 3.716195 CGGTGCTGACCATCCCCA 61.716 66.667 0.00 0.00 43.33 4.96
450 452 3.717294 ACGGTGCTGACCATCCCC 61.717 66.667 0.00 0.00 43.33 4.81
451 453 2.436646 CACGGTGCTGACCATCCC 60.437 66.667 0.00 0.00 43.33 3.85
452 454 2.257409 ATCCACGGTGCTGACCATCC 62.257 60.000 1.68 0.00 43.33 3.51
453 455 0.811616 GATCCACGGTGCTGACCATC 60.812 60.000 1.68 0.00 43.33 3.51
454 456 1.221840 GATCCACGGTGCTGACCAT 59.778 57.895 1.68 0.00 43.33 3.55
455 457 2.662596 GATCCACGGTGCTGACCA 59.337 61.111 1.68 0.00 43.33 4.02
456 458 2.509336 CGATCCACGGTGCTGACC 60.509 66.667 1.68 0.00 39.14 4.02
466 468 3.385111 ACCTTCCTTAGATGACGATCCAC 59.615 47.826 0.00 0.00 0.00 4.02
467 469 3.384789 CACCTTCCTTAGATGACGATCCA 59.615 47.826 0.00 0.00 0.00 3.41
468 470 3.243907 CCACCTTCCTTAGATGACGATCC 60.244 52.174 0.00 0.00 0.00 3.36
469 471 3.385111 ACCACCTTCCTTAGATGACGATC 59.615 47.826 0.00 0.00 0.00 3.69
470 472 3.375699 ACCACCTTCCTTAGATGACGAT 58.624 45.455 0.00 0.00 0.00 3.73
471 473 2.758979 GACCACCTTCCTTAGATGACGA 59.241 50.000 0.00 0.00 0.00 4.20
472 474 2.479730 CGACCACCTTCCTTAGATGACG 60.480 54.545 0.00 0.00 0.00 4.35
473 475 2.496470 ACGACCACCTTCCTTAGATGAC 59.504 50.000 0.00 0.00 0.00 3.06
474 476 2.496070 CACGACCACCTTCCTTAGATGA 59.504 50.000 0.00 0.00 0.00 2.92
475 477 2.418746 CCACGACCACCTTCCTTAGATG 60.419 54.545 0.00 0.00 0.00 2.90
476 478 1.831736 CCACGACCACCTTCCTTAGAT 59.168 52.381 0.00 0.00 0.00 1.98
477 479 1.263356 CCACGACCACCTTCCTTAGA 58.737 55.000 0.00 0.00 0.00 2.10
478 480 0.974383 ACCACGACCACCTTCCTTAG 59.026 55.000 0.00 0.00 0.00 2.18
479 481 1.426751 AACCACGACCACCTTCCTTA 58.573 50.000 0.00 0.00 0.00 2.69
480 482 1.426751 TAACCACGACCACCTTCCTT 58.573 50.000 0.00 0.00 0.00 3.36
481 483 1.278127 CATAACCACGACCACCTTCCT 59.722 52.381 0.00 0.00 0.00 3.36
482 484 1.734163 CATAACCACGACCACCTTCC 58.266 55.000 0.00 0.00 0.00 3.46
483 485 1.084289 GCATAACCACGACCACCTTC 58.916 55.000 0.00 0.00 0.00 3.46
484 486 0.690762 AGCATAACCACGACCACCTT 59.309 50.000 0.00 0.00 0.00 3.50
485 487 0.690762 AAGCATAACCACGACCACCT 59.309 50.000 0.00 0.00 0.00 4.00
486 488 0.802494 CAAGCATAACCACGACCACC 59.198 55.000 0.00 0.00 0.00 4.61
487 489 0.802494 CCAAGCATAACCACGACCAC 59.198 55.000 0.00 0.00 0.00 4.16
488 490 0.958382 GCCAAGCATAACCACGACCA 60.958 55.000 0.00 0.00 0.00 4.02
489 491 0.958382 TGCCAAGCATAACCACGACC 60.958 55.000 0.00 0.00 31.71 4.79
490 492 0.447801 CTGCCAAGCATAACCACGAC 59.552 55.000 0.00 0.00 38.13 4.34
491 493 0.323302 TCTGCCAAGCATAACCACGA 59.677 50.000 0.00 0.00 38.13 4.35
492 494 0.729116 CTCTGCCAAGCATAACCACG 59.271 55.000 0.00 0.00 38.13 4.94
493 495 1.470098 CACTCTGCCAAGCATAACCAC 59.530 52.381 0.00 0.00 38.13 4.16
494 496 1.350684 TCACTCTGCCAAGCATAACCA 59.649 47.619 0.00 0.00 38.13 3.67
495 497 2.113860 TCACTCTGCCAAGCATAACC 57.886 50.000 0.00 0.00 38.13 2.85
496 498 2.357009 CCATCACTCTGCCAAGCATAAC 59.643 50.000 0.00 0.00 38.13 1.89
497 499 2.025981 ACCATCACTCTGCCAAGCATAA 60.026 45.455 0.00 0.00 38.13 1.90
498 500 1.561076 ACCATCACTCTGCCAAGCATA 59.439 47.619 0.00 0.00 38.13 3.14
499 501 0.330604 ACCATCACTCTGCCAAGCAT 59.669 50.000 0.00 0.00 38.13 3.79
500 502 0.111061 AACCATCACTCTGCCAAGCA 59.889 50.000 0.00 0.00 36.92 3.91
501 503 0.807496 GAACCATCACTCTGCCAAGC 59.193 55.000 0.00 0.00 0.00 4.01
502 504 1.457346 GGAACCATCACTCTGCCAAG 58.543 55.000 0.00 0.00 0.00 3.61
503 505 0.321564 CGGAACCATCACTCTGCCAA 60.322 55.000 0.00 0.00 0.00 4.52
504 506 1.296392 CGGAACCATCACTCTGCCA 59.704 57.895 0.00 0.00 0.00 4.92
505 507 2.109126 GCGGAACCATCACTCTGCC 61.109 63.158 0.00 0.00 37.89 4.85
506 508 1.078848 AGCGGAACCATCACTCTGC 60.079 57.895 0.00 0.00 43.11 4.26
507 509 0.247460 TCAGCGGAACCATCACTCTG 59.753 55.000 0.00 0.00 0.00 3.35
508 510 0.976641 TTCAGCGGAACCATCACTCT 59.023 50.000 0.00 0.00 0.00 3.24
509 511 1.734465 CTTTCAGCGGAACCATCACTC 59.266 52.381 0.00 0.00 31.35 3.51
510 512 1.611673 CCTTTCAGCGGAACCATCACT 60.612 52.381 0.00 0.00 31.35 3.41
511 513 0.804989 CCTTTCAGCGGAACCATCAC 59.195 55.000 0.00 0.00 31.35 3.06
512 514 0.690192 TCCTTTCAGCGGAACCATCA 59.310 50.000 0.00 0.00 31.35 3.07
513 515 1.087501 GTCCTTTCAGCGGAACCATC 58.912 55.000 0.00 0.00 31.35 3.51
514 516 0.673644 CGTCCTTTCAGCGGAACCAT 60.674 55.000 0.00 0.00 31.35 3.55
515 517 1.301401 CGTCCTTTCAGCGGAACCA 60.301 57.895 0.00 0.00 31.35 3.67
516 518 0.883370 AACGTCCTTTCAGCGGAACC 60.883 55.000 0.00 0.00 31.35 3.62
517 519 0.511653 GAACGTCCTTTCAGCGGAAC 59.488 55.000 0.00 0.00 31.35 3.62
518 520 0.601841 GGAACGTCCTTTCAGCGGAA 60.602 55.000 0.00 0.00 32.53 4.30
519 521 1.005394 GGAACGTCCTTTCAGCGGA 60.005 57.895 0.00 0.00 32.53 5.54
520 522 1.004918 AGGAACGTCCTTTCAGCGG 60.005 57.895 0.00 0.00 46.91 5.52
521 523 1.291877 CCAGGAACGTCCTTTCAGCG 61.292 60.000 4.08 0.00 46.91 5.18
522 524 1.578206 GCCAGGAACGTCCTTTCAGC 61.578 60.000 4.08 2.85 46.91 4.26
523 525 0.955919 GGCCAGGAACGTCCTTTCAG 60.956 60.000 0.00 0.00 46.91 3.02
524 526 1.072505 GGCCAGGAACGTCCTTTCA 59.927 57.895 0.00 0.00 46.91 2.69
525 527 1.674651 GGGCCAGGAACGTCCTTTC 60.675 63.158 4.39 0.00 46.91 2.62
526 528 2.125766 GAGGGCCAGGAACGTCCTTT 62.126 60.000 6.18 0.00 46.91 3.11
527 529 2.529389 AGGGCCAGGAACGTCCTT 60.529 61.111 6.18 0.00 46.91 3.36
529 531 4.097361 GGAGGGCCAGGAACGTCC 62.097 72.222 6.18 0.00 36.58 4.79
530 532 4.452733 CGGAGGGCCAGGAACGTC 62.453 72.222 6.18 0.00 0.00 4.34
543 545 3.419759 CGACAAAACCGCCCGGAG 61.420 66.667 14.44 0.00 38.96 4.63
544 546 3.869473 CTCGACAAAACCGCCCGGA 62.869 63.158 14.44 0.00 38.96 5.14
545 547 3.419759 CTCGACAAAACCGCCCGG 61.420 66.667 4.96 4.96 42.03 5.73
546 548 3.419759 CCTCGACAAAACCGCCCG 61.420 66.667 0.00 0.00 0.00 6.13
547 549 3.053896 CCCTCGACAAAACCGCCC 61.054 66.667 0.00 0.00 0.00 6.13
548 550 2.281276 ACCCTCGACAAAACCGCC 60.281 61.111 0.00 0.00 0.00 6.13
549 551 2.943653 CACCCTCGACAAAACCGC 59.056 61.111 0.00 0.00 0.00 5.68
550 552 1.164041 AAGCACCCTCGACAAAACCG 61.164 55.000 0.00 0.00 0.00 4.44
551 553 0.591659 GAAGCACCCTCGACAAAACC 59.408 55.000 0.00 0.00 0.00 3.27
552 554 1.594331 AGAAGCACCCTCGACAAAAC 58.406 50.000 0.00 0.00 0.00 2.43
553 555 2.289444 CCTAGAAGCACCCTCGACAAAA 60.289 50.000 0.00 0.00 0.00 2.44
554 556 1.275291 CCTAGAAGCACCCTCGACAAA 59.725 52.381 0.00 0.00 0.00 2.83
555 557 0.895530 CCTAGAAGCACCCTCGACAA 59.104 55.000 0.00 0.00 0.00 3.18
556 558 1.605058 GCCTAGAAGCACCCTCGACA 61.605 60.000 0.00 0.00 0.00 4.35
557 559 1.142097 GCCTAGAAGCACCCTCGAC 59.858 63.158 0.00 0.00 0.00 4.20
558 560 2.058595 GGCCTAGAAGCACCCTCGA 61.059 63.158 0.00 0.00 0.00 4.04
559 561 2.501610 GGCCTAGAAGCACCCTCG 59.498 66.667 0.00 0.00 0.00 4.63
560 562 2.501610 CGGCCTAGAAGCACCCTC 59.498 66.667 0.00 0.00 0.00 4.30
561 563 2.898472 ATCCGGCCTAGAAGCACCCT 62.898 60.000 0.00 0.00 0.00 4.34
562 564 1.984288 AATCCGGCCTAGAAGCACCC 61.984 60.000 0.00 0.00 0.00 4.61
563 565 0.756903 TAATCCGGCCTAGAAGCACC 59.243 55.000 0.00 0.00 0.00 5.01
564 566 1.138266 TGTAATCCGGCCTAGAAGCAC 59.862 52.381 0.00 0.00 0.00 4.40
565 567 1.412710 CTGTAATCCGGCCTAGAAGCA 59.587 52.381 0.00 0.00 0.00 3.91
566 568 1.413077 ACTGTAATCCGGCCTAGAAGC 59.587 52.381 0.00 0.00 0.00 3.86
567 569 4.142790 TCTACTGTAATCCGGCCTAGAAG 58.857 47.826 0.00 0.00 0.00 2.85
568 570 4.174704 TCTACTGTAATCCGGCCTAGAA 57.825 45.455 0.00 0.00 0.00 2.10
569 571 3.870538 TCTACTGTAATCCGGCCTAGA 57.129 47.619 0.00 0.00 0.00 2.43
570 572 3.890147 AGTTCTACTGTAATCCGGCCTAG 59.110 47.826 0.00 0.00 0.00 3.02
571 573 3.887716 GAGTTCTACTGTAATCCGGCCTA 59.112 47.826 0.00 0.00 0.00 3.93
572 574 2.694109 GAGTTCTACTGTAATCCGGCCT 59.306 50.000 0.00 0.00 0.00 5.19
573 575 2.694109 AGAGTTCTACTGTAATCCGGCC 59.306 50.000 0.00 0.00 0.00 6.13
574 576 3.380637 TCAGAGTTCTACTGTAATCCGGC 59.619 47.826 0.00 0.00 36.81 6.13
575 577 5.125739 AGTTCAGAGTTCTACTGTAATCCGG 59.874 44.000 0.00 0.00 36.81 5.14
576 578 6.030849 CAGTTCAGAGTTCTACTGTAATCCG 58.969 44.000 4.58 0.00 36.81 4.18
577 579 5.808030 GCAGTTCAGAGTTCTACTGTAATCC 59.192 44.000 11.64 0.00 40.02 3.01
578 580 6.390721 TGCAGTTCAGAGTTCTACTGTAATC 58.609 40.000 11.64 0.09 40.02 1.75
579 581 6.346477 TGCAGTTCAGAGTTCTACTGTAAT 57.654 37.500 11.64 0.00 40.02 1.89
580 582 5.279006 CCTGCAGTTCAGAGTTCTACTGTAA 60.279 44.000 13.81 3.33 45.72 2.41
581 583 4.218635 CCTGCAGTTCAGAGTTCTACTGTA 59.781 45.833 13.81 7.79 45.72 2.74
582 584 3.006323 CCTGCAGTTCAGAGTTCTACTGT 59.994 47.826 13.81 0.00 45.72 3.55
583 585 3.006323 ACCTGCAGTTCAGAGTTCTACTG 59.994 47.826 13.81 7.42 45.72 2.74
584 586 3.006323 CACCTGCAGTTCAGAGTTCTACT 59.994 47.826 13.81 0.00 45.72 2.57
585 587 3.321497 CACCTGCAGTTCAGAGTTCTAC 58.679 50.000 13.81 0.00 45.72 2.59
586 588 2.300152 CCACCTGCAGTTCAGAGTTCTA 59.700 50.000 13.81 0.00 45.72 2.10
627 629 0.924090 GTTCAGAGTTCTATGGCGCG 59.076 55.000 0.00 0.00 0.00 6.86
676 689 5.675684 TGGCTTCTGATTACTATGTGTCA 57.324 39.130 0.00 0.00 0.00 3.58
723 738 3.983741 AGCACTAATGAATCCGAGTAGC 58.016 45.455 0.00 0.00 0.00 3.58
823 907 1.739562 GACAGAGAAGTGGCGGCAG 60.740 63.158 13.91 0.25 0.00 4.85
891 980 3.407698 GAGAGCGAGGTGAGATAGATCA 58.592 50.000 0.00 0.00 0.00 2.92
1222 1333 1.710996 TTGATGTTGGTGGGGACGGT 61.711 55.000 0.00 0.00 0.00 4.83
1259 1379 1.608717 CTTGGCTCCGCTAGGACACT 61.609 60.000 0.00 0.00 42.75 3.55
1274 1394 0.103208 CGGACTCTTCGGATCCTTGG 59.897 60.000 10.75 0.00 0.00 3.61
1419 1539 4.919653 GCAGATCGAGCCTTGTCA 57.080 55.556 0.00 0.00 0.00 3.58
1680 1806 0.965866 TCTGCTTCGATCACCCGAGT 60.966 55.000 0.00 0.00 39.90 4.18
2063 2231 6.097915 TCAATATATTCTGAAGACGGACCC 57.902 41.667 0.00 0.00 0.00 4.46
2403 2572 0.756442 CGATTTGGGCATGGGGATGT 60.756 55.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.