Multiple sequence alignment - TraesCS6B01G328600

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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 TraesCS6B01G328600 chr6B 100.000 6242 0 0 1 6242 578407192 578400951 0.000000e+00 11527.0
1 TraesCS6B01G328600 chr6B 90.495 747 55 8 5509 6242 578302399 578301656 0.000000e+00 972.0
2 TraesCS6B01G328600 chr6B 88.326 454 43 8 5794 6242 578213611 578213163 2.560000e-148 536.0
3 TraesCS6B01G328600 chr6A 89.811 2640 150 65 2849 5430 532339617 532337039 0.000000e+00 3275.0
4 TraesCS6B01G328600 chr6A 91.169 1676 87 22 1 1639 532342703 532341052 0.000000e+00 2218.0
5 TraesCS6B01G328600 chr6A 87.705 854 43 22 5427 6242 532319119 532318290 0.000000e+00 939.0
6 TraesCS6B01G328600 chr6A 87.193 773 67 14 1638 2397 532341022 532340269 0.000000e+00 850.0
7 TraesCS6B01G328600 chr6A 81.782 752 89 31 5519 6242 532162928 532162197 2.510000e-163 586.0
8 TraesCS6B01G328600 chr6A 91.304 368 26 5 2478 2844 532340086 532339724 1.210000e-136 497.0
9 TraesCS6B01G328600 chr6A 97.143 35 1 0 5396 5430 532336396 532336362 6.760000e-05 60.2
10 TraesCS6B01G328600 chr6D 89.446 2454 127 43 1 2399 387049821 387047445 0.000000e+00 2976.0
11 TraesCS6B01G328600 chr6D 90.666 1982 108 35 4294 6242 387045011 387043074 0.000000e+00 2564.0
12 TraesCS6B01G328600 chr6D 91.408 1804 50 40 2480 4236 387046772 387045027 0.000000e+00 2375.0
13 TraesCS6B01G328600 chr6D 84.992 613 59 22 5656 6242 386950972 386950367 5.390000e-165 592.0
14 TraesCS6B01G328600 chr5D 88.855 332 31 4 3 329 549548943 549548613 2.710000e-108 403.0
15 TraesCS6B01G328600 chr5D 75.587 426 83 17 1 422 14736093 14735685 2.300000e-44 191.0
16 TraesCS6B01G328600 chr5D 83.516 91 15 0 2 92 9499152 9499242 1.110000e-12 86.1
17 TraesCS6B01G328600 chr5A 85.559 367 48 5 59 422 553342862 553342498 4.570000e-101 379.0
18 TraesCS6B01G328600 chr5A 78.997 319 53 6 44 362 664815577 664815273 8.200000e-49 206.0
19 TraesCS6B01G328600 chr5A 78.333 180 37 2 245 424 353974683 353974506 1.420000e-21 115.0
20 TraesCS6B01G328600 chr2A 82.609 368 53 8 1 366 758333553 758333911 1.310000e-81 315.0
21 TraesCS6B01G328600 chr3B 79.310 377 51 9 47 422 129399441 129399091 8.090000e-59 239.0
22 TraesCS6B01G328600 chr2B 84.737 190 24 5 1 187 770200356 770200543 1.070000e-42 185.0
23 TraesCS6B01G328600 chr7B 79.310 290 38 12 154 422 708434898 708435186 3.840000e-42 183.0
24 TraesCS6B01G328600 chr1D 77.500 240 30 14 193 423 386167749 386167973 8.500000e-24 122.0
25 TraesCS6B01G328600 chr4B 85.437 103 15 0 320 422 588548561 588548663 2.380000e-19 108.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G328600 chr6B 578400951 578407192 6241 True 11527.000000 11527 100.000000 1 6242 1 chr6B.!!$R3 6241
1 TraesCS6B01G328600 chr6B 578301656 578302399 743 True 972.000000 972 90.495000 5509 6242 1 chr6B.!!$R2 733
2 TraesCS6B01G328600 chr6A 532336362 532342703 6341 True 1380.040000 3275 91.324000 1 5430 5 chr6A.!!$R3 5429
3 TraesCS6B01G328600 chr6A 532318290 532319119 829 True 939.000000 939 87.705000 5427 6242 1 chr6A.!!$R2 815
4 TraesCS6B01G328600 chr6A 532162197 532162928 731 True 586.000000 586 81.782000 5519 6242 1 chr6A.!!$R1 723
5 TraesCS6B01G328600 chr6D 387043074 387049821 6747 True 2638.333333 2976 90.506667 1 6242 3 chr6D.!!$R2 6241
6 TraesCS6B01G328600 chr6D 386950367 386950972 605 True 592.000000 592 84.992000 5656 6242 1 chr6D.!!$R1 586

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
692 721 1.151668 CAGGAACCAGAGCTCGTTTG 58.848 55.0 8.37 0.78 0.00 2.93 F
1933 2023 0.389948 AGCCATCGACCGTTCTCAAC 60.390 55.0 0.00 0.00 0.00 3.18 F
2828 3585 0.041238 CCCCCTCCCCTTCCTTTTTC 59.959 60.0 0.00 0.00 0.00 2.29 F
3873 4760 0.108662 CAGATGTGAGCGCACCTACA 60.109 55.0 18.33 9.39 44.51 2.74 F
4473 5391 0.038455 TACCCCAACCCCACGAAATG 59.962 55.0 0.00 0.00 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 3241 0.232303 AAGCGCGTTTCTCTTTCACG 59.768 50.0 8.43 0.0 36.98 4.35 R
3653 4531 0.028902 GCACGCCACGAAAAAGAGTT 59.971 50.0 0.00 0.0 0.00 3.01 R
3880 4767 0.101399 GGAGCGTGACATCGACATCT 59.899 55.0 0.00 0.0 0.00 2.90 R
5197 6121 0.318762 ACTGTCAAGAAGGAGACGGC 59.681 55.0 0.00 0.0 43.32 5.68 R
5738 6745 0.459899 ATATTCGGCTGAGTGCGACA 59.540 50.0 0.00 0.0 44.05 4.35 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
79 80 9.422196 GCTCATTATAGACGTGAATAACAAAAC 57.578 33.333 0.00 0.00 0.00 2.43
337 341 3.181499 GGATTAAAGCTCGACTCGACTCA 60.181 47.826 0.00 0.00 0.00 3.41
372 381 1.235948 AAGTCGAGTCGAGCCGAGTT 61.236 55.000 17.12 18.27 39.77 3.01
453 462 7.092716 GGTCATCAATTACACTGAATTTGCTT 58.907 34.615 0.00 0.00 0.00 3.91
460 470 7.951530 ATTACACTGAATTTGCTTCCAAAAG 57.048 32.000 0.00 0.00 43.58 2.27
478 488 9.748708 TTCCAAAAGAAATTCAATTACACTGAG 57.251 29.630 0.00 0.00 0.00 3.35
499 509 3.004315 AGGTTGTGGTTTTGCGTAATGAG 59.996 43.478 0.00 0.00 0.00 2.90
509 519 2.722094 TGCGTAATGAGCTCCCAAAAT 58.278 42.857 12.15 0.00 35.28 1.82
515 525 5.448632 CGTAATGAGCTCCCAAAATTACACC 60.449 44.000 23.20 7.01 34.73 4.16
524 553 2.227865 CCAAAATTACACCACCACTCCG 59.772 50.000 0.00 0.00 0.00 4.63
570 599 3.450817 ACCTTGAAACCCCAACAGAAAAG 59.549 43.478 0.00 0.00 0.00 2.27
587 616 5.748630 CAGAAAAGCTTTGTTAGTTCCAACC 59.251 40.000 13.54 0.00 0.00 3.77
594 623 3.290948 TGTTAGTTCCAACCAGCACTT 57.709 42.857 0.00 0.00 0.00 3.16
595 624 2.948979 TGTTAGTTCCAACCAGCACTTG 59.051 45.455 0.00 0.00 0.00 3.16
596 625 1.604604 TAGTTCCAACCAGCACTTGC 58.395 50.000 0.00 0.00 42.49 4.01
639 668 7.069826 CCACATTACATTTCCCTTTCCACATAT 59.930 37.037 0.00 0.00 0.00 1.78
672 701 4.613850 GCTTCCGACTCTTGATTCAAAACC 60.614 45.833 0.01 0.00 0.00 3.27
692 721 1.151668 CAGGAACCAGAGCTCGTTTG 58.848 55.000 8.37 0.78 0.00 2.93
697 726 2.622064 ACCAGAGCTCGTTTGAAGTT 57.378 45.000 8.37 0.00 0.00 2.66
772 806 4.455877 CCTAGTTCCATTCACACCAAGAAC 59.544 45.833 0.00 0.00 35.08 3.01
778 814 1.384525 TTCACACCAAGAACCAACCG 58.615 50.000 0.00 0.00 0.00 4.44
1238 1278 3.234041 CGACGCGCTCGAGTTCAG 61.234 66.667 21.09 6.07 46.14 3.02
1271 1311 1.931172 GCCGCATACTCAACGTAACAT 59.069 47.619 0.00 0.00 0.00 2.71
1283 1323 5.891474 CAACGTAACATAAGCATTCGTTG 57.109 39.130 11.75 11.75 45.78 4.10
1337 1377 3.750652 CCTCTTCTGTTTGAGCTTCCTTC 59.249 47.826 0.00 0.00 0.00 3.46
1347 1387 4.280436 TGAGCTTCCTTCAATTCCGTTA 57.720 40.909 0.00 0.00 0.00 3.18
1357 1397 4.593597 TCAATTCCGTTACGCAAGATTC 57.406 40.909 0.00 0.00 43.62 2.52
1388 1428 5.018240 CGTGTACGTTGCTAGTAAGTACTC 58.982 45.833 21.60 18.84 38.63 2.59
1389 1429 5.327891 GTGTACGTTGCTAGTAAGTACTCC 58.672 45.833 21.60 14.29 38.63 3.85
1396 1436 6.238429 CGTTGCTAGTAAGTACTCCTAGAAGG 60.238 46.154 23.77 17.50 37.73 3.46
1404 1444 9.549984 AGTAAGTACTCCTAGAAGGAAGAAATT 57.450 33.333 0.00 0.00 45.28 1.82
1470 1510 3.921677 TCTGAACGTAATCAGTGGTTCC 58.078 45.455 15.12 0.00 45.65 3.62
1478 1518 2.094762 ATCAGTGGTTCCGCAGTTAC 57.905 50.000 5.19 0.00 0.00 2.50
1497 1537 6.688813 CAGTTACAAGTTCTCTGAAACTTTGC 59.311 38.462 12.25 6.39 44.95 3.68
1505 1545 4.947645 TCTCTGAAACTTTGCCCAAATTG 58.052 39.130 0.00 0.00 0.00 2.32
1520 1560 3.613737 CCAAATTGATTAAGCGTTGCTGG 59.386 43.478 0.00 0.00 39.62 4.85
1531 1571 3.939066 AGCGTTGCTGGTAAGATTAAGT 58.061 40.909 0.00 0.00 37.57 2.24
1669 1743 1.801771 CGTAAGCAATCAACCGGTTCA 59.198 47.619 19.24 4.48 0.00 3.18
1803 1887 1.080298 GAATGGTGGCTGCTTGCAC 60.080 57.895 0.00 0.00 45.15 4.57
1820 1904 3.084039 TGCACAGCTTTCCCTCATTAAG 58.916 45.455 0.00 0.00 0.00 1.85
1825 1909 5.529060 CACAGCTTTCCCTCATTAAGTATCC 59.471 44.000 0.00 0.00 0.00 2.59
1827 1911 6.122277 CAGCTTTCCCTCATTAAGTATCCAA 58.878 40.000 0.00 0.00 0.00 3.53
1893 1983 0.391661 AACTGCGCCAATCATCGACT 60.392 50.000 4.18 0.00 0.00 4.18
1911 2001 3.370061 CGACTTCTCCCCGATAAAAACAC 59.630 47.826 0.00 0.00 0.00 3.32
1915 2005 3.670625 TCTCCCCGATAAAAACACACAG 58.329 45.455 0.00 0.00 0.00 3.66
1933 2023 0.389948 AGCCATCGACCGTTCTCAAC 60.390 55.000 0.00 0.00 0.00 3.18
1940 2030 4.203950 TCGACCGTTCTCAACATTTTTG 57.796 40.909 0.00 0.00 0.00 2.44
1941 2031 3.872182 TCGACCGTTCTCAACATTTTTGA 59.128 39.130 0.00 0.00 0.00 2.69
1987 2077 8.606602 GGATGAATTTTATTGGCTTGACATTTC 58.393 33.333 0.00 0.00 0.00 2.17
2079 2170 6.835174 TGGATCAAAATCAACCATCCAAAAA 58.165 32.000 0.00 0.00 40.07 1.94
2087 2178 8.782339 AAATCAACCATCCAAAAATCAAGATC 57.218 30.769 0.00 0.00 0.00 2.75
2095 2186 8.566260 CCATCCAAAAATCAAGATCAGATAGTC 58.434 37.037 0.00 0.00 0.00 2.59
2096 2187 7.776933 TCCAAAAATCAAGATCAGATAGTCG 57.223 36.000 0.00 0.00 0.00 4.18
2097 2188 7.331026 TCCAAAAATCAAGATCAGATAGTCGT 58.669 34.615 0.00 0.00 0.00 4.34
2099 2190 9.098355 CCAAAAATCAAGATCAGATAGTCGTAA 57.902 33.333 0.00 0.00 0.00 3.18
2201 2295 6.029346 AGTCAAATTTGGCTCCACAATTAG 57.971 37.500 19.49 0.00 39.25 1.73
2305 2400 1.536766 AGACGTACATCAACGAACCGA 59.463 47.619 3.10 0.00 45.68 4.69
2307 2402 2.725723 GACGTACATCAACGAACCGAAA 59.274 45.455 3.10 0.00 45.68 3.46
2308 2403 2.727798 ACGTACATCAACGAACCGAAAG 59.272 45.455 3.10 0.00 45.68 2.62
2311 2406 4.084952 CGTACATCAACGAACCGAAAGAAA 60.085 41.667 0.00 0.00 45.68 2.52
2338 2433 9.449550 AAAAACTTAAAAATATGCAAAGCAAGC 57.550 25.926 0.00 0.00 43.62 4.01
2359 2454 7.698130 GCAAGCATTCTTCGATGTTAGTATTTT 59.302 33.333 0.00 0.00 0.00 1.82
2361 2456 7.920738 AGCATTCTTCGATGTTAGTATTTTCC 58.079 34.615 0.00 0.00 0.00 3.13
2368 2466 6.703319 TCGATGTTAGTATTTTCCAAGGACA 58.297 36.000 0.00 0.00 0.00 4.02
2369 2467 7.162761 TCGATGTTAGTATTTTCCAAGGACAA 58.837 34.615 0.00 0.00 0.00 3.18
2381 2479 1.131126 CAAGGACAACAATAGCTGGCG 59.869 52.381 0.00 0.00 0.00 5.69
2386 2484 0.521242 CAACAATAGCTGGCGAACGC 60.521 55.000 10.81 10.81 41.06 4.84
2399 2497 1.959226 GAACGCTCGCTGTTTGGGA 60.959 57.895 0.00 0.00 36.19 4.37
2400 2498 2.171489 GAACGCTCGCTGTTTGGGAC 62.171 60.000 0.00 0.00 33.86 4.46
2428 3175 6.785337 TCCGAAGAAGAAAGGACATATACA 57.215 37.500 0.00 0.00 0.00 2.29
2430 3177 7.617225 TCCGAAGAAGAAAGGACATATACAAA 58.383 34.615 0.00 0.00 0.00 2.83
2431 3178 8.265055 TCCGAAGAAGAAAGGACATATACAAAT 58.735 33.333 0.00 0.00 0.00 2.32
2432 3179 8.893727 CCGAAGAAGAAAGGACATATACAAATT 58.106 33.333 0.00 0.00 0.00 1.82
2439 3186 8.680903 AGAAAGGACATATACAAATTTCTGCTG 58.319 33.333 0.00 0.00 35.00 4.41
2440 3187 8.579850 AAAGGACATATACAAATTTCTGCTGA 57.420 30.769 0.00 0.00 0.00 4.26
2441 3188 8.579850 AAGGACATATACAAATTTCTGCTGAA 57.420 30.769 1.33 1.33 0.00 3.02
2442 3189 8.579850 AGGACATATACAAATTTCTGCTGAAA 57.420 30.769 19.39 19.39 44.99 2.69
2443 3190 8.680903 AGGACATATACAAATTTCTGCTGAAAG 58.319 33.333 21.19 12.04 44.25 2.62
2444 3191 8.677300 GGACATATACAAATTTCTGCTGAAAGA 58.323 33.333 21.19 2.87 44.25 2.52
2445 3192 9.713740 GACATATACAAATTTCTGCTGAAAGAG 57.286 33.333 21.19 15.65 44.25 2.85
2522 3269 7.644551 TGAAAGAGAAACGCGCTTAATTAAAAA 59.355 29.630 5.73 0.00 35.45 1.94
2523 3270 7.548673 AAGAGAAACGCGCTTAATTAAAAAG 57.451 32.000 5.73 0.00 34.70 2.27
2547 3294 2.202783 GATTTGGCGGGCATGCAC 60.203 61.111 21.36 16.51 36.28 4.57
2582 3331 0.179234 TGTCGGAGCTGTTCAACCAA 59.821 50.000 0.00 0.00 0.00 3.67
2810 3559 4.179579 GCCATCGCAAGGTTCGCC 62.180 66.667 0.00 0.00 38.47 5.54
2826 3583 2.558147 GCCCCCTCCCCTTCCTTTT 61.558 63.158 0.00 0.00 0.00 2.27
2828 3585 0.041238 CCCCCTCCCCTTCCTTTTTC 59.959 60.000 0.00 0.00 0.00 2.29
2844 3601 7.941795 TCCTTTTTCTTTCTCACTAAGTACG 57.058 36.000 0.00 0.00 0.00 3.67
2847 3604 8.274248 CCTTTTTCTTTCTCACTAAGTACGAAC 58.726 37.037 0.00 0.00 0.00 3.95
2852 3609 6.646653 TCTTTCTCACTAAGTACGAACTACGA 59.353 38.462 0.00 0.00 45.77 3.43
2856 3613 6.309980 TCTCACTAAGTACGAACTACGAAGAG 59.690 42.308 0.00 0.00 45.77 2.85
2889 3748 0.586802 GACTTTGACTGGTTCCACGC 59.413 55.000 0.00 0.00 0.00 5.34
2993 3852 9.274065 CAGAAAATAACGTGGTTTATTTAGAGC 57.726 33.333 3.95 0.00 39.62 4.09
3019 3878 6.828785 ACTGTATTAATTTAGTGCCAGGAAGG 59.171 38.462 0.00 0.00 41.84 3.46
3027 3886 1.911269 TGCCAGGAAGGTGCTACGA 60.911 57.895 0.00 0.00 40.61 3.43
3031 3890 1.066143 CCAGGAAGGTGCTACGATGTT 60.066 52.381 0.00 0.00 0.00 2.71
3183 4049 2.433239 ACCCGTAGTTTTCAGACAGTGT 59.567 45.455 0.00 0.00 0.00 3.55
3189 4055 2.939103 AGTTTTCAGACAGTGTGCTGAC 59.061 45.455 18.91 11.91 45.28 3.51
3190 4056 2.677836 GTTTTCAGACAGTGTGCTGACA 59.322 45.455 18.91 13.09 45.28 3.58
3191 4057 2.229675 TTCAGACAGTGTGCTGACAG 57.770 50.000 18.91 0.00 45.28 3.51
3235 4104 2.572104 AGACACCTTGTATGAACCCTCC 59.428 50.000 0.00 0.00 0.00 4.30
3244 4113 4.331968 TGTATGAACCCTCCAACATGAAC 58.668 43.478 0.00 0.00 0.00 3.18
3487 4361 1.152030 AGGTCCAGGTCCAAGCTCA 60.152 57.895 5.43 0.00 0.00 4.26
3580 4454 2.359531 CTCGTCTCATCCAAGGAGGTAC 59.640 54.545 0.25 0.69 39.02 3.34
3582 4456 3.201487 TCGTCTCATCCAAGGAGGTACTA 59.799 47.826 0.25 0.00 41.55 1.82
3583 4457 3.952323 CGTCTCATCCAAGGAGGTACTAA 59.048 47.826 0.25 0.00 41.55 2.24
3584 4458 4.202030 CGTCTCATCCAAGGAGGTACTAAC 60.202 50.000 0.25 0.00 41.55 2.34
3586 4460 4.956700 TCTCATCCAAGGAGGTACTAACTG 59.043 45.833 0.25 0.00 41.55 3.16
3587 4461 4.942944 TCATCCAAGGAGGTACTAACTGA 58.057 43.478 0.25 0.00 41.55 3.41
3591 4465 7.622081 TCATCCAAGGAGGTACTAACTGATTAA 59.378 37.037 0.25 0.00 41.55 1.40
3592 4466 7.989947 TCCAAGGAGGTACTAACTGATTAAT 57.010 36.000 0.00 0.00 41.55 1.40
3605 4479 9.110502 ACTAACTGATTAATTTAACTGGCTAGC 57.889 33.333 6.04 6.04 0.00 3.42
3624 4502 5.004535 GCTAGCACTGTCGTTTAGTGATTAC 59.995 44.000 10.63 6.05 46.52 1.89
3806 4693 2.060383 CATCACCTCCCTGCTCCGA 61.060 63.158 0.00 0.00 0.00 4.55
3873 4760 0.108662 CAGATGTGAGCGCACCTACA 60.109 55.000 18.33 9.39 44.51 2.74
3874 4761 0.826715 AGATGTGAGCGCACCTACAT 59.173 50.000 18.33 14.03 44.51 2.29
3875 4762 1.202463 AGATGTGAGCGCACCTACATC 60.202 52.381 25.43 25.43 45.98 3.06
3877 4764 0.536724 TGTGAGCGCACCTACATCAT 59.463 50.000 18.33 0.00 44.51 2.45
3878 4765 1.212616 GTGAGCGCACCTACATCATC 58.787 55.000 11.47 0.00 39.14 2.92
3880 4767 2.034685 GTGAGCGCACCTACATCATCTA 59.965 50.000 11.47 0.00 39.14 1.98
3881 4768 2.294512 TGAGCGCACCTACATCATCTAG 59.705 50.000 11.47 0.00 0.00 2.43
3895 4798 4.474226 TCATCTAGATGTCGATGTCACG 57.526 45.455 27.80 2.70 39.72 4.35
3955 4858 5.063880 AGTGCACCGTAGAAAATTTCTTCT 58.936 37.500 14.63 0.00 41.14 2.85
3986 4890 6.955963 CGAGAATCAATGTTACAAGCAAGTAC 59.044 38.462 0.00 0.00 33.17 2.73
4021 4925 7.116662 GCTCAATAATTGCATTCAAAAGTGACA 59.883 33.333 0.00 0.00 35.56 3.58
4238 5144 4.884164 CAGGTATTTTCAATCAGAGACCCC 59.116 45.833 0.00 0.00 0.00 4.95
4255 5161 1.613610 CCCCTCGTCCTCACTCCTA 59.386 63.158 0.00 0.00 0.00 2.94
4265 5171 3.027412 TCCTCACTCCTACTCAGATTGC 58.973 50.000 0.00 0.00 0.00 3.56
4400 5318 1.302511 GCACCTCGAGGGCAAGAAA 60.303 57.895 34.04 0.00 40.27 2.52
4451 5369 2.221169 TGAAGTTTGCTTGCTCGTGAT 58.779 42.857 0.00 0.00 34.61 3.06
4453 5371 3.812609 TGAAGTTTGCTTGCTCGTGATAA 59.187 39.130 0.00 0.00 34.61 1.75
4455 5373 5.641636 TGAAGTTTGCTTGCTCGTGATAATA 59.358 36.000 0.00 0.00 34.61 0.98
4456 5374 5.470845 AGTTTGCTTGCTCGTGATAATAC 57.529 39.130 0.00 0.00 0.00 1.89
4461 5379 3.804036 CTTGCTCGTGATAATACCCCAA 58.196 45.455 0.00 0.00 0.00 4.12
4462 5380 3.188159 TGCTCGTGATAATACCCCAAC 57.812 47.619 0.00 0.00 0.00 3.77
4463 5381 2.158871 TGCTCGTGATAATACCCCAACC 60.159 50.000 0.00 0.00 0.00 3.77
4464 5382 2.809299 GCTCGTGATAATACCCCAACCC 60.809 54.545 0.00 0.00 0.00 4.11
4465 5383 1.770061 TCGTGATAATACCCCAACCCC 59.230 52.381 0.00 0.00 0.00 4.95
4466 5384 1.491332 CGTGATAATACCCCAACCCCA 59.509 52.381 0.00 0.00 0.00 4.96
4467 5385 2.747135 CGTGATAATACCCCAACCCCAC 60.747 54.545 0.00 0.00 0.00 4.61
4469 5387 1.770061 GATAATACCCCAACCCCACGA 59.230 52.381 0.00 0.00 0.00 4.35
4470 5388 1.666365 TAATACCCCAACCCCACGAA 58.334 50.000 0.00 0.00 0.00 3.85
4471 5389 0.778720 AATACCCCAACCCCACGAAA 59.221 50.000 0.00 0.00 0.00 3.46
4472 5390 1.004436 ATACCCCAACCCCACGAAAT 58.996 50.000 0.00 0.00 0.00 2.17
4473 5391 0.038455 TACCCCAACCCCACGAAATG 59.962 55.000 0.00 0.00 0.00 2.32
4494 5412 0.450983 AGCTCTACGCGTGACTAACC 59.549 55.000 24.59 3.48 45.59 2.85
4501 5419 0.108804 CGCGTGACTAACCCAGTGAT 60.109 55.000 0.00 0.00 37.72 3.06
4503 5421 2.537401 GCGTGACTAACCCAGTGATAC 58.463 52.381 0.00 0.00 37.72 2.24
4564 5482 3.124921 GCCACCCCGACGTTCATG 61.125 66.667 0.00 0.00 0.00 3.07
4725 5646 3.986006 GCACCACTCCCACGACGA 61.986 66.667 0.00 0.00 0.00 4.20
5197 6121 2.097038 CAAGTTCTCCCTGCTCGCG 61.097 63.158 0.00 0.00 0.00 5.87
5217 6141 1.270358 GCCGTCTCCTTCTTGACAGTT 60.270 52.381 0.00 0.00 33.18 3.16
5218 6142 2.678324 CCGTCTCCTTCTTGACAGTTC 58.322 52.381 0.00 0.00 33.18 3.01
5307 6240 3.997021 TGCTTCTCTCGTTTCTCATTTCC 59.003 43.478 0.00 0.00 0.00 3.13
5308 6241 3.372514 GCTTCTCTCGTTTCTCATTTCCC 59.627 47.826 0.00 0.00 0.00 3.97
5310 6243 3.173965 TCTCTCGTTTCTCATTTCCCCT 58.826 45.455 0.00 0.00 0.00 4.79
5311 6244 3.583086 TCTCTCGTTTCTCATTTCCCCTT 59.417 43.478 0.00 0.00 0.00 3.95
5312 6245 3.674997 TCTCGTTTCTCATTTCCCCTTG 58.325 45.455 0.00 0.00 0.00 3.61
5314 6247 1.135689 CGTTTCTCATTTCCCCTTGCG 60.136 52.381 0.00 0.00 0.00 4.85
5340 6284 5.637006 TTTTGGTTCGATCCTGTAAATGG 57.363 39.130 13.55 0.00 0.00 3.16
5346 6290 2.236146 TCGATCCTGTAAATGGTGCAGT 59.764 45.455 0.00 0.00 38.23 4.40
5358 6302 1.010797 GTGCAGTGCAACGAGTGTG 60.011 57.895 21.67 0.00 45.86 3.82
5361 6305 0.041839 GCAGTGCAACGAGTGTGAAG 60.042 55.000 11.09 0.00 45.86 3.02
5368 6312 3.057019 GCAACGAGTGTGAAGTCATACA 58.943 45.455 10.33 0.00 39.95 2.29
5369 6313 3.121944 GCAACGAGTGTGAAGTCATACAG 59.878 47.826 10.33 6.56 39.95 2.74
5370 6314 4.299155 CAACGAGTGTGAAGTCATACAGT 58.701 43.478 10.33 7.10 39.95 3.55
5371 6315 5.458015 CAACGAGTGTGAAGTCATACAGTA 58.542 41.667 10.33 0.00 39.95 2.74
5372 6316 5.044428 ACGAGTGTGAAGTCATACAGTAC 57.956 43.478 10.33 0.00 39.95 2.73
5373 6317 4.760715 ACGAGTGTGAAGTCATACAGTACT 59.239 41.667 10.33 0.00 39.95 2.73
5374 6318 5.936372 ACGAGTGTGAAGTCATACAGTACTA 59.064 40.000 10.33 0.00 39.95 1.82
5375 6319 6.128336 ACGAGTGTGAAGTCATACAGTACTAC 60.128 42.308 10.33 0.00 39.95 2.73
5376 6320 6.092396 CGAGTGTGAAGTCATACAGTACTACT 59.908 42.308 10.33 0.00 39.95 2.57
5424 6368 8.680903 TGATAGAGCAAGGAAAAAGATTCATTC 58.319 33.333 0.00 0.00 0.00 2.67
5460 6404 3.297134 TCAAGCTGAAGTTGGGTCTTT 57.703 42.857 0.00 0.00 0.00 2.52
5488 6432 6.137415 ACATTTCAAATTTTCAATGCAAGCG 58.863 32.000 14.90 0.00 30.96 4.68
5506 6450 3.347216 AGCGCAGGATTAACAAGAACAT 58.653 40.909 11.47 0.00 0.00 2.71
5507 6451 3.127548 AGCGCAGGATTAACAAGAACATG 59.872 43.478 11.47 0.00 0.00 3.21
5514 6458 5.048504 AGGATTAACAAGAACATGTGCAGTG 60.049 40.000 6.60 6.29 32.81 3.66
5530 6474 3.871006 TGCAGTGCGAATATGACCTAAAG 59.129 43.478 11.20 0.00 0.00 1.85
5546 6490 4.352893 ACCTAAAGAGCAGGGGAAAACTAA 59.647 41.667 0.00 0.00 37.51 2.24
5548 6492 2.498644 AGAGCAGGGGAAAACTAAGC 57.501 50.000 0.00 0.00 0.00 3.09
5564 6508 9.713740 GAAAACTAAGCATGATTACAGATCAAG 57.286 33.333 0.00 0.00 0.00 3.02
5585 6529 3.440173 AGCCACAGAAATACATTCAACGG 59.560 43.478 0.00 0.00 40.72 4.44
5609 6572 2.455557 CATCCAATGCCCACAAGGTTA 58.544 47.619 0.00 0.00 38.26 2.85
5611 6574 1.427368 TCCAATGCCCACAAGGTTAGT 59.573 47.619 0.00 0.00 38.26 2.24
5615 6578 4.079253 CAATGCCCACAAGGTTAGTAGTT 58.921 43.478 0.00 0.00 38.26 2.24
5617 6580 2.289195 TGCCCACAAGGTTAGTAGTTCG 60.289 50.000 0.00 0.00 38.26 3.95
5619 6582 3.804759 GCCCACAAGGTTAGTAGTTCGTT 60.805 47.826 0.00 0.00 38.26 3.85
5620 6583 3.992427 CCCACAAGGTTAGTAGTTCGTTC 59.008 47.826 0.00 0.00 0.00 3.95
5621 6584 3.992427 CCACAAGGTTAGTAGTTCGTTCC 59.008 47.826 0.00 0.00 0.00 3.62
5622 6585 3.992427 CACAAGGTTAGTAGTTCGTTCCC 59.008 47.826 0.00 0.00 0.00 3.97
5623 6586 3.642848 ACAAGGTTAGTAGTTCGTTCCCA 59.357 43.478 0.00 0.00 0.00 4.37
5624 6587 3.949842 AGGTTAGTAGTTCGTTCCCAC 57.050 47.619 0.00 0.00 0.00 4.61
5635 6604 0.392461 CGTTCCCACCCCACATGTAG 60.392 60.000 0.00 0.00 0.00 2.74
5738 6745 2.878406 CAAGACCAACAACGACCTGATT 59.122 45.455 0.00 0.00 0.00 2.57
5764 6771 2.282555 CACTCAGCCGAATATCGTGTTG 59.717 50.000 0.00 0.07 38.40 3.33
5782 6789 3.059884 GTTGCGTCTCATTCTGTTCTCA 58.940 45.455 0.00 0.00 0.00 3.27
5783 6790 2.677199 TGCGTCTCATTCTGTTCTCAC 58.323 47.619 0.00 0.00 0.00 3.51
5793 6800 1.131315 TCTGTTCTCACGATCGAGCAG 59.869 52.381 24.34 16.21 39.09 4.24
5795 6802 1.539827 TGTTCTCACGATCGAGCAGAA 59.460 47.619 24.34 20.29 32.75 3.02
5796 6803 2.030274 TGTTCTCACGATCGAGCAGAAA 60.030 45.455 24.34 12.19 32.75 2.52
5872 6995 1.070758 AGATGTGGCCGGTGATCATAC 59.929 52.381 1.90 0.00 0.00 2.39
5886 7009 5.455326 GGTGATCATACCCTTCATTGTAGCT 60.455 44.000 0.00 0.00 34.56 3.32
5894 7017 2.771943 CCTTCATTGTAGCTACCCCAGA 59.228 50.000 21.01 10.73 0.00 3.86
5899 7022 2.921834 TGTAGCTACCCCAGAACTCT 57.078 50.000 21.01 0.00 0.00 3.24
6201 7324 3.895232 ACTGTAGTCTTGGTAGCCATG 57.105 47.619 0.00 0.00 31.53 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 190 6.927936 TGTTGTTGATTGTTGTCATTTATGGG 59.072 34.615 0.00 0.00 0.00 4.00
337 341 5.124138 ACTCGACTTGAACTCGATGACTAAT 59.876 40.000 0.00 0.00 39.36 1.73
343 347 2.159693 TCGACTCGACTTGAACTCGATG 60.160 50.000 0.00 0.00 39.36 3.84
346 350 1.872029 CTCGACTCGACTTGAACTCG 58.128 55.000 0.00 0.00 0.00 4.18
453 462 8.359642 CCTCAGTGTAATTGAATTTCTTTTGGA 58.640 33.333 0.00 0.00 29.84 3.53
460 470 6.863126 CCACAACCTCAGTGTAATTGAATTTC 59.137 38.462 0.00 0.00 29.84 2.17
478 488 3.305110 CTCATTACGCAAAACCACAACC 58.695 45.455 0.00 0.00 0.00 3.77
499 509 2.029380 GTGGTGGTGTAATTTTGGGAGC 60.029 50.000 0.00 0.00 0.00 4.70
509 519 1.459921 ACCCGGAGTGGTGGTGTAA 60.460 57.895 0.73 0.00 37.20 2.41
515 525 2.032071 GGTTGACCCGGAGTGGTG 59.968 66.667 0.73 0.00 39.24 4.17
570 599 2.360801 TGCTGGTTGGAACTAACAAAGC 59.639 45.455 15.39 15.39 39.89 3.51
587 616 1.014044 ATGTACCGTCGCAAGTGCTG 61.014 55.000 1.21 0.00 39.32 4.41
594 623 1.005512 ACTTGCATGTACCGTCGCA 60.006 52.632 2.92 0.00 0.00 5.10
595 624 1.693083 GGACTTGCATGTACCGTCGC 61.693 60.000 5.05 0.00 0.00 5.19
596 625 0.389296 TGGACTTGCATGTACCGTCG 60.389 55.000 12.16 0.00 0.00 5.12
597 626 1.076332 GTGGACTTGCATGTACCGTC 58.924 55.000 12.16 0.00 0.00 4.79
598 627 0.394938 TGTGGACTTGCATGTACCGT 59.605 50.000 12.16 0.00 0.00 4.83
599 628 1.737838 ATGTGGACTTGCATGTACCG 58.262 50.000 12.16 0.00 0.00 4.02
672 701 0.035458 AAACGAGCTCTGGTTCCTGG 59.965 55.000 12.85 0.00 31.13 4.45
772 806 2.548904 TGTTAATGTTCGGTTCGGTTGG 59.451 45.455 0.00 0.00 0.00 3.77
778 814 4.457949 ACAGGGATTGTTAATGTTCGGTTC 59.542 41.667 0.00 0.00 36.31 3.62
891 927 0.674895 AGCTAGGCGGCAAGTTGAAG 60.675 55.000 13.08 0.04 34.17 3.02
892 928 0.611200 TAGCTAGGCGGCAAGTTGAA 59.389 50.000 13.08 0.00 34.17 2.69
1238 1278 4.460873 GCGGCGTGCTAACCTTGC 62.461 66.667 9.37 0.00 41.73 4.01
1271 1311 3.688673 TGATCATGCACAACGAATGCTTA 59.311 39.130 10.66 0.00 43.77 3.09
1283 1323 3.811722 TCGAAAACTGTGATCATGCAC 57.188 42.857 0.00 0.00 39.22 4.57
1316 1356 4.384056 TGAAGGAAGCTCAAACAGAAGAG 58.616 43.478 0.00 0.00 35.01 2.85
1337 1377 3.342269 CGAATCTTGCGTAACGGAATTG 58.658 45.455 0.00 0.00 36.50 2.32
1347 1387 0.645355 CGTATGTGCGAATCTTGCGT 59.355 50.000 0.00 0.00 34.24 5.24
1382 1422 6.960542 TCCAATTTCTTCCTTCTAGGAGTACT 59.039 38.462 0.00 0.00 46.73 2.73
1384 1424 6.127026 GCTCCAATTTCTTCCTTCTAGGAGTA 60.127 42.308 0.00 0.00 46.73 2.59
1386 1426 5.122519 GCTCCAATTTCTTCCTTCTAGGAG 58.877 45.833 0.00 0.00 46.73 3.69
1388 1428 4.203226 GGCTCCAATTTCTTCCTTCTAGG 58.797 47.826 0.00 0.00 36.46 3.02
1389 1429 4.848357 TGGCTCCAATTTCTTCCTTCTAG 58.152 43.478 0.00 0.00 0.00 2.43
1396 1436 3.502211 TCTCGTTTGGCTCCAATTTCTTC 59.498 43.478 1.72 0.00 35.70 2.87
1404 1444 2.357034 GCGTCTCGTTTGGCTCCA 60.357 61.111 0.00 0.00 0.00 3.86
1448 1488 4.312443 GGAACCACTGATTACGTTCAGAA 58.688 43.478 21.17 0.00 44.88 3.02
1456 1496 2.094762 ACTGCGGAACCACTGATTAC 57.905 50.000 0.00 0.00 0.00 1.89
1470 1510 4.508124 AGTTTCAGAGAACTTGTAACTGCG 59.492 41.667 0.00 0.00 36.49 5.18
1478 1518 3.381272 TGGGCAAAGTTTCAGAGAACTTG 59.619 43.478 4.01 1.31 46.23 3.16
1497 1537 3.613737 CAGCAACGCTTAATCAATTTGGG 59.386 43.478 0.00 0.00 36.40 4.12
1505 1545 5.485662 AATCTTACCAGCAACGCTTAATC 57.514 39.130 0.00 0.00 36.40 1.75
1520 1560 7.435068 TCCAGTTTCTTGCACTTAATCTTAC 57.565 36.000 0.00 0.00 0.00 2.34
1531 1571 1.949525 GTCTTGCTCCAGTTTCTTGCA 59.050 47.619 0.00 0.00 0.00 4.08
1652 1726 2.582052 TCTTGAACCGGTTGATTGCTT 58.418 42.857 27.87 0.00 0.00 3.91
1669 1743 2.922740 TAATCCGGCGGCTAATTCTT 57.077 45.000 23.83 7.94 0.00 2.52
1803 1887 5.684704 TGGATACTTAATGAGGGAAAGCTG 58.315 41.667 0.00 0.00 37.61 4.24
1820 1904 1.756538 CAGCACCCCCAAATTGGATAC 59.243 52.381 14.62 0.00 40.96 2.24
1825 1909 0.831288 TGGTCAGCACCCCCAAATTG 60.831 55.000 0.00 0.00 42.99 2.32
1827 1911 1.228862 GTGGTCAGCACCCCCAAAT 60.229 57.895 0.00 0.00 42.99 2.32
1850 1934 1.067212 GAGAATCACGTAGGACCGCAT 59.933 52.381 0.00 0.00 33.17 4.73
1880 1970 1.587547 GGGAGAAGTCGATGATTGGC 58.412 55.000 0.00 0.00 0.00 4.52
1893 1983 4.069304 CTGTGTGTTTTTATCGGGGAGAA 58.931 43.478 0.00 0.00 0.00 2.87
1911 2001 1.078759 GAGAACGGTCGATGGCTGTG 61.079 60.000 0.00 0.00 0.00 3.66
1915 2005 0.669318 TGTTGAGAACGGTCGATGGC 60.669 55.000 0.00 0.00 0.00 4.40
1987 2077 2.930826 ATGTTGCTTATACTCCCGGG 57.069 50.000 16.85 16.85 0.00 5.73
2079 2170 8.684386 TCTTCTTACGACTATCTGATCTTGAT 57.316 34.615 0.00 0.75 0.00 2.57
2087 2178 7.010552 CCAACCAAATCTTCTTACGACTATCTG 59.989 40.741 0.00 0.00 0.00 2.90
2095 2186 2.817258 TGGCCAACCAAATCTTCTTACG 59.183 45.455 0.61 0.00 45.37 3.18
2314 2409 8.152309 TGCTTGCTTTGCATATTTTTAAGTTT 57.848 26.923 0.00 0.00 38.76 2.66
2315 2410 7.727331 TGCTTGCTTTGCATATTTTTAAGTT 57.273 28.000 0.00 0.00 38.76 2.66
2328 2423 2.336554 TCGAAGAATGCTTGCTTTGC 57.663 45.000 0.00 0.00 33.61 3.68
2333 2428 4.606457 ACTAACATCGAAGAATGCTTGC 57.394 40.909 0.00 0.00 43.58 4.01
2337 2432 7.693952 TGGAAAATACTAACATCGAAGAATGC 58.306 34.615 0.00 0.00 43.58 3.56
2338 2433 9.708222 CTTGGAAAATACTAACATCGAAGAATG 57.292 33.333 0.00 0.00 43.58 2.67
2359 2454 2.879756 GCCAGCTATTGTTGTCCTTGGA 60.880 50.000 0.00 0.00 0.00 3.53
2361 2456 1.131126 CGCCAGCTATTGTTGTCCTTG 59.869 52.381 0.00 0.00 0.00 3.61
2368 2466 0.673644 AGCGTTCGCCAGCTATTGTT 60.674 50.000 13.54 0.00 42.60 2.83
2369 2467 1.079127 AGCGTTCGCCAGCTATTGT 60.079 52.632 13.54 0.00 42.60 2.71
2381 2479 1.959226 TCCCAAACAGCGAGCGTTC 60.959 57.895 0.00 0.00 0.00 3.95
2386 2484 2.678336 GGAAATAGTCCCAAACAGCGAG 59.322 50.000 0.00 0.00 41.10 5.03
2390 2488 4.575885 TCTTCGGAAATAGTCCCAAACAG 58.424 43.478 0.00 0.00 44.60 3.16
2399 2497 6.110411 TGTCCTTTCTTCTTCGGAAATAGT 57.890 37.500 0.00 0.00 33.12 2.12
2400 2498 8.894768 ATATGTCCTTTCTTCTTCGGAAATAG 57.105 34.615 0.00 0.00 31.19 1.73
2418 3165 8.677300 TCTTTCAGCAGAAATTTGTATATGTCC 58.323 33.333 4.61 0.00 42.49 4.02
2484 3231 9.481800 CGCGTTTCTCTTTCACGTATATATATA 57.518 33.333 0.00 0.00 36.29 0.86
2485 3232 7.008086 GCGCGTTTCTCTTTCACGTATATATAT 59.992 37.037 8.43 0.00 36.29 0.86
2486 3233 6.303970 GCGCGTTTCTCTTTCACGTATATATA 59.696 38.462 8.43 0.00 36.29 0.86
2487 3234 5.116680 GCGCGTTTCTCTTTCACGTATATAT 59.883 40.000 8.43 0.00 36.29 0.86
2488 3235 4.438797 GCGCGTTTCTCTTTCACGTATATA 59.561 41.667 8.43 0.00 36.29 0.86
2489 3236 3.242248 GCGCGTTTCTCTTTCACGTATAT 59.758 43.478 8.43 0.00 36.29 0.86
2490 3237 2.595536 GCGCGTTTCTCTTTCACGTATA 59.404 45.455 8.43 0.00 36.29 1.47
2491 3238 1.389106 GCGCGTTTCTCTTTCACGTAT 59.611 47.619 8.43 0.00 36.29 3.06
2492 3239 0.780002 GCGCGTTTCTCTTTCACGTA 59.220 50.000 8.43 0.00 36.29 3.57
2493 3240 0.874607 AGCGCGTTTCTCTTTCACGT 60.875 50.000 8.43 0.00 36.29 4.49
2494 3241 0.232303 AAGCGCGTTTCTCTTTCACG 59.768 50.000 8.43 0.00 36.98 4.35
2495 3242 3.515071 TTAAGCGCGTTTCTCTTTCAC 57.485 42.857 12.68 0.00 0.00 3.18
2522 3269 0.603065 GCCCGCCAAATCAGTTTTCT 59.397 50.000 0.00 0.00 0.00 2.52
2523 3270 0.316841 TGCCCGCCAAATCAGTTTTC 59.683 50.000 0.00 0.00 0.00 2.29
2810 3559 1.084866 AGAAAAAGGAAGGGGAGGGG 58.915 55.000 0.00 0.00 0.00 4.79
2814 3563 4.168088 AGTGAGAAAGAAAAAGGAAGGGGA 59.832 41.667 0.00 0.00 0.00 4.81
2815 3564 4.474394 AGTGAGAAAGAAAAAGGAAGGGG 58.526 43.478 0.00 0.00 0.00 4.79
2826 3583 7.171508 TCGTAGTTCGTACTTAGTGAGAAAGAA 59.828 37.037 0.00 0.00 40.80 2.52
2828 3585 6.825584 TCGTAGTTCGTACTTAGTGAGAAAG 58.174 40.000 0.00 0.00 40.80 2.62
2844 3601 3.087781 ACTGGTACCCTCTTCGTAGTTC 58.912 50.000 10.07 0.00 0.00 3.01
2847 3604 1.134560 GCACTGGTACCCTCTTCGTAG 59.865 57.143 10.07 0.00 0.00 3.51
2852 3609 0.178903 TCCTGCACTGGTACCCTCTT 60.179 55.000 10.07 0.00 0.00 2.85
2856 3613 0.400594 AAAGTCCTGCACTGGTACCC 59.599 55.000 10.07 0.00 34.56 3.69
2993 3852 7.201732 CCTTCCTGGCACTAAATTAATACAGTG 60.202 40.741 18.50 18.50 41.06 3.66
3005 3864 1.278127 GTAGCACCTTCCTGGCACTAA 59.722 52.381 0.00 0.00 40.22 2.24
3043 3902 1.165907 TCAACAAAGACGGGCAGCAG 61.166 55.000 0.00 0.00 0.00 4.24
3044 3903 0.749818 TTCAACAAAGACGGGCAGCA 60.750 50.000 0.00 0.00 0.00 4.41
3045 3904 0.317854 GTTCAACAAAGACGGGCAGC 60.318 55.000 0.00 0.00 0.00 5.25
3183 4049 0.823460 TGTCAGTGTCACTGTCAGCA 59.177 50.000 27.97 19.89 46.03 4.41
3190 4056 2.288457 CGACCAGATTGTCAGTGTCACT 60.288 50.000 0.00 0.00 34.88 3.41
3191 4057 2.061773 CGACCAGATTGTCAGTGTCAC 58.938 52.381 0.00 0.00 34.88 3.67
3235 4104 2.538037 TCAGTGACGTTCGTTCATGTTG 59.462 45.455 0.00 1.79 0.00 3.33
3244 4113 1.548973 GCACAGGTCAGTGACGTTCG 61.549 60.000 15.60 10.65 42.05 3.95
3391 4265 1.838846 GATGGCCCCTGATCTCCGA 60.839 63.158 0.00 0.00 0.00 4.55
3417 4291 3.708220 GAAGAGCTGGTCGCCGAGG 62.708 68.421 0.00 0.00 40.39 4.63
3580 4454 9.109393 TGCTAGCCAGTTAAATTAATCAGTTAG 57.891 33.333 13.29 0.00 0.00 2.34
3581 4455 8.889717 GTGCTAGCCAGTTAAATTAATCAGTTA 58.110 33.333 13.29 0.00 0.00 2.24
3582 4456 7.611855 AGTGCTAGCCAGTTAAATTAATCAGTT 59.388 33.333 13.29 0.00 0.00 3.16
3583 4457 7.066284 CAGTGCTAGCCAGTTAAATTAATCAGT 59.934 37.037 13.29 0.00 0.00 3.41
3584 4458 7.066284 ACAGTGCTAGCCAGTTAAATTAATCAG 59.934 37.037 13.29 0.00 0.00 2.90
3586 4460 7.321745 ACAGTGCTAGCCAGTTAAATTAATC 57.678 36.000 13.29 0.00 0.00 1.75
3587 4461 6.037172 CGACAGTGCTAGCCAGTTAAATTAAT 59.963 38.462 13.29 0.00 0.00 1.40
3591 4465 3.262420 CGACAGTGCTAGCCAGTTAAAT 58.738 45.455 13.29 0.00 0.00 1.40
3592 4466 2.036733 ACGACAGTGCTAGCCAGTTAAA 59.963 45.455 13.29 0.00 0.00 1.52
3604 4478 3.991773 TGGTAATCACTAAACGACAGTGC 59.008 43.478 9.81 0.00 42.58 4.40
3605 4479 5.511088 GTGGTAATCACTAAACGACAGTG 57.489 43.478 8.77 8.77 43.92 3.66
3624 4502 5.700722 TTACTACTACCATATCGCAGTGG 57.299 43.478 0.00 0.00 41.35 4.00
3643 4521 8.782327 CGCCACGAAAAAGAGTTAAATTATTAC 58.218 33.333 0.00 0.00 0.00 1.89
3653 4531 0.028902 GCACGCCACGAAAAAGAGTT 59.971 50.000 0.00 0.00 0.00 3.01
3873 4760 4.614764 GCGTGACATCGACATCTAGATGAT 60.615 45.833 34.16 20.30 45.08 2.45
3874 4761 3.304057 GCGTGACATCGACATCTAGATGA 60.304 47.826 34.16 16.14 45.08 2.92
3875 4762 2.976509 GCGTGACATCGACATCTAGATG 59.023 50.000 27.63 27.63 46.95 2.90
3877 4764 2.288186 GAGCGTGACATCGACATCTAGA 59.712 50.000 0.00 0.00 0.00 2.43
3878 4765 2.603412 GGAGCGTGACATCGACATCTAG 60.603 54.545 0.00 0.00 0.00 2.43
3880 4767 0.101399 GGAGCGTGACATCGACATCT 59.899 55.000 0.00 0.00 0.00 2.90
3881 4768 0.101399 AGGAGCGTGACATCGACATC 59.899 55.000 0.00 0.00 0.00 3.06
3895 4798 2.680339 CAACTAGGCTAAGCAAAGGAGC 59.320 50.000 0.00 0.00 35.39 4.70
3955 4858 7.041440 TGCTTGTAACATTGATTCTCGAAGAAA 60.041 33.333 0.00 0.00 37.82 2.52
3986 4890 2.223340 GCAATTATTGAGCACGGACAGG 60.223 50.000 9.36 0.00 0.00 4.00
4021 4925 2.079158 CAGTCATTTGGCAGATCACGT 58.921 47.619 0.00 0.00 0.00 4.49
4238 5144 0.256464 AGTAGGAGTGAGGACGAGGG 59.744 60.000 0.00 0.00 0.00 4.30
4240 5146 2.093394 TCTGAGTAGGAGTGAGGACGAG 60.093 54.545 0.00 0.00 0.00 4.18
4249 5155 2.763448 GTGGAGCAATCTGAGTAGGAGT 59.237 50.000 0.00 0.00 0.00 3.85
4255 5161 4.100035 TGATAATCGTGGAGCAATCTGAGT 59.900 41.667 0.00 0.00 0.00 3.41
4265 5171 8.824159 ATATTTCTTCAGTGATAATCGTGGAG 57.176 34.615 0.00 0.00 0.00 3.86
4319 5234 9.699703 ACCTGCGTTAACATTACATTTATTTTT 57.300 25.926 6.39 0.00 0.00 1.94
4326 5244 4.076394 ACCACCTGCGTTAACATTACATT 58.924 39.130 6.39 0.00 0.00 2.71
4339 5257 1.227999 ATTCGACACAACCACCTGCG 61.228 55.000 0.00 0.00 0.00 5.18
4422 5340 6.256539 CGAGCAAGCAAACTTCATTATAGAGA 59.743 38.462 0.00 0.00 32.29 3.10
4423 5341 6.036517 ACGAGCAAGCAAACTTCATTATAGAG 59.963 38.462 0.00 0.00 32.29 2.43
4427 5345 4.455533 TCACGAGCAAGCAAACTTCATTAT 59.544 37.500 0.00 0.00 32.29 1.28
4436 5354 3.625764 GGGTATTATCACGAGCAAGCAAA 59.374 43.478 0.00 0.00 0.00 3.68
4437 5355 3.202906 GGGTATTATCACGAGCAAGCAA 58.797 45.455 0.00 0.00 0.00 3.91
4441 5359 3.537580 GTTGGGGTATTATCACGAGCAA 58.462 45.455 0.00 0.00 0.00 3.91
4443 5361 2.490991 GGTTGGGGTATTATCACGAGC 58.509 52.381 0.00 0.00 0.00 5.03
4451 5369 1.666365 TTCGTGGGGTTGGGGTATTA 58.334 50.000 0.00 0.00 0.00 0.98
4453 5371 1.004436 ATTTCGTGGGGTTGGGGTAT 58.996 50.000 0.00 0.00 0.00 2.73
4455 5373 1.228737 CATTTCGTGGGGTTGGGGT 60.229 57.895 0.00 0.00 0.00 4.95
4456 5374 1.981853 CCATTTCGTGGGGTTGGGG 60.982 63.158 0.00 0.00 44.79 4.96
4464 5382 2.392619 GCGTAGAGCTCCATTTCGTGG 61.393 57.143 10.93 0.00 42.53 4.94
4465 5383 0.924090 GCGTAGAGCTCCATTTCGTG 59.076 55.000 10.93 0.00 44.04 4.35
4466 5384 0.525668 CGCGTAGAGCTCCATTTCGT 60.526 55.000 10.93 0.00 45.59 3.85
4467 5385 0.525668 ACGCGTAGAGCTCCATTTCG 60.526 55.000 11.67 10.46 45.59 3.46
4469 5387 0.530744 TCACGCGTAGAGCTCCATTT 59.469 50.000 13.44 0.00 45.59 2.32
4470 5388 0.179134 GTCACGCGTAGAGCTCCATT 60.179 55.000 13.44 0.00 45.59 3.16
4471 5389 1.032657 AGTCACGCGTAGAGCTCCAT 61.033 55.000 13.44 0.00 45.59 3.41
4472 5390 0.392060 TAGTCACGCGTAGAGCTCCA 60.392 55.000 13.44 0.00 45.59 3.86
4473 5391 0.731417 TTAGTCACGCGTAGAGCTCC 59.269 55.000 13.44 0.31 45.59 4.70
4474 5392 1.531470 GGTTAGTCACGCGTAGAGCTC 60.531 57.143 13.44 5.27 45.59 4.09
4475 5393 0.450983 GGTTAGTCACGCGTAGAGCT 59.549 55.000 13.44 10.27 45.59 4.09
4476 5394 0.525029 GGGTTAGTCACGCGTAGAGC 60.525 60.000 13.44 5.80 43.95 4.09
4477 5395 0.806868 TGGGTTAGTCACGCGTAGAG 59.193 55.000 13.44 0.00 41.37 2.43
4478 5396 0.806868 CTGGGTTAGTCACGCGTAGA 59.193 55.000 13.44 9.56 41.37 2.59
4479 5397 0.524862 ACTGGGTTAGTCACGCGTAG 59.475 55.000 13.44 6.92 41.37 3.51
4480 5398 0.241749 CACTGGGTTAGTCACGCGTA 59.758 55.000 13.44 0.00 41.37 4.42
4501 5419 0.391130 GCCTGATGCACGTGAAGGTA 60.391 55.000 22.23 0.00 40.77 3.08
4503 5421 0.108186 TAGCCTGATGCACGTGAAGG 60.108 55.000 22.23 19.36 44.83 3.46
4660 5578 2.094539 CAGACGTGCGCGAACATG 59.905 61.111 28.73 14.38 42.00 3.21
4785 5706 4.295119 GCACGGTGGTGGAGTCGT 62.295 66.667 10.60 0.00 44.54 4.34
4842 5763 2.910479 ACCTGGACTGCACGACGA 60.910 61.111 0.00 0.00 0.00 4.20
4972 5896 4.821589 GGGACTCGCTTCTGGCCG 62.822 72.222 0.00 0.00 37.74 6.13
4973 5897 4.475135 GGGGACTCGCTTCTGGCC 62.475 72.222 0.00 0.00 37.74 5.36
4974 5898 4.475135 GGGGGACTCGCTTCTGGC 62.475 72.222 0.00 0.00 37.64 4.85
5005 5929 1.227999 ACACGCCGGAGTTGATGTTG 61.228 55.000 8.62 0.00 0.00 3.33
5197 6121 0.318762 ACTGTCAAGAAGGAGACGGC 59.681 55.000 0.00 0.00 43.32 5.68
5203 6127 3.309296 ACTCTGGAACTGTCAAGAAGGA 58.691 45.455 0.00 0.00 33.15 3.36
5217 6141 3.074687 AGGAGAACTGTACAGACTCTGGA 59.925 47.826 31.62 0.00 35.51 3.86
5218 6142 3.192422 CAGGAGAACTGTACAGACTCTGG 59.808 52.174 31.62 25.08 42.42 3.86
5326 6270 2.352651 CACTGCACCATTTACAGGATCG 59.647 50.000 0.00 0.00 35.70 3.69
5340 6284 1.010797 CACACTCGTTGCACTGCAC 60.011 57.895 2.26 0.00 38.71 4.57
5346 6290 2.238942 ATGACTTCACACTCGTTGCA 57.761 45.000 0.00 0.00 0.00 4.08
5358 6302 8.923683 GGTTTTTCAGTAGTACTGTATGACTTC 58.076 37.037 25.83 12.13 46.03 3.01
5361 6305 8.086522 TCTGGTTTTTCAGTAGTACTGTATGAC 58.913 37.037 25.83 19.56 46.03 3.06
5368 6312 7.793948 ATACCTCTGGTTTTTCAGTAGTACT 57.206 36.000 0.00 0.00 37.09 2.73
5369 6313 7.876582 ACAATACCTCTGGTTTTTCAGTAGTAC 59.123 37.037 0.00 0.00 37.09 2.73
5370 6314 7.970102 ACAATACCTCTGGTTTTTCAGTAGTA 58.030 34.615 0.00 0.00 37.09 1.82
5371 6315 6.838382 ACAATACCTCTGGTTTTTCAGTAGT 58.162 36.000 0.00 0.00 37.09 2.73
5372 6316 7.745620 AACAATACCTCTGGTTTTTCAGTAG 57.254 36.000 0.00 0.00 37.09 2.57
5373 6317 8.410141 CAAAACAATACCTCTGGTTTTTCAGTA 58.590 33.333 0.00 0.00 40.38 2.74
5374 6318 7.123547 TCAAAACAATACCTCTGGTTTTTCAGT 59.876 33.333 0.00 0.00 40.38 3.41
5375 6319 7.488322 TCAAAACAATACCTCTGGTTTTTCAG 58.512 34.615 0.00 0.00 40.38 3.02
5376 6320 7.411486 TCAAAACAATACCTCTGGTTTTTCA 57.589 32.000 0.00 0.00 40.38 2.69
5377 6321 9.626045 CTATCAAAACAATACCTCTGGTTTTTC 57.374 33.333 0.00 0.00 40.38 2.29
5378 6322 9.362151 TCTATCAAAACAATACCTCTGGTTTTT 57.638 29.630 0.00 0.00 40.38 1.94
5424 6368 6.051074 TCAGCTTGATTGTATGACCAGTATG 58.949 40.000 0.00 0.00 0.00 2.39
5488 6432 4.168760 GCACATGTTCTTGTTAATCCTGC 58.831 43.478 0.00 0.00 0.00 4.85
5498 6442 0.587768 TCGCACTGCACATGTTCTTG 59.412 50.000 0.00 0.00 0.00 3.02
5506 6450 1.066215 AGGTCATATTCGCACTGCACA 60.066 47.619 1.11 0.00 0.00 4.57
5507 6451 1.656652 AGGTCATATTCGCACTGCAC 58.343 50.000 1.11 0.00 0.00 4.57
5514 6458 3.743396 CCTGCTCTTTAGGTCATATTCGC 59.257 47.826 0.00 0.00 0.00 4.70
5530 6474 2.200373 TGCTTAGTTTTCCCCTGCTC 57.800 50.000 0.00 0.00 0.00 4.26
5546 6490 3.881688 GTGGCTTGATCTGTAATCATGCT 59.118 43.478 19.11 0.00 44.02 3.79
5548 6492 5.121105 TCTGTGGCTTGATCTGTAATCATG 58.879 41.667 0.00 0.00 0.00 3.07
5564 6508 3.758300 CCGTTGAATGTATTTCTGTGGC 58.242 45.455 0.00 0.00 35.23 5.01
5609 6572 0.472352 TGGGGTGGGAACGAACTACT 60.472 55.000 0.00 0.00 0.00 2.57
5611 6574 0.763604 TGTGGGGTGGGAACGAACTA 60.764 55.000 0.00 0.00 0.00 2.24
5615 6578 0.836830 TACATGTGGGGTGGGAACGA 60.837 55.000 9.11 0.00 0.00 3.85
5617 6580 0.988832 TCTACATGTGGGGTGGGAAC 59.011 55.000 9.11 0.00 0.00 3.62
5619 6582 1.274126 TGATCTACATGTGGGGTGGGA 60.274 52.381 9.11 0.00 0.00 4.37
5620 6583 1.212375 TGATCTACATGTGGGGTGGG 58.788 55.000 9.11 0.00 0.00 4.61
5621 6584 2.026356 TGTTGATCTACATGTGGGGTGG 60.026 50.000 9.11 0.00 0.00 4.61
5622 6585 3.009723 GTGTTGATCTACATGTGGGGTG 58.990 50.000 13.09 0.00 0.00 4.61
5623 6586 2.642311 TGTGTTGATCTACATGTGGGGT 59.358 45.455 13.09 0.00 0.00 4.95
5624 6587 3.348647 TGTGTTGATCTACATGTGGGG 57.651 47.619 13.09 0.00 0.00 4.96
5635 6604 9.760660 GTAATTGTTAACTCAGATGTGTTGATC 57.239 33.333 7.22 0.00 34.19 2.92
5738 6745 0.459899 ATATTCGGCTGAGTGCGACA 59.540 50.000 0.00 0.00 44.05 4.35
5764 6771 1.651138 CGTGAGAACAGAATGAGACGC 59.349 52.381 0.00 0.00 39.69 5.19
5782 6789 3.246619 GAAGAAGTTTCTGCTCGATCGT 58.753 45.455 15.94 0.00 37.65 3.73
5783 6790 2.600867 GGAAGAAGTTTCTGCTCGATCG 59.399 50.000 9.36 9.36 37.65 3.69
5793 6800 3.997021 TCTCATCAAGCGGAAGAAGTTTC 59.003 43.478 0.00 0.00 0.00 2.78
5795 6802 3.685139 TCTCATCAAGCGGAAGAAGTT 57.315 42.857 0.00 0.00 0.00 2.66
5796 6803 3.685139 TTCTCATCAAGCGGAAGAAGT 57.315 42.857 0.00 0.00 0.00 3.01
5872 6995 1.843851 TGGGGTAGCTACAATGAAGGG 59.156 52.381 24.75 0.00 0.00 3.95
5894 7017 5.030147 TCATGTTACCTATCACCCAGAGTT 58.970 41.667 0.00 0.00 0.00 3.01
5899 7022 5.220521 TGGTATCATGTTACCTATCACCCA 58.779 41.667 26.10 7.65 41.90 4.51
5941 7064 1.126488 GAGATGGTCATGAGGCCTCA 58.874 55.000 36.73 36.73 44.59 3.86
6201 7324 8.821894 GGTCTTATGACACTGATTTGATAGTTC 58.178 37.037 10.60 0.00 44.61 3.01


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

AutoCloner maintained by Alex Coulton.