Multiple sequence alignment - TraesCS7B01G117200

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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 TraesCS7B01G117200 chr7B 100.000 3233 0 0 1 3233 136889781 136886549 0.000000e+00 5971.0
1 TraesCS7B01G117200 chr7B 84.603 604 81 8 3 597 14931169 14931769 9.990000e-165 590.0
2 TraesCS7B01G117200 chr7B 91.667 72 4 1 2281 2350 483280599 483280670 7.380000e-17 99.0
3 TraesCS7B01G117200 chr7B 82.609 115 17 2 2239 2350 589823341 589823455 7.380000e-17 99.0
4 TraesCS7B01G117200 chr7B 89.333 75 5 3 2370 2442 292401852 292401925 1.240000e-14 91.6
5 TraesCS7B01G117200 chr7D 91.241 2249 168 8 1 2248 170609095 170606875 0.000000e+00 3035.0
6 TraesCS7B01G117200 chr7D 86.656 607 71 6 1 597 92216282 92215676 0.000000e+00 664.0
7 TraesCS7B01G117200 chr7D 77.122 271 57 4 1202 1468 170730877 170730608 5.590000e-33 152.0
8 TraesCS7B01G117200 chr7D 85.263 95 10 4 2443 2535 75270897 75270805 9.550000e-16 95.3
9 TraesCS7B01G117200 chr7D 82.692 104 15 3 2572 2674 375815628 375815527 4.440000e-14 89.8
10 TraesCS7B01G117200 chr7A 91.394 1650 86 21 619 2234 173493929 173492302 0.000000e+00 2209.0
11 TraesCS7B01G117200 chr7A 86.820 607 68 9 1 597 94312582 94311978 0.000000e+00 667.0
12 TraesCS7B01G117200 chr2A 86.289 671 81 8 2572 3233 706274164 706273496 0.000000e+00 719.0
13 TraesCS7B01G117200 chr2A 88.889 90 9 1 2447 2535 18632740 18632651 3.410000e-20 110.0
14 TraesCS7B01G117200 chr2A 91.176 68 5 1 2366 2432 630349491 630349424 1.240000e-14 91.6
15 TraesCS7B01G117200 chr2A 83.158 95 15 1 2442 2535 146953528 146953434 5.750000e-13 86.1
16 TraesCS7B01G117200 chr1D 87.059 595 75 2 1 595 460746681 460746089 0.000000e+00 671.0
17 TraesCS7B01G117200 chr1D 85.025 601 84 6 1 597 402432994 402432396 9.920000e-170 606.0
18 TraesCS7B01G117200 chr1D 90.141 71 4 2 2373 2441 141715467 141715536 4.440000e-14 89.8
19 TraesCS7B01G117200 chrUn 86.723 595 79 0 1 595 8093707 8093113 0.000000e+00 662.0
20 TraesCS7B01G117200 chr4A 83.939 660 102 3 2574 3233 690797873 690798528 2.120000e-176 628.0
21 TraesCS7B01G117200 chr4A 88.312 77 7 1 2277 2351 740525387 740525463 1.240000e-14 91.6
22 TraesCS7B01G117200 chr4A 88.312 77 7 1 2277 2351 740529854 740529930 1.240000e-14 91.6
23 TraesCS7B01G117200 chr4A 88.312 77 7 1 2277 2351 740534321 740534397 1.240000e-14 91.6
24 TraesCS7B01G117200 chr3D 85.362 608 75 10 1 604 583051413 583050816 4.580000e-173 617.0
25 TraesCS7B01G117200 chr5D 85.240 603 75 8 3 593 505028722 505028122 2.760000e-170 608.0
26 TraesCS7B01G117200 chr5D 90.000 50 4 1 2572 2621 505445641 505445593 2.690000e-06 63.9
27 TraesCS7B01G117200 chr2D 84.564 596 91 1 1 596 450207464 450206870 9.990000e-165 590.0
28 TraesCS7B01G117200 chr2D 75.852 675 135 23 2574 3229 9373355 9374020 5.200000e-83 318.0
29 TraesCS7B01G117200 chr2D 83.133 83 11 2 2236 2315 121001194 121001112 4.470000e-09 73.1
30 TraesCS7B01G117200 chr6D 85.009 527 71 4 2708 3233 18871201 18870682 2.210000e-146 529.0
31 TraesCS7B01G117200 chr4B 79.464 672 122 12 2572 3232 364350358 364351024 2.270000e-126 462.0
32 TraesCS7B01G117200 chr4B 78.625 669 117 18 2572 3220 23318128 23318790 1.390000e-113 420.0
33 TraesCS7B01G117200 chr4B 86.957 92 9 3 2444 2534 643538604 643538693 2.050000e-17 100.0
34 TraesCS7B01G117200 chr4B 83.158 95 11 5 2443 2535 633145197 633145106 7.430000e-12 82.4
35 TraesCS7B01G117200 chr4B 89.091 55 6 0 2571 2625 112467462 112467516 5.790000e-08 69.4
36 TraesCS7B01G117200 chr5B 91.188 261 22 1 2570 2830 210165056 210164797 1.430000e-93 353.0
37 TraesCS7B01G117200 chr5B 88.506 261 29 1 2570 2830 210151405 210151146 6.730000e-82 315.0
38 TraesCS7B01G117200 chr5B 91.860 86 6 1 2446 2531 20013464 20013380 5.670000e-23 119.0
39 TraesCS7B01G117200 chr5B 87.179 78 8 2 2366 2441 482500956 482500879 1.600000e-13 87.9
40 TraesCS7B01G117200 chr5B 83.696 92 14 1 2443 2534 55517408 55517318 5.750000e-13 86.1
41 TraesCS7B01G117200 chr5B 88.732 71 6 2 2371 2440 661309385 661309454 5.750000e-13 86.1
42 TraesCS7B01G117200 chr6B 86.869 99 10 2 2255 2350 629525652 629525750 1.230000e-19 108.0
43 TraesCS7B01G117200 chr1A 94.915 59 3 0 2374 2432 556139903 556139961 3.430000e-15 93.5
44 TraesCS7B01G117200 chr1A 85.714 77 9 2 2356 2432 486045752 486045826 2.670000e-11 80.5
45 TraesCS7B01G117200 chr2B 88.889 72 4 4 2376 2445 683761986 683761917 5.750000e-13 86.1
46 TraesCS7B01G117200 chr2B 83.824 68 10 1 2241 2307 133533518 133533585 2.690000e-06 63.9
47 TraesCS7B01G117200 chr1B 88.000 75 6 3 2379 2451 29970877 29970950 5.750000e-13 86.1
48 TraesCS7B01G117200 chr1B 90.909 66 3 3 2572 2636 41640010 41639947 5.750000e-13 86.1
49 TraesCS7B01G117200 chr3A 81.308 107 17 2 2239 2342 727378132 727378026 2.070000e-12 84.2
50 TraesCS7B01G117200 chr5A 89.062 64 7 0 2281 2344 367133208 367133271 2.670000e-11 80.5
51 TraesCS7B01G117200 chr5A 81.915 94 11 6 2442 2533 544722086 544721997 1.240000e-09 75.0
52 TraesCS7B01G117200 chr5A 81.915 94 11 6 2442 2533 544787946 544787857 1.240000e-09 75.0
53 TraesCS7B01G117200 chr3B 88.889 54 6 0 2572 2625 782485467 782485520 2.080000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G117200 chr7B 136886549 136889781 3232 True 5971 5971 100.000 1 3233 1 chr7B.!!$R1 3232
1 TraesCS7B01G117200 chr7B 14931169 14931769 600 False 590 590 84.603 3 597 1 chr7B.!!$F1 594
2 TraesCS7B01G117200 chr7D 170606875 170609095 2220 True 3035 3035 91.241 1 2248 1 chr7D.!!$R3 2247
3 TraesCS7B01G117200 chr7D 92215676 92216282 606 True 664 664 86.656 1 597 1 chr7D.!!$R2 596
4 TraesCS7B01G117200 chr7A 173492302 173493929 1627 True 2209 2209 91.394 619 2234 1 chr7A.!!$R2 1615
5 TraesCS7B01G117200 chr7A 94311978 94312582 604 True 667 667 86.820 1 597 1 chr7A.!!$R1 596
6 TraesCS7B01G117200 chr2A 706273496 706274164 668 True 719 719 86.289 2572 3233 1 chr2A.!!$R4 661
7 TraesCS7B01G117200 chr1D 460746089 460746681 592 True 671 671 87.059 1 595 1 chr1D.!!$R2 594
8 TraesCS7B01G117200 chr1D 402432396 402432994 598 True 606 606 85.025 1 597 1 chr1D.!!$R1 596
9 TraesCS7B01G117200 chrUn 8093113 8093707 594 True 662 662 86.723 1 595 1 chrUn.!!$R1 594
10 TraesCS7B01G117200 chr4A 690797873 690798528 655 False 628 628 83.939 2574 3233 1 chr4A.!!$F1 659
11 TraesCS7B01G117200 chr3D 583050816 583051413 597 True 617 617 85.362 1 604 1 chr3D.!!$R1 603
12 TraesCS7B01G117200 chr5D 505028122 505028722 600 True 608 608 85.240 3 593 1 chr5D.!!$R1 590
13 TraesCS7B01G117200 chr2D 450206870 450207464 594 True 590 590 84.564 1 596 1 chr2D.!!$R2 595
14 TraesCS7B01G117200 chr2D 9373355 9374020 665 False 318 318 75.852 2574 3229 1 chr2D.!!$F1 655
15 TraesCS7B01G117200 chr6D 18870682 18871201 519 True 529 529 85.009 2708 3233 1 chr6D.!!$R1 525
16 TraesCS7B01G117200 chr4B 364350358 364351024 666 False 462 462 79.464 2572 3232 1 chr4B.!!$F3 660
17 TraesCS7B01G117200 chr4B 23318128 23318790 662 False 420 420 78.625 2572 3220 1 chr4B.!!$F1 648

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
474 497 0.817654 CGACACATGCAGACTAGGGA 59.182 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2514 0.032017 ATGGAACGGAGGGAGTAGCT 60.032 55.0 0.0 0.0 0.0 3.32 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
64 65 3.326006 AGATCATGATCGGGTACATGCTT 59.674 43.478 26.09 5.13 42.17 3.91
110 111 3.533606 CCATGAAGGTGATCGTCTTCT 57.466 47.619 20.95 9.82 39.85 2.85
177 179 4.124351 CTTCGCCGTGACCGCCTA 62.124 66.667 0.00 0.00 0.00 3.93
231 234 7.810759 TGTTGGTTTAAGACTTGAGTTTTGTTC 59.189 33.333 0.00 0.00 0.00 3.18
232 235 6.548171 TGGTTTAAGACTTGAGTTTTGTTCG 58.452 36.000 0.00 0.00 0.00 3.95
245 248 8.301730 TGAGTTTTGTTCGAAACTTATCGTAT 57.698 30.769 16.26 0.00 46.73 3.06
306 312 3.789224 GTGTTTGTGCCTAAGTTTGTTCG 59.211 43.478 0.00 0.00 0.00 3.95
388 408 2.292267 CCACACAACTATCCTGGATGC 58.708 52.381 19.42 0.00 0.00 3.91
402 422 3.244146 CCTGGATGCAACCAAACAATCAA 60.244 43.478 17.27 0.00 39.59 2.57
416 436 5.675684 AACAATCAAACTTGTGTTTCCCT 57.324 34.783 0.00 0.00 43.75 4.20
450 473 2.094078 GCAACCAAATAGCATGCCTTCA 60.094 45.455 15.66 0.00 0.00 3.02
467 490 3.189080 CCTTCAATTTCGACACATGCAGA 59.811 43.478 0.00 0.00 0.00 4.26
472 495 2.654749 TTCGACACATGCAGACTAGG 57.345 50.000 0.00 0.00 0.00 3.02
474 497 0.817654 CGACACATGCAGACTAGGGA 59.182 55.000 0.00 0.00 0.00 4.20
539 562 2.694397 TCATATGCTAAGCCAGACCCT 58.306 47.619 0.00 0.00 0.00 4.34
543 566 6.022958 TCATATGCTAAGCCAGACCCTATTA 58.977 40.000 0.00 0.00 0.00 0.98
553 576 7.541916 AGCCAGACCCTATTAAGATAAGTAC 57.458 40.000 0.00 0.00 0.00 2.73
582 605 5.658190 AGTGCCTAAAAATGATGCAGGTAAT 59.342 36.000 0.00 0.00 31.69 1.89
598 621 4.634004 CAGGTAATCAAACGCATCCTTACA 59.366 41.667 0.00 0.00 0.00 2.41
611 634 3.965379 TCCTTACAACCATAGCGTTGA 57.035 42.857 8.36 0.00 44.88 3.18
630 653 5.198274 GTTGAAAAACACGTGACAGATCTC 58.802 41.667 25.01 9.31 0.00 2.75
677 702 1.893137 GGAATGGTTGGTGAACTTCCC 59.107 52.381 0.00 0.00 33.31 3.97
683 708 2.230660 GTTGGTGAACTTCCCTTCCTG 58.769 52.381 0.00 0.00 0.00 3.86
697 722 2.266376 TTCCTGGATCTCGACACGCG 62.266 60.000 3.53 3.53 42.69 6.01
757 810 1.207593 GCGCACCTGTTTAGCACTG 59.792 57.895 0.30 0.00 0.00 3.66
813 866 3.236816 CCGCATACTAATTACGTACCGG 58.763 50.000 0.00 0.00 32.55 5.28
884 937 3.060615 GCCACTTCCAGCTGCCAG 61.061 66.667 8.66 8.54 0.00 4.85
1083 1140 2.903357 CACTATGTGCTCCCCGCT 59.097 61.111 0.00 0.00 40.11 5.52
1649 1720 2.823147 CCTAGACGAGCCGGACGT 60.823 66.667 22.89 22.89 46.58 4.34
1777 1848 2.579201 GCTGCCTCGCTCCTAACA 59.421 61.111 0.00 0.00 0.00 2.41
2022 2093 1.255667 TACAGGTGGAGGAGTTCGCC 61.256 60.000 0.00 0.00 35.75 5.54
2071 2142 1.445716 GGTGAGGATGCTGCTGATGC 61.446 60.000 0.00 0.00 40.20 3.91
2154 2225 0.388649 CGGAGAAGTTCAGGGTGTCG 60.389 60.000 5.50 0.00 0.00 4.35
2211 2282 0.038618 ACGAGTGCAACGACATGCTA 60.039 50.000 18.81 0.00 46.54 3.49
2212 2283 1.067693 CGAGTGCAACGACATGCTAA 58.932 50.000 8.56 0.00 46.54 3.09
2214 2285 2.535534 CGAGTGCAACGACATGCTAATG 60.536 50.000 8.56 0.00 46.54 1.90
2234 2305 1.064060 GCACATGCTGATCGGTTAACC 59.936 52.381 15.13 15.13 38.21 2.85
2236 2307 2.746904 CACATGCTGATCGGTTAACCAA 59.253 45.455 24.14 6.59 35.14 3.67
2244 2315 5.622914 GCTGATCGGTTAACCAACAGTACTA 60.623 44.000 27.60 8.06 36.29 1.82
2248 2319 5.772521 TCGGTTAACCAACAGTACTACTTC 58.227 41.667 24.14 0.00 36.29 3.01
2249 2320 4.925646 CGGTTAACCAACAGTACTACTTCC 59.074 45.833 24.14 0.00 36.29 3.46
2250 2321 4.925646 GGTTAACCAACAGTACTACTTCCG 59.074 45.833 20.12 0.00 36.29 4.30
2251 2322 5.509670 GGTTAACCAACAGTACTACTTCCGT 60.510 44.000 20.12 0.00 36.29 4.69
2252 2323 4.677673 AACCAACAGTACTACTTCCGTT 57.322 40.909 0.00 0.00 0.00 4.44
2253 2324 4.677673 ACCAACAGTACTACTTCCGTTT 57.322 40.909 0.00 0.00 0.00 3.60
2254 2325 4.625028 ACCAACAGTACTACTTCCGTTTC 58.375 43.478 0.00 0.00 0.00 2.78
2255 2326 4.099881 ACCAACAGTACTACTTCCGTTTCA 59.900 41.667 0.00 0.00 0.00 2.69
2256 2327 5.051816 CCAACAGTACTACTTCCGTTTCAA 58.948 41.667 0.00 0.00 0.00 2.69
2257 2328 5.524646 CCAACAGTACTACTTCCGTTTCAAA 59.475 40.000 0.00 0.00 0.00 2.69
2258 2329 6.037391 CCAACAGTACTACTTCCGTTTCAAAA 59.963 38.462 0.00 0.00 0.00 2.44
2259 2330 7.414319 CCAACAGTACTACTTCCGTTTCAAAAA 60.414 37.037 0.00 0.00 0.00 1.94
2260 2331 7.242914 ACAGTACTACTTCCGTTTCAAAAAG 57.757 36.000 0.00 0.00 0.00 2.27
2261 2332 6.134061 CAGTACTACTTCCGTTTCAAAAAGC 58.866 40.000 0.00 0.00 0.00 3.51
2262 2333 6.018180 CAGTACTACTTCCGTTTCAAAAAGCT 60.018 38.462 0.00 0.00 0.00 3.74
2263 2334 5.830000 ACTACTTCCGTTTCAAAAAGCTT 57.170 34.783 0.00 0.00 0.00 3.74
2264 2335 5.578776 ACTACTTCCGTTTCAAAAAGCTTG 58.421 37.500 0.00 0.00 0.00 4.01
2265 2336 4.450082 ACTTCCGTTTCAAAAAGCTTGT 57.550 36.364 0.00 0.00 0.00 3.16
2266 2337 4.421058 ACTTCCGTTTCAAAAAGCTTGTC 58.579 39.130 0.00 0.00 0.00 3.18
2267 2338 4.157840 ACTTCCGTTTCAAAAAGCTTGTCT 59.842 37.500 0.00 0.00 0.00 3.41
2268 2339 4.712122 TCCGTTTCAAAAAGCTTGTCTT 57.288 36.364 0.00 0.00 36.34 3.01
2269 2340 4.420168 TCCGTTTCAAAAAGCTTGTCTTG 58.580 39.130 0.00 4.79 34.67 3.02
2270 2341 4.082463 TCCGTTTCAAAAAGCTTGTCTTGT 60.082 37.500 0.00 0.00 34.67 3.16
2271 2342 5.124138 TCCGTTTCAAAAAGCTTGTCTTGTA 59.876 36.000 0.00 0.00 34.67 2.41
2272 2343 5.977129 CCGTTTCAAAAAGCTTGTCTTGTAT 59.023 36.000 0.00 0.00 34.67 2.29
2273 2344 6.475402 CCGTTTCAAAAAGCTTGTCTTGTATT 59.525 34.615 0.00 0.00 34.67 1.89
2274 2345 7.646130 CCGTTTCAAAAAGCTTGTCTTGTATTA 59.354 33.333 0.00 0.00 34.67 0.98
2275 2346 9.180678 CGTTTCAAAAAGCTTGTCTTGTATTAT 57.819 29.630 0.00 0.00 34.67 1.28
2284 2355 9.988350 AAGCTTGTCTTGTATTATTGAAATACG 57.012 29.630 0.00 0.00 36.24 3.06
2285 2356 8.612619 AGCTTGTCTTGTATTATTGAAATACGG 58.387 33.333 4.06 0.97 36.24 4.02
2286 2357 8.609176 GCTTGTCTTGTATTATTGAAATACGGA 58.391 33.333 4.06 2.83 36.24 4.69
2289 2360 9.607988 TGTCTTGTATTATTGAAATACGGATGT 57.392 29.630 4.06 0.00 36.24 3.06
2307 2378 8.644318 ACGGATGTATCTAACACTAAAATGTC 57.356 34.615 0.00 0.00 42.09 3.06
2308 2379 8.475639 ACGGATGTATCTAACACTAAAATGTCT 58.524 33.333 0.00 0.00 42.09 3.41
2309 2380 9.961265 CGGATGTATCTAACACTAAAATGTCTA 57.039 33.333 0.00 0.00 42.09 2.59
2391 2462 8.579850 TTACTTTACTATTACTCCCTTCGTCA 57.420 34.615 0.00 0.00 0.00 4.35
2392 2463 6.861144 ACTTTACTATTACTCCCTTCGTCAC 58.139 40.000 0.00 0.00 0.00 3.67
2393 2464 5.490139 TTACTATTACTCCCTTCGTCACG 57.510 43.478 0.00 0.00 0.00 4.35
2394 2465 3.614092 ACTATTACTCCCTTCGTCACGA 58.386 45.455 0.00 0.00 0.00 4.35
2395 2466 4.012374 ACTATTACTCCCTTCGTCACGAA 58.988 43.478 13.02 13.02 43.75 3.85
2396 2467 3.947910 ATTACTCCCTTCGTCACGAAA 57.052 42.857 14.73 0.00 45.23 3.46
2397 2468 3.947910 TTACTCCCTTCGTCACGAAAT 57.052 42.857 14.73 0.19 45.23 2.17
2398 2469 5.587388 ATTACTCCCTTCGTCACGAAATA 57.413 39.130 14.73 1.34 45.23 1.40
2399 2470 3.227810 ACTCCCTTCGTCACGAAATAC 57.772 47.619 14.73 0.00 45.23 1.89
2400 2471 2.824341 ACTCCCTTCGTCACGAAATACT 59.176 45.455 14.73 0.00 45.23 2.12
2401 2472 3.257624 ACTCCCTTCGTCACGAAATACTT 59.742 43.478 14.73 0.00 45.23 2.24
2402 2473 3.581755 TCCCTTCGTCACGAAATACTTG 58.418 45.455 14.73 0.66 45.23 3.16
2403 2474 3.006110 TCCCTTCGTCACGAAATACTTGT 59.994 43.478 14.73 0.00 45.23 3.16
2404 2475 3.367025 CCCTTCGTCACGAAATACTTGTC 59.633 47.826 14.73 0.00 45.23 3.18
2405 2476 3.985279 CCTTCGTCACGAAATACTTGTCA 59.015 43.478 14.73 0.00 45.23 3.58
2406 2477 4.625742 CCTTCGTCACGAAATACTTGTCAT 59.374 41.667 14.73 0.00 45.23 3.06
2407 2478 5.220228 CCTTCGTCACGAAATACTTGTCATC 60.220 44.000 14.73 0.00 45.23 2.92
2408 2479 4.800784 TCGTCACGAAATACTTGTCATCA 58.199 39.130 0.00 0.00 31.06 3.07
2409 2480 5.224135 TCGTCACGAAATACTTGTCATCAA 58.776 37.500 0.00 0.00 31.06 2.57
2410 2481 5.692654 TCGTCACGAAATACTTGTCATCAAA 59.307 36.000 0.00 0.00 31.06 2.69
2411 2482 6.201234 TCGTCACGAAATACTTGTCATCAAAA 59.799 34.615 0.00 0.00 31.06 2.44
2412 2483 7.015289 CGTCACGAAATACTTGTCATCAAAAT 58.985 34.615 0.00 0.00 32.87 1.82
2413 2484 7.006476 CGTCACGAAATACTTGTCATCAAAATG 59.994 37.037 0.00 0.00 32.87 2.32
2414 2485 7.271223 GTCACGAAATACTTGTCATCAAAATGG 59.729 37.037 0.00 0.00 33.42 3.16
2415 2486 7.174080 TCACGAAATACTTGTCATCAAAATGGA 59.826 33.333 0.00 0.00 33.42 3.41
2416 2487 7.970061 CACGAAATACTTGTCATCAAAATGGAT 59.030 33.333 0.00 0.00 33.42 3.41
2417 2488 9.173021 ACGAAATACTTGTCATCAAAATGGATA 57.827 29.630 0.00 0.00 33.42 2.59
2424 2495 8.526147 ACTTGTCATCAAAATGGATAAAAGAGG 58.474 33.333 0.00 0.00 33.42 3.69
2425 2496 8.648698 TTGTCATCAAAATGGATAAAAGAGGA 57.351 30.769 0.00 0.00 33.42 3.71
2426 2497 8.827832 TGTCATCAAAATGGATAAAAGAGGAT 57.172 30.769 0.00 0.00 33.42 3.24
2427 2498 8.689061 TGTCATCAAAATGGATAAAAGAGGATG 58.311 33.333 0.00 0.00 33.42 3.51
2428 2499 8.689972 GTCATCAAAATGGATAAAAGAGGATGT 58.310 33.333 0.00 0.00 33.42 3.06
2429 2500 9.919416 TCATCAAAATGGATAAAAGAGGATGTA 57.081 29.630 0.00 0.00 33.42 2.29
2432 2503 9.056005 TCAAAATGGATAAAAGAGGATGTATCG 57.944 33.333 0.00 0.00 0.00 2.92
2433 2504 9.056005 CAAAATGGATAAAAGAGGATGTATCGA 57.944 33.333 0.00 0.00 0.00 3.59
2434 2505 8.839310 AAATGGATAAAAGAGGATGTATCGAG 57.161 34.615 0.00 0.00 0.00 4.04
2435 2506 6.978674 TGGATAAAAGAGGATGTATCGAGT 57.021 37.500 0.00 0.00 0.00 4.18
2436 2507 8.651589 ATGGATAAAAGAGGATGTATCGAGTA 57.348 34.615 0.00 0.00 0.00 2.59
2437 2508 7.883217 TGGATAAAAGAGGATGTATCGAGTAC 58.117 38.462 0.00 0.00 0.00 2.73
2438 2509 7.724506 TGGATAAAAGAGGATGTATCGAGTACT 59.275 37.037 0.00 0.00 34.27 2.73
2439 2510 9.228949 GGATAAAAGAGGATGTATCGAGTACTA 57.771 37.037 0.00 0.00 34.27 1.82
2445 2516 8.271312 AGAGGATGTATCGAGTACTAATTAGC 57.729 38.462 12.54 0.00 34.27 3.09
2446 2517 8.104566 AGAGGATGTATCGAGTACTAATTAGCT 58.895 37.037 12.54 2.42 34.27 3.32
2447 2518 9.381033 GAGGATGTATCGAGTACTAATTAGCTA 57.619 37.037 12.54 0.00 34.27 3.32
2448 2519 9.165035 AGGATGTATCGAGTACTAATTAGCTAC 57.835 37.037 12.54 12.93 34.27 3.58
2449 2520 9.165035 GGATGTATCGAGTACTAATTAGCTACT 57.835 37.037 19.20 19.20 34.27 2.57
2451 2522 8.545229 TGTATCGAGTACTAATTAGCTACTCC 57.455 38.462 27.53 20.72 35.69 3.85
2452 2523 7.605691 TGTATCGAGTACTAATTAGCTACTCCC 59.394 40.741 27.53 20.13 35.69 4.30
2453 2524 6.185114 TCGAGTACTAATTAGCTACTCCCT 57.815 41.667 27.53 12.38 35.69 4.20
2454 2525 6.229733 TCGAGTACTAATTAGCTACTCCCTC 58.770 44.000 27.53 16.68 35.69 4.30
2455 2526 5.412286 CGAGTACTAATTAGCTACTCCCTCC 59.588 48.000 27.53 16.17 35.69 4.30
2456 2527 5.315348 AGTACTAATTAGCTACTCCCTCCG 58.685 45.833 12.54 0.00 0.00 4.63
2457 2528 4.181799 ACTAATTAGCTACTCCCTCCGT 57.818 45.455 12.54 0.00 0.00 4.69
2458 2529 4.544683 ACTAATTAGCTACTCCCTCCGTT 58.455 43.478 12.54 0.00 0.00 4.44
2459 2530 4.583907 ACTAATTAGCTACTCCCTCCGTTC 59.416 45.833 12.54 0.00 0.00 3.95
2460 2531 1.772836 TTAGCTACTCCCTCCGTTCC 58.227 55.000 0.00 0.00 0.00 3.62
2461 2532 0.627451 TAGCTACTCCCTCCGTTCCA 59.373 55.000 0.00 0.00 0.00 3.53
2462 2533 0.032017 AGCTACTCCCTCCGTTCCAT 60.032 55.000 0.00 0.00 0.00 3.41
2463 2534 1.217183 AGCTACTCCCTCCGTTCCATA 59.783 52.381 0.00 0.00 0.00 2.74
2464 2535 2.037144 GCTACTCCCTCCGTTCCATAA 58.963 52.381 0.00 0.00 0.00 1.90
2465 2536 2.633481 GCTACTCCCTCCGTTCCATAAT 59.367 50.000 0.00 0.00 0.00 1.28
2466 2537 3.830755 GCTACTCCCTCCGTTCCATAATA 59.169 47.826 0.00 0.00 0.00 0.98
2467 2538 4.466726 GCTACTCCCTCCGTTCCATAATAT 59.533 45.833 0.00 0.00 0.00 1.28
2468 2539 5.655532 GCTACTCCCTCCGTTCCATAATATA 59.344 44.000 0.00 0.00 0.00 0.86
2469 2540 5.997384 ACTCCCTCCGTTCCATAATATAC 57.003 43.478 0.00 0.00 0.00 1.47
2470 2541 4.461781 ACTCCCTCCGTTCCATAATATACG 59.538 45.833 0.00 0.00 0.00 3.06
2471 2542 4.665451 TCCCTCCGTTCCATAATATACGA 58.335 43.478 0.00 0.00 36.16 3.43
2472 2543 4.460382 TCCCTCCGTTCCATAATATACGAC 59.540 45.833 0.00 0.00 36.16 4.34
2473 2544 4.409570 CCTCCGTTCCATAATATACGACG 58.590 47.826 0.00 0.00 36.16 5.12
2474 2545 4.083110 CCTCCGTTCCATAATATACGACGT 60.083 45.833 5.52 5.52 36.16 4.34
2475 2546 5.437289 TCCGTTCCATAATATACGACGTT 57.563 39.130 5.50 0.00 36.16 3.99
2476 2547 5.830912 TCCGTTCCATAATATACGACGTTT 58.169 37.500 5.50 0.00 36.16 3.60
2477 2548 6.272318 TCCGTTCCATAATATACGACGTTTT 58.728 36.000 5.50 0.69 36.16 2.43
2478 2549 6.756074 TCCGTTCCATAATATACGACGTTTTT 59.244 34.615 5.50 0.31 36.16 1.94
2525 2596 7.941795 AACGTTTTATATTATGAGACGGAGG 57.058 36.000 13.58 0.00 33.74 4.30
2526 2597 6.453092 ACGTTTTATATTATGAGACGGAGGG 58.547 40.000 13.58 0.00 33.74 4.30
2527 2598 6.266103 ACGTTTTATATTATGAGACGGAGGGA 59.734 38.462 13.58 0.00 33.74 4.20
2528 2599 6.807230 CGTTTTATATTATGAGACGGAGGGAG 59.193 42.308 4.26 0.00 0.00 4.30
2529 2600 7.523380 CGTTTTATATTATGAGACGGAGGGAGT 60.523 40.741 4.26 0.00 0.00 3.85
2530 2601 8.800332 GTTTTATATTATGAGACGGAGGGAGTA 58.200 37.037 0.00 0.00 0.00 2.59
2531 2602 8.577048 TTTATATTATGAGACGGAGGGAGTAG 57.423 38.462 0.00 0.00 0.00 2.57
2532 2603 2.273538 TATGAGACGGAGGGAGTAGC 57.726 55.000 0.00 0.00 0.00 3.58
2533 2604 0.553819 ATGAGACGGAGGGAGTAGCT 59.446 55.000 0.00 0.00 0.00 3.32
2534 2605 0.331954 TGAGACGGAGGGAGTAGCTT 59.668 55.000 0.00 0.00 0.00 3.74
2535 2606 0.741915 GAGACGGAGGGAGTAGCTTG 59.258 60.000 0.00 0.00 0.00 4.01
2536 2607 0.684805 AGACGGAGGGAGTAGCTTGG 60.685 60.000 0.00 0.00 0.00 3.61
2537 2608 0.971447 GACGGAGGGAGTAGCTTGGT 60.971 60.000 0.00 0.00 0.00 3.67
2538 2609 0.333993 ACGGAGGGAGTAGCTTGGTA 59.666 55.000 0.00 0.00 0.00 3.25
2539 2610 1.272872 ACGGAGGGAGTAGCTTGGTAA 60.273 52.381 0.00 0.00 0.00 2.85
2540 2611 2.040178 CGGAGGGAGTAGCTTGGTAAT 58.960 52.381 0.00 0.00 0.00 1.89
2541 2612 2.434702 CGGAGGGAGTAGCTTGGTAATT 59.565 50.000 0.00 0.00 0.00 1.40
2542 2613 3.118371 CGGAGGGAGTAGCTTGGTAATTT 60.118 47.826 0.00 0.00 0.00 1.82
2543 2614 4.200092 GGAGGGAGTAGCTTGGTAATTTG 58.800 47.826 0.00 0.00 0.00 2.32
2544 2615 4.080526 GGAGGGAGTAGCTTGGTAATTTGA 60.081 45.833 0.00 0.00 0.00 2.69
2545 2616 5.398012 GGAGGGAGTAGCTTGGTAATTTGAT 60.398 44.000 0.00 0.00 0.00 2.57
2546 2617 5.440610 AGGGAGTAGCTTGGTAATTTGATG 58.559 41.667 0.00 0.00 0.00 3.07
2547 2618 4.580580 GGGAGTAGCTTGGTAATTTGATGG 59.419 45.833 0.00 0.00 0.00 3.51
2548 2619 5.437060 GGAGTAGCTTGGTAATTTGATGGA 58.563 41.667 0.00 0.00 0.00 3.41
2549 2620 5.297029 GGAGTAGCTTGGTAATTTGATGGAC 59.703 44.000 0.00 0.00 0.00 4.02
2550 2621 5.193679 AGTAGCTTGGTAATTTGATGGACC 58.806 41.667 0.00 0.00 0.00 4.46
2551 2622 3.016736 AGCTTGGTAATTTGATGGACCG 58.983 45.455 0.00 0.00 34.49 4.79
2552 2623 3.013921 GCTTGGTAATTTGATGGACCGA 58.986 45.455 0.00 0.00 34.49 4.69
2553 2624 3.065371 GCTTGGTAATTTGATGGACCGAG 59.935 47.826 5.90 5.90 43.70 4.63
2554 2625 3.992943 TGGTAATTTGATGGACCGAGT 57.007 42.857 0.00 0.00 34.49 4.18
2555 2626 5.423704 TTGGTAATTTGATGGACCGAGTA 57.576 39.130 0.00 0.00 34.49 2.59
2556 2627 5.623956 TGGTAATTTGATGGACCGAGTAT 57.376 39.130 0.00 0.00 34.49 2.12
2557 2628 5.364778 TGGTAATTTGATGGACCGAGTATG 58.635 41.667 0.00 0.00 34.49 2.39
2558 2629 5.104693 TGGTAATTTGATGGACCGAGTATGT 60.105 40.000 0.00 0.00 34.49 2.29
2559 2630 5.236478 GGTAATTTGATGGACCGAGTATGTG 59.764 44.000 0.00 0.00 0.00 3.21
2560 2631 2.309528 TTGATGGACCGAGTATGTGC 57.690 50.000 0.00 0.00 0.00 4.57
2561 2632 1.485124 TGATGGACCGAGTATGTGCT 58.515 50.000 0.00 0.00 0.00 4.40
2562 2633 1.831106 TGATGGACCGAGTATGTGCTT 59.169 47.619 0.00 0.00 0.00 3.91
2563 2634 2.236146 TGATGGACCGAGTATGTGCTTT 59.764 45.455 0.00 0.00 0.00 3.51
2564 2635 2.380084 TGGACCGAGTATGTGCTTTC 57.620 50.000 0.00 0.00 0.00 2.62
2565 2636 1.621317 TGGACCGAGTATGTGCTTTCA 59.379 47.619 0.00 0.00 0.00 2.69
2566 2637 2.037902 TGGACCGAGTATGTGCTTTCAA 59.962 45.455 0.00 0.00 0.00 2.69
2567 2638 2.415512 GGACCGAGTATGTGCTTTCAAC 59.584 50.000 0.00 0.00 0.00 3.18
2568 2639 3.326747 GACCGAGTATGTGCTTTCAACT 58.673 45.455 0.00 0.00 0.00 3.16
2569 2640 4.491676 GACCGAGTATGTGCTTTCAACTA 58.508 43.478 0.00 0.00 0.00 2.24
2570 2641 4.243270 ACCGAGTATGTGCTTTCAACTAC 58.757 43.478 0.00 0.00 0.00 2.73
2696 2784 1.324736 GGCGCAACGAGATAAAGAGTG 59.675 52.381 10.83 0.00 0.00 3.51
2712 2802 0.846693 AGTGTGGAGGGTTCAAAGCT 59.153 50.000 0.00 0.00 0.00 3.74
2761 2852 1.270518 CCTAGGCATTAGAGCACGCAT 60.271 52.381 0.00 0.00 35.83 4.73
2793 2885 1.742308 AAAGAGCACTCCCACCCTAA 58.258 50.000 0.00 0.00 0.00 2.69
2794 2886 1.742308 AAGAGCACTCCCACCCTAAA 58.258 50.000 0.00 0.00 0.00 1.85
2796 2888 0.035343 GAGCACTCCCACCCTAAACC 60.035 60.000 0.00 0.00 0.00 3.27
2797 2889 0.475828 AGCACTCCCACCCTAAACCT 60.476 55.000 0.00 0.00 0.00 3.50
2798 2890 0.404426 GCACTCCCACCCTAAACCTT 59.596 55.000 0.00 0.00 0.00 3.50
2811 2903 2.813226 AAACCTTGCATCGCCGGCTA 62.813 55.000 26.68 15.56 0.00 3.93
2841 2933 3.135225 CCACGTACACTTGGTGAATTCA 58.865 45.455 3.38 3.38 36.96 2.57
2847 2939 6.262273 ACGTACACTTGGTGAATTCATTCTTT 59.738 34.615 12.12 0.00 36.96 2.52
2907 2999 0.107312 GGACTCCACTGCTGCATGAT 60.107 55.000 1.31 0.00 0.00 2.45
2925 3017 8.260270 TGCATGATGATAGAGCATTTGTATAC 57.740 34.615 0.00 0.00 0.00 1.47
2955 3047 2.807045 GTGCGTCAGGAGAGTGCG 60.807 66.667 0.00 0.00 0.00 5.34
2960 3058 1.153862 GTCAGGAGAGTGCGCTCAG 60.154 63.158 28.02 14.83 44.00 3.35
2985 3083 1.359848 AGTTTATTGCGAGTGAGCCG 58.640 50.000 0.00 0.00 36.02 5.52
3016 3114 0.401738 ACGGCGCCCCTATACTAGTA 59.598 55.000 23.46 4.77 0.00 1.82
3021 3119 2.624838 GCGCCCCTATACTAGTACACAA 59.375 50.000 4.31 0.00 0.00 3.33
3027 3125 5.419788 CCCCTATACTAGTACACAACACACA 59.580 44.000 4.31 0.00 0.00 3.72
3032 3130 3.869246 ACTAGTACACAACACACACTTGC 59.131 43.478 0.00 0.00 0.00 4.01
3070 3168 5.488341 GAATCAAGTAGCCCTACAAGTTCA 58.512 41.667 8.06 0.00 38.48 3.18
3081 3179 3.259374 CCTACAAGTTCAGAAGAGGAGCA 59.741 47.826 0.00 0.00 0.00 4.26
3133 3233 2.048127 GCGCTCCAGACGAACCTT 60.048 61.111 0.00 0.00 0.00 3.50
3181 3281 1.497309 TTGCATTCTCGGGGTTCCCT 61.497 55.000 7.87 0.00 42.67 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 0.320421 GGGTCAGCAGCTTGAACGTA 60.320 55.000 0.00 0.00 35.59 3.57
120 121 0.395312 CTTGGTAACCACCTCCACGT 59.605 55.000 0.00 0.00 45.98 4.49
177 179 1.600916 GAACGGGCAACAGGAGCTT 60.601 57.895 0.00 0.00 39.74 3.74
231 234 7.173863 AGCCAACATAATACGATAAGTTTCG 57.826 36.000 0.00 6.08 44.56 3.46
245 248 7.168302 CGTGTCACAAATTTTAAGCCAACATAA 59.832 33.333 3.42 0.00 0.00 1.90
268 272 5.676744 CACAAACACAAGTCTTAATCACGTG 59.323 40.000 9.94 9.94 0.00 4.49
269 273 5.729454 GCACAAACACAAGTCTTAATCACGT 60.729 40.000 0.00 0.00 0.00 4.49
306 312 8.237267 CACACATGGAAAGAACTAAATTAGACC 58.763 37.037 7.06 0.00 0.00 3.85
359 379 4.595781 AGGATAGTTGTGTGGTAACCTTCA 59.404 41.667 0.00 0.00 0.00 3.02
361 381 4.263331 CCAGGATAGTTGTGTGGTAACCTT 60.263 45.833 0.00 0.00 0.00 3.50
388 408 6.479095 AACACAAGTTTGATTGTTTGGTTG 57.521 33.333 0.00 0.00 41.41 3.77
402 422 8.418662 GGACTTATTTAAAGGGAAACACAAGTT 58.581 33.333 0.00 0.00 40.40 2.66
416 436 7.030768 GCTATTTGGTTGCGGACTTATTTAAA 58.969 34.615 0.00 0.00 0.00 1.52
450 473 3.935203 CCTAGTCTGCATGTGTCGAAATT 59.065 43.478 0.00 0.00 0.00 1.82
467 490 1.133976 GTTGCATGCATCCTCCCTAGT 60.134 52.381 23.37 0.00 0.00 2.57
472 495 1.068127 GATTGGTTGCATGCATCCTCC 59.932 52.381 35.85 26.90 36.89 4.30
474 497 1.855295 TGATTGGTTGCATGCATCCT 58.145 45.000 35.85 23.67 36.89 3.24
519 542 2.694397 AGGGTCTGGCTTAGCATATGA 58.306 47.619 6.97 0.00 0.00 2.15
528 551 7.255871 CGTACTTATCTTAATAGGGTCTGGCTT 60.256 40.741 0.00 0.00 0.00 4.35
539 562 7.270047 AGGCACTTTGCGTACTTATCTTAATA 58.730 34.615 0.00 0.00 46.21 0.98
543 566 3.939066 AGGCACTTTGCGTACTTATCTT 58.061 40.909 0.00 0.00 46.21 2.40
553 576 3.061161 GCATCATTTTTAGGCACTTTGCG 59.939 43.478 0.00 0.00 46.21 4.85
582 605 2.852449 TGGTTGTAAGGATGCGTTTGA 58.148 42.857 0.00 0.00 0.00 2.69
598 621 3.065648 ACGTGTTTTTCAACGCTATGGTT 59.934 39.130 0.00 0.00 40.69 3.67
611 634 5.811399 TTTGAGATCTGTCACGTGTTTTT 57.189 34.783 16.51 0.00 0.00 1.94
630 653 9.188588 AGCATTCGATAATGAGCATTTTATTTG 57.811 29.630 0.52 0.00 44.50 2.32
647 671 2.026641 CCAACCATTCCAGCATTCGAT 58.973 47.619 0.00 0.00 0.00 3.59
677 702 0.526524 GCGTGTCGAGATCCAGGAAG 60.527 60.000 0.00 0.00 0.00 3.46
697 722 5.810074 GGTAGAGCTTCAATCTTCTTGACTC 59.190 44.000 0.00 0.00 0.00 3.36
704 729 3.172229 AGCGGTAGAGCTTCAATCTTC 57.828 47.619 0.00 0.00 46.80 2.87
757 810 1.439679 GTGGATTCCACGTGACCTTC 58.560 55.000 19.65 8.08 44.95 3.46
780 833 3.053831 AGTATGCGGCTTACACTTGTT 57.946 42.857 22.94 3.77 0.00 2.83
813 866 1.337447 TGGTGACTAGTTAGCGTTGCC 60.337 52.381 11.66 0.00 0.00 4.52
865 918 2.598394 GGCAGCTGGAAGTGGCAA 60.598 61.111 17.12 0.00 39.23 4.52
1029 1086 0.463833 GGGCAATCGACGGGAGATTT 60.464 55.000 0.00 0.00 36.30 2.17
1032 1089 1.622607 AATGGGCAATCGACGGGAGA 61.623 55.000 0.00 0.00 0.00 3.71
1248 1305 1.280206 GGCACGTCTCGTTGGTGTAC 61.280 60.000 0.00 0.00 38.32 2.90
1380 1437 2.125147 CTCATGGCGCCGAGGAAA 60.125 61.111 23.90 2.33 0.00 3.13
1546 1603 1.737008 GGAACGGCGACCAGAAGTC 60.737 63.158 16.62 0.00 42.54 3.01
1547 1604 2.156051 GAGGAACGGCGACCAGAAGT 62.156 60.000 16.62 0.00 0.00 3.01
1548 1605 1.446272 GAGGAACGGCGACCAGAAG 60.446 63.158 16.62 0.00 0.00 2.85
1549 1606 2.654877 GAGGAACGGCGACCAGAA 59.345 61.111 16.62 0.00 0.00 3.02
1550 1607 3.744719 CGAGGAACGGCGACCAGA 61.745 66.667 16.62 0.00 38.46 3.86
1635 1706 4.052229 CCAACGTCCGGCTCGTCT 62.052 66.667 20.77 11.06 40.69 4.18
1770 1841 1.822990 GTGAGGTCGGTGATGTTAGGA 59.177 52.381 0.00 0.00 0.00 2.94
1773 1844 0.108992 GCGTGAGGTCGGTGATGTTA 60.109 55.000 0.00 0.00 0.00 2.41
1887 1958 3.450559 CTCGTAGTGCGACGGCGAT 62.451 63.158 18.90 0.43 45.68 4.58
2071 2142 2.655364 CATAGCCTCCGTCGCGTG 60.655 66.667 5.77 0.00 0.00 5.34
2105 2176 2.436115 GGTACTTGCTCGGGTGGC 60.436 66.667 0.00 0.00 0.00 5.01
2154 2225 1.738099 CCAGTGTAGGCAGTCACGC 60.738 63.158 0.00 0.00 39.25 5.34
2195 2266 1.131126 GCATTAGCATGTCGTTGCACT 59.869 47.619 9.65 0.00 45.23 4.40
2211 2282 1.466856 AACCGATCAGCATGTGCATT 58.533 45.000 7.83 0.00 45.16 3.56
2212 2283 2.330440 TAACCGATCAGCATGTGCAT 57.670 45.000 7.83 0.00 45.16 3.96
2214 2285 1.064060 GGTTAACCGATCAGCATGTGC 59.936 52.381 9.34 0.00 42.49 4.57
2244 2315 5.336451 AAGACAAGCTTTTTGAAACGGAAGT 60.336 36.000 0.00 0.00 39.29 3.01
2248 2319 4.173256 ACAAGACAAGCTTTTTGAAACGG 58.827 39.130 17.41 0.00 33.60 4.44
2249 2320 7.449934 AATACAAGACAAGCTTTTTGAAACG 57.550 32.000 17.41 0.00 33.60 3.60
2258 2329 9.988350 CGTATTTCAATAATACAAGACAAGCTT 57.012 29.630 0.00 0.00 37.29 3.74
2259 2330 8.612619 CCGTATTTCAATAATACAAGACAAGCT 58.387 33.333 8.02 0.00 33.81 3.74
2260 2331 8.609176 TCCGTATTTCAATAATACAAGACAAGC 58.391 33.333 8.02 0.00 33.81 4.01
2263 2334 9.607988 ACATCCGTATTTCAATAATACAAGACA 57.392 29.630 8.02 0.00 33.81 3.41
2281 2352 9.740239 GACATTTTAGTGTTAGATACATCCGTA 57.260 33.333 0.00 0.00 39.39 4.02
2282 2353 8.475639 AGACATTTTAGTGTTAGATACATCCGT 58.524 33.333 0.00 0.00 39.39 4.69
2283 2354 8.873215 AGACATTTTAGTGTTAGATACATCCG 57.127 34.615 0.00 0.00 39.39 4.18
2365 2436 9.193806 TGACGAAGGGAGTAATAGTAAAGTAAT 57.806 33.333 0.00 0.00 0.00 1.89
2366 2437 8.462016 GTGACGAAGGGAGTAATAGTAAAGTAA 58.538 37.037 0.00 0.00 0.00 2.24
2367 2438 7.201644 CGTGACGAAGGGAGTAATAGTAAAGTA 60.202 40.741 0.00 0.00 0.00 2.24
2368 2439 6.404074 CGTGACGAAGGGAGTAATAGTAAAGT 60.404 42.308 0.00 0.00 0.00 2.66
2369 2440 5.970023 CGTGACGAAGGGAGTAATAGTAAAG 59.030 44.000 0.00 0.00 0.00 1.85
2370 2441 5.647658 TCGTGACGAAGGGAGTAATAGTAAA 59.352 40.000 4.69 0.00 31.06 2.01
2371 2442 5.185454 TCGTGACGAAGGGAGTAATAGTAA 58.815 41.667 4.69 0.00 31.06 2.24
2372 2443 4.769688 TCGTGACGAAGGGAGTAATAGTA 58.230 43.478 4.69 0.00 31.06 1.82
2373 2444 3.614092 TCGTGACGAAGGGAGTAATAGT 58.386 45.455 4.69 0.00 31.06 2.12
2374 2445 4.627611 TTCGTGACGAAGGGAGTAATAG 57.372 45.455 17.28 0.00 41.05 1.73
2375 2446 5.587388 ATTTCGTGACGAAGGGAGTAATA 57.413 39.130 20.17 2.97 46.43 0.98
2376 2447 3.947910 TTTCGTGACGAAGGGAGTAAT 57.052 42.857 20.17 0.00 46.43 1.89
2377 2448 3.947910 ATTTCGTGACGAAGGGAGTAA 57.052 42.857 20.17 4.49 46.43 2.24
2378 2449 4.012374 AGTATTTCGTGACGAAGGGAGTA 58.988 43.478 20.17 5.25 46.43 2.59
2379 2450 2.824341 AGTATTTCGTGACGAAGGGAGT 59.176 45.455 20.17 9.78 46.43 3.85
2380 2451 3.505464 AGTATTTCGTGACGAAGGGAG 57.495 47.619 20.17 0.00 46.43 4.30
2381 2452 3.006110 ACAAGTATTTCGTGACGAAGGGA 59.994 43.478 20.17 6.79 46.43 4.20
2382 2453 3.323243 ACAAGTATTTCGTGACGAAGGG 58.677 45.455 20.17 9.90 46.43 3.95
2383 2454 3.985279 TGACAAGTATTTCGTGACGAAGG 59.015 43.478 20.17 9.59 46.43 3.46
2384 2455 5.344933 TGATGACAAGTATTTCGTGACGAAG 59.655 40.000 20.17 10.35 46.43 3.79
2385 2456 5.224135 TGATGACAAGTATTTCGTGACGAA 58.776 37.500 17.28 17.28 44.28 3.85
2386 2457 4.800784 TGATGACAAGTATTTCGTGACGA 58.199 39.130 2.39 2.39 0.00 4.20
2387 2458 5.509605 TTGATGACAAGTATTTCGTGACG 57.490 39.130 0.00 0.00 0.00 4.35
2388 2459 7.271223 CCATTTTGATGACAAGTATTTCGTGAC 59.729 37.037 0.00 0.00 37.32 3.67
2389 2460 7.174080 TCCATTTTGATGACAAGTATTTCGTGA 59.826 33.333 0.00 0.00 37.32 4.35
2390 2461 7.304735 TCCATTTTGATGACAAGTATTTCGTG 58.695 34.615 0.00 0.00 37.32 4.35
2391 2462 7.447374 TCCATTTTGATGACAAGTATTTCGT 57.553 32.000 0.00 0.00 37.32 3.85
2398 2469 8.526147 CCTCTTTTATCCATTTTGATGACAAGT 58.474 33.333 0.00 0.00 37.32 3.16
2399 2470 8.742777 TCCTCTTTTATCCATTTTGATGACAAG 58.257 33.333 0.00 0.00 37.32 3.16
2400 2471 8.648698 TCCTCTTTTATCCATTTTGATGACAA 57.351 30.769 0.00 0.00 0.00 3.18
2401 2472 8.689061 CATCCTCTTTTATCCATTTTGATGACA 58.311 33.333 0.00 0.00 0.00 3.58
2402 2473 8.689972 ACATCCTCTTTTATCCATTTTGATGAC 58.310 33.333 0.00 0.00 32.39 3.06
2403 2474 8.827832 ACATCCTCTTTTATCCATTTTGATGA 57.172 30.769 0.00 0.00 32.39 2.92
2406 2477 9.056005 CGATACATCCTCTTTTATCCATTTTGA 57.944 33.333 0.00 0.00 0.00 2.69
2407 2478 9.056005 TCGATACATCCTCTTTTATCCATTTTG 57.944 33.333 0.00 0.00 0.00 2.44
2408 2479 9.277783 CTCGATACATCCTCTTTTATCCATTTT 57.722 33.333 0.00 0.00 0.00 1.82
2409 2480 8.432805 ACTCGATACATCCTCTTTTATCCATTT 58.567 33.333 0.00 0.00 0.00 2.32
2410 2481 7.967908 ACTCGATACATCCTCTTTTATCCATT 58.032 34.615 0.00 0.00 0.00 3.16
2411 2482 7.546250 ACTCGATACATCCTCTTTTATCCAT 57.454 36.000 0.00 0.00 0.00 3.41
2412 2483 6.978674 ACTCGATACATCCTCTTTTATCCA 57.021 37.500 0.00 0.00 0.00 3.41
2413 2484 8.113173 AGTACTCGATACATCCTCTTTTATCC 57.887 38.462 0.00 0.00 36.09 2.59
2419 2490 8.732531 GCTAATTAGTACTCGATACATCCTCTT 58.267 37.037 13.91 0.00 36.09 2.85
2420 2491 8.104566 AGCTAATTAGTACTCGATACATCCTCT 58.895 37.037 13.91 0.00 36.09 3.69
2421 2492 8.271312 AGCTAATTAGTACTCGATACATCCTC 57.729 38.462 13.91 0.00 36.09 3.71
2422 2493 9.165035 GTAGCTAATTAGTACTCGATACATCCT 57.835 37.037 13.91 0.50 36.09 3.24
2423 2494 9.165035 AGTAGCTAATTAGTACTCGATACATCC 57.835 37.037 13.91 0.00 36.09 3.51
2425 2496 9.165035 GGAGTAGCTAATTAGTACTCGATACAT 57.835 37.037 27.12 10.77 42.42 2.29
2426 2497 7.605691 GGGAGTAGCTAATTAGTACTCGATACA 59.394 40.741 27.12 3.33 42.42 2.29
2427 2498 7.823799 AGGGAGTAGCTAATTAGTACTCGATAC 59.176 40.741 27.12 21.64 42.42 2.24
2428 2499 7.915930 AGGGAGTAGCTAATTAGTACTCGATA 58.084 38.462 27.12 5.57 42.42 2.92
2429 2500 6.781943 AGGGAGTAGCTAATTAGTACTCGAT 58.218 40.000 27.12 21.31 42.42 3.59
2430 2501 6.185114 AGGGAGTAGCTAATTAGTACTCGA 57.815 41.667 27.12 7.42 42.42 4.04
2431 2502 5.412286 GGAGGGAGTAGCTAATTAGTACTCG 59.588 48.000 27.12 6.16 42.42 4.18
2432 2503 5.412286 CGGAGGGAGTAGCTAATTAGTACTC 59.588 48.000 26.79 26.79 41.29 2.59
2433 2504 5.163109 ACGGAGGGAGTAGCTAATTAGTACT 60.163 44.000 19.20 19.20 0.00 2.73
2434 2505 5.069318 ACGGAGGGAGTAGCTAATTAGTAC 58.931 45.833 13.91 13.47 0.00 2.73
2435 2506 5.316158 ACGGAGGGAGTAGCTAATTAGTA 57.684 43.478 13.91 3.08 0.00 1.82
2436 2507 4.181799 ACGGAGGGAGTAGCTAATTAGT 57.818 45.455 13.91 3.98 0.00 2.24
2437 2508 4.022155 GGAACGGAGGGAGTAGCTAATTAG 60.022 50.000 8.20 8.20 0.00 1.73
2438 2509 3.893813 GGAACGGAGGGAGTAGCTAATTA 59.106 47.826 0.00 0.00 0.00 1.40
2439 2510 2.699321 GGAACGGAGGGAGTAGCTAATT 59.301 50.000 0.00 0.00 0.00 1.40
2440 2511 2.317973 GGAACGGAGGGAGTAGCTAAT 58.682 52.381 0.00 0.00 0.00 1.73
2441 2512 1.006281 TGGAACGGAGGGAGTAGCTAA 59.994 52.381 0.00 0.00 0.00 3.09
2442 2513 0.627451 TGGAACGGAGGGAGTAGCTA 59.373 55.000 0.00 0.00 0.00 3.32
2443 2514 0.032017 ATGGAACGGAGGGAGTAGCT 60.032 55.000 0.00 0.00 0.00 3.32
2444 2515 1.700955 TATGGAACGGAGGGAGTAGC 58.299 55.000 0.00 0.00 0.00 3.58
2445 2516 6.183360 CGTATATTATGGAACGGAGGGAGTAG 60.183 46.154 0.00 0.00 0.00 2.57
2446 2517 5.649395 CGTATATTATGGAACGGAGGGAGTA 59.351 44.000 0.00 0.00 0.00 2.59
2447 2518 4.461781 CGTATATTATGGAACGGAGGGAGT 59.538 45.833 0.00 0.00 0.00 3.85
2448 2519 4.703575 TCGTATATTATGGAACGGAGGGAG 59.296 45.833 0.00 0.00 36.08 4.30
2449 2520 4.460382 GTCGTATATTATGGAACGGAGGGA 59.540 45.833 0.00 0.00 36.08 4.20
2450 2521 4.673580 CGTCGTATATTATGGAACGGAGGG 60.674 50.000 0.00 0.00 36.08 4.30
2451 2522 4.083110 ACGTCGTATATTATGGAACGGAGG 60.083 45.833 0.00 0.00 36.08 4.30
2452 2523 5.039480 ACGTCGTATATTATGGAACGGAG 57.961 43.478 0.00 0.00 36.08 4.63
2453 2524 5.437289 AACGTCGTATATTATGGAACGGA 57.563 39.130 0.00 0.00 36.08 4.69
2454 2525 6.515043 AAAACGTCGTATATTATGGAACGG 57.485 37.500 0.00 0.00 36.08 4.44
2499 2570 8.823818 CCTCCGTCTCATAATATAAAACGTTTT 58.176 33.333 27.65 27.65 0.00 2.43
2500 2571 7.440255 CCCTCCGTCTCATAATATAAAACGTTT 59.560 37.037 7.96 7.96 0.00 3.60
2501 2572 6.927381 CCCTCCGTCTCATAATATAAAACGTT 59.073 38.462 0.00 0.00 0.00 3.99
2502 2573 6.266103 TCCCTCCGTCTCATAATATAAAACGT 59.734 38.462 0.00 0.00 0.00 3.99
2503 2574 6.684686 TCCCTCCGTCTCATAATATAAAACG 58.315 40.000 0.00 0.00 0.00 3.60
2504 2575 7.668492 ACTCCCTCCGTCTCATAATATAAAAC 58.332 38.462 0.00 0.00 0.00 2.43
2505 2576 7.850935 ACTCCCTCCGTCTCATAATATAAAA 57.149 36.000 0.00 0.00 0.00 1.52
2506 2577 7.122353 GCTACTCCCTCCGTCTCATAATATAAA 59.878 40.741 0.00 0.00 0.00 1.40
2507 2578 6.602406 GCTACTCCCTCCGTCTCATAATATAA 59.398 42.308 0.00 0.00 0.00 0.98
2508 2579 6.069556 AGCTACTCCCTCCGTCTCATAATATA 60.070 42.308 0.00 0.00 0.00 0.86
2509 2580 4.951094 GCTACTCCCTCCGTCTCATAATAT 59.049 45.833 0.00 0.00 0.00 1.28
2510 2581 4.043059 AGCTACTCCCTCCGTCTCATAATA 59.957 45.833 0.00 0.00 0.00 0.98
2511 2582 3.158676 GCTACTCCCTCCGTCTCATAAT 58.841 50.000 0.00 0.00 0.00 1.28
2512 2583 2.175069 AGCTACTCCCTCCGTCTCATAA 59.825 50.000 0.00 0.00 0.00 1.90
2513 2584 1.775459 AGCTACTCCCTCCGTCTCATA 59.225 52.381 0.00 0.00 0.00 2.15
2514 2585 0.553819 AGCTACTCCCTCCGTCTCAT 59.446 55.000 0.00 0.00 0.00 2.90
2515 2586 0.331954 AAGCTACTCCCTCCGTCTCA 59.668 55.000 0.00 0.00 0.00 3.27
2516 2587 0.741915 CAAGCTACTCCCTCCGTCTC 59.258 60.000 0.00 0.00 0.00 3.36
2517 2588 0.684805 CCAAGCTACTCCCTCCGTCT 60.685 60.000 0.00 0.00 0.00 4.18
2518 2589 0.971447 ACCAAGCTACTCCCTCCGTC 60.971 60.000 0.00 0.00 0.00 4.79
2519 2590 0.333993 TACCAAGCTACTCCCTCCGT 59.666 55.000 0.00 0.00 0.00 4.69
2520 2591 1.481871 TTACCAAGCTACTCCCTCCG 58.518 55.000 0.00 0.00 0.00 4.63
2521 2592 4.080526 TCAAATTACCAAGCTACTCCCTCC 60.081 45.833 0.00 0.00 0.00 4.30
2522 2593 5.099042 TCAAATTACCAAGCTACTCCCTC 57.901 43.478 0.00 0.00 0.00 4.30
2523 2594 5.440610 CATCAAATTACCAAGCTACTCCCT 58.559 41.667 0.00 0.00 0.00 4.20
2524 2595 4.580580 CCATCAAATTACCAAGCTACTCCC 59.419 45.833 0.00 0.00 0.00 4.30
2525 2596 5.297029 GTCCATCAAATTACCAAGCTACTCC 59.703 44.000 0.00 0.00 0.00 3.85
2526 2597 5.297029 GGTCCATCAAATTACCAAGCTACTC 59.703 44.000 0.00 0.00 32.04 2.59
2527 2598 5.193679 GGTCCATCAAATTACCAAGCTACT 58.806 41.667 0.00 0.00 32.04 2.57
2528 2599 4.035208 CGGTCCATCAAATTACCAAGCTAC 59.965 45.833 0.00 0.00 32.04 3.58
2529 2600 4.080807 TCGGTCCATCAAATTACCAAGCTA 60.081 41.667 0.00 0.00 32.04 3.32
2530 2601 3.016736 CGGTCCATCAAATTACCAAGCT 58.983 45.455 0.00 0.00 32.04 3.74
2531 2602 3.013921 TCGGTCCATCAAATTACCAAGC 58.986 45.455 0.00 0.00 32.04 4.01
2532 2603 4.261801 ACTCGGTCCATCAAATTACCAAG 58.738 43.478 0.00 0.00 32.04 3.61
2533 2604 4.295141 ACTCGGTCCATCAAATTACCAA 57.705 40.909 0.00 0.00 32.04 3.67
2534 2605 3.992943 ACTCGGTCCATCAAATTACCA 57.007 42.857 0.00 0.00 32.04 3.25
2535 2606 5.236478 CACATACTCGGTCCATCAAATTACC 59.764 44.000 0.00 0.00 0.00 2.85
2536 2607 5.277345 GCACATACTCGGTCCATCAAATTAC 60.277 44.000 0.00 0.00 0.00 1.89
2537 2608 4.814234 GCACATACTCGGTCCATCAAATTA 59.186 41.667 0.00 0.00 0.00 1.40
2538 2609 3.627577 GCACATACTCGGTCCATCAAATT 59.372 43.478 0.00 0.00 0.00 1.82
2539 2610 3.118261 AGCACATACTCGGTCCATCAAAT 60.118 43.478 0.00 0.00 0.00 2.32
2540 2611 2.236146 AGCACATACTCGGTCCATCAAA 59.764 45.455 0.00 0.00 0.00 2.69
2541 2612 1.831106 AGCACATACTCGGTCCATCAA 59.169 47.619 0.00 0.00 0.00 2.57
2542 2613 1.485124 AGCACATACTCGGTCCATCA 58.515 50.000 0.00 0.00 0.00 3.07
2543 2614 2.604046 AAGCACATACTCGGTCCATC 57.396 50.000 0.00 0.00 0.00 3.51
2544 2615 2.236146 TGAAAGCACATACTCGGTCCAT 59.764 45.455 0.00 0.00 0.00 3.41
2545 2616 1.621317 TGAAAGCACATACTCGGTCCA 59.379 47.619 0.00 0.00 0.00 4.02
2546 2617 2.380084 TGAAAGCACATACTCGGTCC 57.620 50.000 0.00 0.00 0.00 4.46
2547 2618 3.326747 AGTTGAAAGCACATACTCGGTC 58.673 45.455 0.00 0.00 0.00 4.79
2548 2619 3.402628 AGTTGAAAGCACATACTCGGT 57.597 42.857 0.00 0.00 0.00 4.69
2549 2620 4.495422 AGTAGTTGAAAGCACATACTCGG 58.505 43.478 0.00 0.00 0.00 4.63
2550 2621 6.467723 AAAGTAGTTGAAAGCACATACTCG 57.532 37.500 0.00 0.00 29.70 4.18
2583 2654 1.147153 GGGCGCTCCTAGCATCTTT 59.853 57.895 7.64 0.00 42.58 2.52
2625 2696 1.079819 TTGCTACTCTGCCTGTCGC 60.080 57.895 0.00 0.00 38.31 5.19
2696 2784 0.895559 CCCAGCTTTGAACCCTCCAC 60.896 60.000 0.00 0.00 0.00 4.02
2712 2802 1.671054 GTAACTTGCTCGCTGCCCA 60.671 57.895 0.00 0.00 42.00 5.36
2761 2852 0.029300 GCTCTTTTGTGTTGCGAGCA 59.971 50.000 0.00 0.00 44.74 4.26
2793 2885 3.323758 TAGCCGGCGATGCAAGGTT 62.324 57.895 23.20 0.95 32.15 3.50
2794 2886 3.781307 TAGCCGGCGATGCAAGGT 61.781 61.111 23.20 1.83 32.15 3.50
2796 2888 2.363711 TAGGTAGCCGGCGATGCAAG 62.364 60.000 23.20 0.00 0.00 4.01
2797 2889 2.363711 CTAGGTAGCCGGCGATGCAA 62.364 60.000 23.20 5.48 0.00 4.08
2798 2890 2.835895 TAGGTAGCCGGCGATGCA 60.836 61.111 23.20 4.70 0.00 3.96
2811 2903 2.677524 TGTACGTGGCGGCTAGGT 60.678 61.111 15.71 15.71 0.00 3.08
2907 2999 9.626045 CTAACATCGTATACAAATGCTCTATCA 57.374 33.333 12.79 0.00 0.00 2.15
2925 3017 1.421410 GACGCACCCAGCTAACATCG 61.421 60.000 0.00 0.00 42.61 3.84
2955 3047 3.682858 TCGCAATAAACTTACCACTGAGC 59.317 43.478 0.00 0.00 0.00 4.26
2960 3058 4.435651 GCTCACTCGCAATAAACTTACCAC 60.436 45.833 0.00 0.00 0.00 4.16
2985 3083 1.156034 GGCGCCGTTATGGTCCTTAC 61.156 60.000 12.58 0.00 41.21 2.34
2999 3097 1.543358 GTGTACTAGTATAGGGGCGCC 59.457 57.143 21.18 21.18 44.97 6.53
3016 3114 1.739466 CAGAGCAAGTGTGTGTTGTGT 59.261 47.619 0.00 0.00 0.00 3.72
3021 3119 0.179045 GGGACAGAGCAAGTGTGTGT 60.179 55.000 0.00 0.00 31.30 3.72
3027 3125 1.484444 GGTCCAGGGACAGAGCAAGT 61.484 60.000 19.43 0.00 46.20 3.16
3032 3130 0.461961 GATTCGGTCCAGGGACAGAG 59.538 60.000 19.43 10.38 46.43 3.35
3070 3168 1.985116 GGACCCGTGCTCCTCTTCT 60.985 63.158 0.00 0.00 0.00 2.85
3125 3225 2.193536 GCCCACTTGCAAGGTTCGT 61.194 57.895 29.18 6.94 0.00 3.85
3133 3233 2.877097 TCTTTCTATGCCCACTTGCA 57.123 45.000 0.00 0.00 46.94 4.08
3181 3281 1.522806 GGGTCCGTGCGCATTATGA 60.523 57.895 15.91 5.09 0.00 2.15


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

AutoCloner maintained by Alex Coulton.