Multiple sequence alignment - TraesCS7D01G223700

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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 TraesCS7D01G223700 chr7D 100.000 3176 0 0 1 3176 184524875 184521700 0.000000e+00 5866.0
1 TraesCS7D01G223700 chr7D 88.638 2394 176 44 21 2349 184499376 184501738 0.000000e+00 2826.0
2 TraesCS7D01G223700 chr7D 88.750 80 5 2 821 900 575506521 575506596 9.380000e-16 95.3
3 TraesCS7D01G223700 chr7D 90.411 73 3 2 821 893 2078468 2078400 3.370000e-15 93.5
4 TraesCS7D01G223700 chr7B 95.082 2440 98 11 8 2435 153744651 153742222 0.000000e+00 3821.0
5 TraesCS7D01G223700 chr7B 89.627 1446 87 23 894 2285 153581848 153583284 0.000000e+00 1781.0
6 TraesCS7D01G223700 chr7B 84.663 815 66 17 21 794 153581045 153581841 0.000000e+00 758.0
7 TraesCS7D01G223700 chr7B 91.781 365 30 0 2802 3166 153741707 153741343 2.830000e-140 508.0
8 TraesCS7D01G223700 chr7B 74.703 1261 255 45 924 2161 133707846 133706627 1.310000e-138 503.0
9 TraesCS7D01G223700 chr7B 87.692 130 9 5 2371 2497 153583393 153583518 9.180000e-31 145.0
10 TraesCS7D01G223700 chr7B 90.826 109 4 4 2459 2562 153742227 153742120 1.190000e-29 141.0
11 TraesCS7D01G223700 chr7A 89.197 2305 168 42 21 2274 186098218 186095944 0.000000e+00 2802.0
12 TraesCS7D01G223700 chr7A 92.118 1459 89 19 905 2343 185975455 185976907 0.000000e+00 2034.0
13 TraesCS7D01G223700 chr7A 92.626 773 32 4 2 767 185974639 185975393 0.000000e+00 1088.0
14 TraesCS7D01G223700 chr7A 86.957 368 39 6 2719 3079 185976921 185977286 3.810000e-109 405.0
15 TraesCS7D01G223700 chr7A 79.615 260 21 11 2244 2500 186095939 186095709 1.180000e-34 158.0
16 TraesCS7D01G223700 chr6D 73.413 1260 264 49 952 2174 114224865 114226090 3.810000e-109 405.0
17 TraesCS7D01G223700 chr6A 73.270 1272 254 61 952 2174 142773005 142774239 1.380000e-103 387.0
18 TraesCS7D01G223700 chr6B 73.692 688 148 28 1505 2174 203894892 203895564 1.470000e-58 237.0
19 TraesCS7D01G223700 chrUn 72.616 734 155 31 924 1637 91795842 91795135 1.930000e-47 200.0
20 TraesCS7D01G223700 chrUn 87.500 80 6 2 821 900 99396836 99396911 4.360000e-14 89.8
21 TraesCS7D01G223700 chr3D 90.566 106 10 0 1944 2049 474664327 474664222 1.190000e-29 141.0
22 TraesCS7D01G223700 chr5A 89.873 79 4 1 821 899 603501790 603501716 7.250000e-17 99.0
23 TraesCS7D01G223700 chr5A 82.727 110 16 3 2589 2697 595400743 595400850 9.380000e-16 95.3
24 TraesCS7D01G223700 chr3A 91.781 73 2 1 821 893 574856726 574856794 7.250000e-17 99.0
25 TraesCS7D01G223700 chr4D 88.608 79 5 2 821 899 322032096 322032022 3.370000e-15 93.5
26 TraesCS7D01G223700 chr2A 96.226 53 2 0 2594 2646 770021645 770021697 1.570000e-13 87.9
27 TraesCS7D01G223700 chr5B 86.364 66 2 4 2611 2675 583301596 583301655 7.350000e-07 65.8


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 TraesCS7D01G223700 chr7D 184521700 184524875 3175 True 5866.000000 5866 100.000000 1 3176 1 chr7D.!!$R2 3175
1 TraesCS7D01G223700 chr7D 184499376 184501738 2362 False 2826.000000 2826 88.638000 21 2349 1 chr7D.!!$F1 2328
2 TraesCS7D01G223700 chr7B 153741343 153744651 3308 True 1490.000000 3821 92.563000 8 3166 3 chr7B.!!$R2 3158
3 TraesCS7D01G223700 chr7B 153581045 153583518 2473 False 894.666667 1781 87.327333 21 2497 3 chr7B.!!$F1 2476
4 TraesCS7D01G223700 chr7B 133706627 133707846 1219 True 503.000000 503 74.703000 924 2161 1 chr7B.!!$R1 1237
5 TraesCS7D01G223700 chr7A 186095709 186098218 2509 True 1480.000000 2802 84.406000 21 2500 2 chr7A.!!$R1 2479
6 TraesCS7D01G223700 chr7A 185974639 185977286 2647 False 1175.666667 2034 90.567000 2 3079 3 chr7A.!!$F1 3077
7 TraesCS7D01G223700 chr6D 114224865 114226090 1225 False 405.000000 405 73.413000 952 2174 1 chr6D.!!$F1 1222
8 TraesCS7D01G223700 chr6A 142773005 142774239 1234 False 387.000000 387 73.270000 952 2174 1 chr6A.!!$F1 1222
9 TraesCS7D01G223700 chr6B 203894892 203895564 672 False 237.000000 237 73.692000 1505 2174 1 chr6B.!!$F1 669

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
354 373 1.205064 CGCTGCTTATATGTGCGCC 59.795 57.895 4.18 0.0 40.15 6.53 F
518 544 1.471684 GTCCTCGACGTACCTCATGTT 59.528 52.381 0.00 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1879 1.22184 GCCGATGAGCCTCAGGAAA 59.778 57.895 0.0 0.0 0.0 3.13 R
2409 2678 0.10212 CGGCACCTGAAAACAAGCAA 59.898 50.000 0.0 0.0 0.0 3.91 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
141 149 1.448893 GCGACCGGCAATGAAGGTA 60.449 57.895 0.00 0.00 42.87 3.08
157 165 9.739276 CAATGAAGGTATAAGCCAATTAGGATA 57.261 33.333 0.00 0.00 41.22 2.59
163 172 7.294958 AGGTATAAGCCAATTAGGATACAAGGT 59.705 37.037 0.00 0.00 41.22 3.50
164 173 8.599792 GGTATAAGCCAATTAGGATACAAGGTA 58.400 37.037 0.00 0.00 41.22 3.08
354 373 1.205064 CGCTGCTTATATGTGCGCC 59.795 57.895 4.18 0.00 40.15 6.53
424 443 4.640201 GCACAAGGCTGAGAATAACCATTA 59.360 41.667 0.00 0.00 40.25 1.90
449 475 6.466812 TGTATGCCCACTTACATATCTGATG 58.533 40.000 0.00 0.00 32.98 3.07
518 544 1.471684 GTCCTCGACGTACCTCATGTT 59.528 52.381 0.00 0.00 0.00 2.71
842 917 6.096846 AGTTGTTGAAATATATTGCCCACCTC 59.903 38.462 0.00 0.00 0.00 3.85
877 952 5.007626 TCAGTTCGGACTTTTGAATGAGTTG 59.992 40.000 0.00 0.00 32.54 3.16
888 963 4.824479 TGAATGAGTTGACTGGAGCATA 57.176 40.909 0.00 0.00 0.00 3.14
1637 1797 1.544825 TTCCTCTCCTTCGGCACCAG 61.545 60.000 0.00 0.00 0.00 4.00
1710 1879 2.842936 CCCCGCCGGAACCTCTAT 60.843 66.667 5.05 0.00 0.00 1.98
1998 2167 1.374947 CCTGGAGCTCGGGTTTGAA 59.625 57.895 7.83 0.00 37.13 2.69
2185 2357 1.563655 CGCTGCTGATCGATCAAGC 59.436 57.895 29.84 29.84 37.32 4.01
2188 2361 1.220169 CTGCTGATCGATCAAGCCCG 61.220 60.000 29.99 20.60 36.18 6.13
2199 2372 2.674380 AAGCCCGCTCAAAGCAGG 60.674 61.111 0.00 0.00 42.58 4.85
2231 2435 2.354656 CATCGCATGCATGGCAGC 60.355 61.111 27.34 12.51 43.65 5.25
2292 2552 2.431057 GTCACTAGGTAGATGGTGTGGG 59.569 54.545 0.00 0.00 33.71 4.61
2355 2624 8.694394 CAGCAGCTACATAAGTTTTTCTTTTTC 58.306 33.333 0.00 0.00 37.56 2.29
2357 2626 9.249457 GCAGCTACATAAGTTTTTCTTTTTCTT 57.751 29.630 0.00 0.00 37.56 2.52
2393 2662 9.199982 GAACAACAGCTACATAAGTTAGTGTTA 57.800 33.333 0.00 0.00 29.98 2.41
2394 2663 9.720769 AACAACAGCTACATAAGTTAGTGTTAT 57.279 29.630 0.00 0.00 28.83 1.89
2399 2668 8.969267 CAGCTACATAAGTTAGTGTTATACTGC 58.031 37.037 0.00 0.00 40.65 4.40
2400 2669 8.142551 AGCTACATAAGTTAGTGTTATACTGCC 58.857 37.037 0.00 0.00 40.65 4.85
2401 2670 8.142551 GCTACATAAGTTAGTGTTATACTGCCT 58.857 37.037 0.00 0.00 40.65 4.75
2402 2671 9.680315 CTACATAAGTTAGTGTTATACTGCCTC 57.320 37.037 0.00 0.00 40.65 4.70
2403 2672 7.201145 ACATAAGTTAGTGTTATACTGCCTCG 58.799 38.462 0.00 0.00 40.65 4.63
2404 2673 4.650754 AGTTAGTGTTATACTGCCTCGG 57.349 45.455 0.00 0.00 40.65 4.63
2405 2674 3.121544 GTTAGTGTTATACTGCCTCGGC 58.878 50.000 0.00 0.00 40.65 5.54
2415 2684 2.796651 GCCTCGGCATCTTGCTTG 59.203 61.111 2.41 0.00 44.28 4.01
2416 2685 2.042831 GCCTCGGCATCTTGCTTGT 61.043 57.895 2.41 0.00 44.28 3.16
2417 2686 1.589716 GCCTCGGCATCTTGCTTGTT 61.590 55.000 2.41 0.00 44.28 2.83
2418 2687 0.883833 CCTCGGCATCTTGCTTGTTT 59.116 50.000 0.00 0.00 44.28 2.83
2419 2688 1.270550 CCTCGGCATCTTGCTTGTTTT 59.729 47.619 0.00 0.00 44.28 2.43
2420 2689 2.589014 CTCGGCATCTTGCTTGTTTTC 58.411 47.619 0.00 0.00 44.28 2.29
2421 2690 1.952990 TCGGCATCTTGCTTGTTTTCA 59.047 42.857 0.00 0.00 44.28 2.69
2422 2691 2.030893 TCGGCATCTTGCTTGTTTTCAG 60.031 45.455 0.00 0.00 44.28 3.02
2423 2692 2.680577 GGCATCTTGCTTGTTTTCAGG 58.319 47.619 0.00 0.00 44.28 3.86
2424 2693 2.036346 GGCATCTTGCTTGTTTTCAGGT 59.964 45.455 0.00 0.00 44.28 4.00
2425 2694 3.054878 GCATCTTGCTTGTTTTCAGGTG 58.945 45.455 0.00 0.00 40.96 4.00
2426 2695 2.869233 TCTTGCTTGTTTTCAGGTGC 57.131 45.000 0.00 0.00 0.00 5.01
2427 2696 1.408702 TCTTGCTTGTTTTCAGGTGCC 59.591 47.619 0.00 0.00 0.00 5.01
2428 2697 0.102120 TTGCTTGTTTTCAGGTGCCG 59.898 50.000 0.00 0.00 0.00 5.69
2429 2698 1.034838 TGCTTGTTTTCAGGTGCCGT 61.035 50.000 0.00 0.00 0.00 5.68
2430 2699 0.948678 GCTTGTTTTCAGGTGCCGTA 59.051 50.000 0.00 0.00 0.00 4.02
2431 2700 1.539827 GCTTGTTTTCAGGTGCCGTAT 59.460 47.619 0.00 0.00 0.00 3.06
2432 2701 2.414161 GCTTGTTTTCAGGTGCCGTATC 60.414 50.000 0.00 0.00 0.00 2.24
2433 2702 2.552599 TGTTTTCAGGTGCCGTATCA 57.447 45.000 0.00 0.00 0.00 2.15
2434 2703 2.852449 TGTTTTCAGGTGCCGTATCAA 58.148 42.857 0.00 0.00 0.00 2.57
2435 2704 2.550606 TGTTTTCAGGTGCCGTATCAAC 59.449 45.455 0.00 0.00 0.00 3.18
2436 2705 1.816074 TTTCAGGTGCCGTATCAACC 58.184 50.000 0.00 0.00 0.00 3.77
2437 2706 0.390603 TTCAGGTGCCGTATCAACCG 60.391 55.000 0.00 0.00 0.00 4.44
2438 2707 1.216977 CAGGTGCCGTATCAACCGA 59.783 57.895 0.00 0.00 0.00 4.69
2439 2708 0.179084 CAGGTGCCGTATCAACCGAT 60.179 55.000 0.00 0.00 35.50 4.18
2440 2709 1.067974 CAGGTGCCGTATCAACCGATA 59.932 52.381 0.00 0.00 32.73 2.92
2441 2710 1.340248 AGGTGCCGTATCAACCGATAG 59.660 52.381 0.00 0.00 34.73 2.08
2442 2711 1.338973 GGTGCCGTATCAACCGATAGA 59.661 52.381 0.00 0.00 34.73 1.98
2443 2712 2.391879 GTGCCGTATCAACCGATAGAC 58.608 52.381 0.00 0.00 34.73 2.59
2444 2713 1.338973 TGCCGTATCAACCGATAGACC 59.661 52.381 0.00 0.00 34.73 3.85
2445 2714 1.338973 GCCGTATCAACCGATAGACCA 59.661 52.381 0.00 0.00 34.73 4.02
2446 2715 2.223876 GCCGTATCAACCGATAGACCAA 60.224 50.000 0.00 0.00 34.73 3.67
2447 2716 3.378339 CCGTATCAACCGATAGACCAAC 58.622 50.000 0.00 0.00 34.73 3.77
2448 2717 3.040795 CGTATCAACCGATAGACCAACG 58.959 50.000 0.00 0.00 34.73 4.10
2449 2718 3.488047 CGTATCAACCGATAGACCAACGT 60.488 47.826 0.00 0.00 34.73 3.99
2450 2719 2.357327 TCAACCGATAGACCAACGTG 57.643 50.000 0.00 0.00 39.76 4.49
2451 2720 0.719465 CAACCGATAGACCAACGTGC 59.281 55.000 0.00 0.00 39.76 5.34
2452 2721 0.606604 AACCGATAGACCAACGTGCT 59.393 50.000 0.00 0.00 39.76 4.40
2453 2722 0.606604 ACCGATAGACCAACGTGCTT 59.393 50.000 0.00 0.00 39.76 3.91
2454 2723 0.999406 CCGATAGACCAACGTGCTTG 59.001 55.000 0.00 0.00 39.76 4.01
2469 2738 9.790389 CCAACGTGCTTGGTATATTAAAATAAA 57.210 29.630 0.00 0.00 44.30 1.40
2486 2755 9.935241 TTAAAATAAATAAAGCAGGTCATTGCA 57.065 25.926 0.52 0.00 46.47 4.08
2487 2756 8.845413 AAAATAAATAAAGCAGGTCATTGCAA 57.155 26.923 0.00 0.00 46.47 4.08
2488 2757 8.845413 AAATAAATAAAGCAGGTCATTGCAAA 57.155 26.923 1.71 0.00 46.47 3.68
2489 2758 9.452287 AAATAAATAAAGCAGGTCATTGCAAAT 57.548 25.926 1.71 0.00 46.47 2.32
2490 2759 9.452287 AATAAATAAAGCAGGTCATTGCAAATT 57.548 25.926 1.71 0.00 46.47 1.82
2491 2760 6.730960 AATAAAGCAGGTCATTGCAAATTG 57.269 33.333 1.71 0.00 46.47 2.32
2492 2761 3.756933 AAGCAGGTCATTGCAAATTGT 57.243 38.095 1.71 0.00 46.47 2.71
2493 2762 3.034721 AGCAGGTCATTGCAAATTGTG 57.965 42.857 1.71 0.00 46.47 3.33
2494 2763 2.366266 AGCAGGTCATTGCAAATTGTGT 59.634 40.909 1.71 0.00 46.47 3.72
2495 2764 3.132925 GCAGGTCATTGCAAATTGTGTT 58.867 40.909 1.71 0.00 43.53 3.32
2496 2765 3.184986 GCAGGTCATTGCAAATTGTGTTC 59.815 43.478 1.71 0.00 43.53 3.18
2497 2766 4.624015 CAGGTCATTGCAAATTGTGTTCT 58.376 39.130 1.71 0.00 0.00 3.01
2498 2767 5.051816 CAGGTCATTGCAAATTGTGTTCTT 58.948 37.500 1.71 0.00 0.00 2.52
2499 2768 5.524646 CAGGTCATTGCAAATTGTGTTCTTT 59.475 36.000 1.71 0.00 0.00 2.52
2500 2769 6.037391 CAGGTCATTGCAAATTGTGTTCTTTT 59.963 34.615 1.71 0.00 0.00 2.27
2501 2770 7.224362 CAGGTCATTGCAAATTGTGTTCTTTTA 59.776 33.333 1.71 0.00 0.00 1.52
2502 2771 7.768120 AGGTCATTGCAAATTGTGTTCTTTTAA 59.232 29.630 1.71 0.00 0.00 1.52
2503 2772 8.063630 GGTCATTGCAAATTGTGTTCTTTTAAG 58.936 33.333 1.71 0.00 0.00 1.85
2504 2773 8.816144 GTCATTGCAAATTGTGTTCTTTTAAGA 58.184 29.630 1.71 0.00 0.00 2.10
2505 2774 9.545105 TCATTGCAAATTGTGTTCTTTTAAGAT 57.455 25.926 1.71 0.00 34.49 2.40
2535 2804 8.822805 AGTAGTTTATTCCAAGATAACAGGACA 58.177 33.333 0.00 0.00 0.00 4.02
2536 2805 9.614792 GTAGTTTATTCCAAGATAACAGGACAT 57.385 33.333 0.00 0.00 0.00 3.06
2538 2807 9.178758 AGTTTATTCCAAGATAACAGGACATTC 57.821 33.333 0.00 0.00 0.00 2.67
2539 2808 7.786178 TTATTCCAAGATAACAGGACATTCG 57.214 36.000 0.00 0.00 0.00 3.34
2540 2809 5.414789 TTCCAAGATAACAGGACATTCGA 57.585 39.130 0.00 0.00 0.00 3.71
2541 2810 5.011090 TCCAAGATAACAGGACATTCGAG 57.989 43.478 0.00 0.00 0.00 4.04
2542 2811 4.709886 TCCAAGATAACAGGACATTCGAGA 59.290 41.667 0.00 0.00 0.00 4.04
2543 2812 5.046529 CCAAGATAACAGGACATTCGAGAG 58.953 45.833 0.00 0.00 0.00 3.20
2544 2813 4.927978 AGATAACAGGACATTCGAGAGG 57.072 45.455 0.00 0.00 0.00 3.69
2545 2814 2.961526 TAACAGGACATTCGAGAGGC 57.038 50.000 0.00 0.00 0.00 4.70
2546 2815 0.976641 AACAGGACATTCGAGAGGCA 59.023 50.000 0.00 0.00 0.00 4.75
2547 2816 0.976641 ACAGGACATTCGAGAGGCAA 59.023 50.000 0.00 0.00 0.00 4.52
2548 2817 1.066573 ACAGGACATTCGAGAGGCAAG 60.067 52.381 0.00 0.00 0.00 4.01
2549 2818 1.205655 CAGGACATTCGAGAGGCAAGA 59.794 52.381 0.00 0.00 0.00 3.02
2550 2819 1.480137 AGGACATTCGAGAGGCAAGAG 59.520 52.381 0.00 0.00 0.00 2.85
2551 2820 1.478510 GGACATTCGAGAGGCAAGAGA 59.521 52.381 0.00 0.00 0.00 3.10
2552 2821 2.102252 GGACATTCGAGAGGCAAGAGAT 59.898 50.000 0.00 0.00 0.00 2.75
2553 2822 3.380142 GACATTCGAGAGGCAAGAGATC 58.620 50.000 0.00 0.00 0.00 2.75
2554 2823 2.102252 ACATTCGAGAGGCAAGAGATCC 59.898 50.000 0.00 0.00 0.00 3.36
2555 2824 2.151502 TTCGAGAGGCAAGAGATCCT 57.848 50.000 0.00 0.00 34.90 3.24
2564 2833 5.398603 AGGCAAGAGATCCTCAATATACG 57.601 43.478 0.00 0.00 32.06 3.06
2565 2834 4.221703 AGGCAAGAGATCCTCAATATACGG 59.778 45.833 0.00 0.00 32.06 4.02
2566 2835 4.499183 GCAAGAGATCCTCAATATACGGG 58.501 47.826 0.00 0.00 32.06 5.28
2567 2836 4.621747 GCAAGAGATCCTCAATATACGGGG 60.622 50.000 0.00 0.00 32.06 5.73
2568 2837 4.405756 AGAGATCCTCAATATACGGGGT 57.594 45.455 0.00 0.00 32.06 4.95
2569 2838 4.345854 AGAGATCCTCAATATACGGGGTC 58.654 47.826 0.00 0.00 32.06 4.46
2570 2839 3.442076 AGATCCTCAATATACGGGGTCC 58.558 50.000 0.00 0.00 29.82 4.46
2571 2840 3.077695 AGATCCTCAATATACGGGGTCCT 59.922 47.826 0.00 0.00 29.82 3.85
2572 2841 2.885616 TCCTCAATATACGGGGTCCTC 58.114 52.381 0.00 0.00 0.00 3.71
2573 2842 2.449730 TCCTCAATATACGGGGTCCTCT 59.550 50.000 0.00 0.00 0.00 3.69
2574 2843 2.563179 CCTCAATATACGGGGTCCTCTG 59.437 54.545 0.00 0.00 0.00 3.35
2575 2844 3.231818 CTCAATATACGGGGTCCTCTGT 58.768 50.000 0.00 0.00 0.00 3.41
2576 2845 3.228453 TCAATATACGGGGTCCTCTGTC 58.772 50.000 0.00 0.00 0.00 3.51
2577 2846 1.906990 ATATACGGGGTCCTCTGTCG 58.093 55.000 0.00 0.00 0.00 4.35
2578 2847 0.839277 TATACGGGGTCCTCTGTCGA 59.161 55.000 0.00 0.00 0.00 4.20
2579 2848 0.465824 ATACGGGGTCCTCTGTCGAG 60.466 60.000 0.00 0.00 37.01 4.04
2580 2849 3.827898 CGGGGTCCTCTGTCGAGC 61.828 72.222 0.00 0.00 35.90 5.03
2581 2850 3.462678 GGGGTCCTCTGTCGAGCC 61.463 72.222 0.00 0.00 45.36 4.70
2582 2851 2.680352 GGGTCCTCTGTCGAGCCA 60.680 66.667 9.16 0.00 45.40 4.75
2583 2852 2.060980 GGGTCCTCTGTCGAGCCAT 61.061 63.158 9.16 0.00 45.40 4.40
2584 2853 1.617947 GGGTCCTCTGTCGAGCCATT 61.618 60.000 9.16 0.00 45.40 3.16
2585 2854 0.250513 GGTCCTCTGTCGAGCCATTT 59.749 55.000 0.00 0.00 35.90 2.32
2586 2855 1.339151 GGTCCTCTGTCGAGCCATTTT 60.339 52.381 0.00 0.00 35.90 1.82
2587 2856 1.734465 GTCCTCTGTCGAGCCATTTTG 59.266 52.381 0.00 0.00 35.90 2.44
2588 2857 0.449388 CCTCTGTCGAGCCATTTTGC 59.551 55.000 0.00 0.00 35.90 3.68
2589 2858 1.446907 CTCTGTCGAGCCATTTTGCT 58.553 50.000 0.00 0.00 46.37 3.91
2590 2859 1.808945 CTCTGTCGAGCCATTTTGCTT 59.191 47.619 0.00 0.00 42.95 3.91
2591 2860 1.806542 TCTGTCGAGCCATTTTGCTTC 59.193 47.619 0.00 0.00 42.95 3.86
2592 2861 0.516877 TGTCGAGCCATTTTGCTTCG 59.483 50.000 0.00 0.00 42.95 3.79
2593 2862 0.517316 GTCGAGCCATTTTGCTTCGT 59.483 50.000 0.00 0.00 42.95 3.85
2594 2863 1.069227 GTCGAGCCATTTTGCTTCGTT 60.069 47.619 0.00 0.00 42.95 3.85
2595 2864 2.158841 GTCGAGCCATTTTGCTTCGTTA 59.841 45.455 0.00 0.00 42.95 3.18
2596 2865 3.006940 TCGAGCCATTTTGCTTCGTTAT 58.993 40.909 0.00 0.00 42.95 1.89
2597 2866 3.100817 CGAGCCATTTTGCTTCGTTATG 58.899 45.455 0.00 0.00 42.95 1.90
2598 2867 3.426159 CGAGCCATTTTGCTTCGTTATGT 60.426 43.478 0.00 0.00 42.95 2.29
2599 2868 4.096732 AGCCATTTTGCTTCGTTATGTC 57.903 40.909 0.00 0.00 38.85 3.06
2600 2869 3.758554 AGCCATTTTGCTTCGTTATGTCT 59.241 39.130 0.00 0.00 38.85 3.41
2601 2870 4.098416 GCCATTTTGCTTCGTTATGTCTC 58.902 43.478 0.00 0.00 0.00 3.36
2602 2871 4.379394 GCCATTTTGCTTCGTTATGTCTCA 60.379 41.667 0.00 0.00 0.00 3.27
2603 2872 5.327091 CCATTTTGCTTCGTTATGTCTCAG 58.673 41.667 0.00 0.00 0.00 3.35
2604 2873 5.106555 CCATTTTGCTTCGTTATGTCTCAGT 60.107 40.000 0.00 0.00 0.00 3.41
2605 2874 5.591643 TTTTGCTTCGTTATGTCTCAGTC 57.408 39.130 0.00 0.00 0.00 3.51
2606 2875 3.934457 TGCTTCGTTATGTCTCAGTCA 57.066 42.857 0.00 0.00 0.00 3.41
2607 2876 4.251543 TGCTTCGTTATGTCTCAGTCAA 57.748 40.909 0.00 0.00 0.00 3.18
2608 2877 4.820897 TGCTTCGTTATGTCTCAGTCAAT 58.179 39.130 0.00 0.00 0.00 2.57
2609 2878 5.961272 TGCTTCGTTATGTCTCAGTCAATA 58.039 37.500 0.00 0.00 0.00 1.90
2610 2879 5.805486 TGCTTCGTTATGTCTCAGTCAATAC 59.195 40.000 0.00 0.00 0.00 1.89
2611 2880 6.037098 GCTTCGTTATGTCTCAGTCAATACT 58.963 40.000 0.00 0.00 35.91 2.12
2612 2881 7.148137 TGCTTCGTTATGTCTCAGTCAATACTA 60.148 37.037 0.00 0.00 33.48 1.82
2613 2882 7.863375 GCTTCGTTATGTCTCAGTCAATACTAT 59.137 37.037 0.00 0.00 33.48 2.12
2640 2909 9.690913 ATTCCTTTGATCTTGTATGAAGATTCA 57.309 29.630 0.00 0.00 42.14 2.57
2700 2969 9.416794 CTATATATGTGTCACTTGAATGAGACC 57.583 37.037 4.27 0.00 41.11 3.85
2701 2970 4.630644 ATGTGTCACTTGAATGAGACCT 57.369 40.909 4.27 0.00 41.11 3.85
2702 2971 5.745312 ATGTGTCACTTGAATGAGACCTA 57.255 39.130 4.27 0.00 41.11 3.08
2703 2972 5.139435 TGTGTCACTTGAATGAGACCTAG 57.861 43.478 4.27 0.00 41.11 3.02
2704 2973 4.588951 TGTGTCACTTGAATGAGACCTAGT 59.411 41.667 4.27 0.00 41.11 2.57
2705 2974 5.164954 GTGTCACTTGAATGAGACCTAGTC 58.835 45.833 0.00 0.00 37.00 2.59
2706 2975 4.832823 TGTCACTTGAATGAGACCTAGTCA 59.167 41.667 0.00 0.00 34.60 3.41
2707 2976 5.164954 GTCACTTGAATGAGACCTAGTCAC 58.835 45.833 0.00 0.00 34.60 3.67
2708 2977 4.832823 TCACTTGAATGAGACCTAGTCACA 59.167 41.667 0.00 0.00 37.52 3.58
2709 2978 4.926238 CACTTGAATGAGACCTAGTCACAC 59.074 45.833 0.00 0.00 36.15 3.82
2710 2979 4.021016 ACTTGAATGAGACCTAGTCACACC 60.021 45.833 0.00 0.00 36.15 4.16
2711 2980 2.832129 TGAATGAGACCTAGTCACACCC 59.168 50.000 0.00 0.00 36.15 4.61
2712 2981 2.930109 ATGAGACCTAGTCACACCCT 57.070 50.000 0.00 0.00 36.15 4.34
2713 2982 2.696526 TGAGACCTAGTCACACCCTT 57.303 50.000 0.00 0.00 34.60 3.95
2714 2983 2.972348 TGAGACCTAGTCACACCCTTT 58.028 47.619 0.00 0.00 34.60 3.11
2715 2984 2.897969 TGAGACCTAGTCACACCCTTTC 59.102 50.000 0.00 0.00 34.60 2.62
2730 2999 2.618816 CCCTTTCTGTTATGCTGCCTCA 60.619 50.000 0.00 0.00 0.00 3.86
2753 3022 1.473258 TCTTGCTTGTTTGCAGGTGT 58.527 45.000 0.00 0.00 44.27 4.16
2762 3031 5.106157 GCTTGTTTGCAGGTGTTGTATATCT 60.106 40.000 0.00 0.00 0.00 1.98
2779 3048 7.879070 TGTATATCTACCGATACACCAAACTC 58.121 38.462 0.00 0.00 34.40 3.01
2781 3050 3.433343 TCTACCGATACACCAAACTCCA 58.567 45.455 0.00 0.00 0.00 3.86
2785 3058 2.073816 CGATACACCAAACTCCACCAC 58.926 52.381 0.00 0.00 0.00 4.16
2823 3600 1.066430 GTTAGCATCGGTGACCTTCCA 60.066 52.381 0.00 0.00 0.00 3.53
2846 3623 1.202031 GCGTTCGTGATCCATGAAACC 60.202 52.381 0.00 0.00 40.42 3.27
2858 3635 1.250154 ATGAAACCCCGGTCGTCGTA 61.250 55.000 0.00 0.00 37.11 3.43
3004 3781 1.030457 CCTCTTGCATCATCTTGGGC 58.970 55.000 0.00 0.00 0.00 5.36
3009 3786 1.451927 GCATCATCTTGGGCGGACA 60.452 57.895 0.00 0.00 0.00 4.02
3025 3802 2.440796 CATTGTCGCCATGGCCCT 60.441 61.111 30.79 8.19 37.98 5.19
3026 3803 1.152984 CATTGTCGCCATGGCCCTA 60.153 57.895 30.79 18.06 37.98 3.53
3041 3818 1.967779 GCCCTAAACAACACCAACCAT 59.032 47.619 0.00 0.00 0.00 3.55
3048 3826 0.746063 CAACACCAACCATGCACAGT 59.254 50.000 0.00 0.00 0.00 3.55
3051 3829 0.031043 CACCAACCATGCACAGTGTG 59.969 55.000 19.27 19.27 36.51 3.82
3075 3853 1.374947 GCAGTGTGCCCAAGAGGTA 59.625 57.895 0.00 0.00 37.42 3.08
3102 3880 1.474077 GATGGTGGTCATTGCCAAGTC 59.526 52.381 2.04 0.00 40.68 3.01
3116 3894 0.393077 CAAGTCACTTGGGTCGACCT 59.607 55.000 32.52 11.62 37.77 3.85
3128 3906 2.821366 CGACCTGAGTGCCATGGC 60.821 66.667 30.54 30.54 42.35 4.40
3157 3935 4.649705 TCGGGAGGAAGGGGCACA 62.650 66.667 0.00 0.00 0.00 4.57
3158 3936 4.410400 CGGGAGGAAGGGGCACAC 62.410 72.222 0.00 0.00 0.00 3.82
3163 3941 0.618458 GAGGAAGGGGCACACATGTA 59.382 55.000 0.00 0.00 0.00 2.29
3166 3944 1.271926 GGAAGGGGCACACATGTAGTT 60.272 52.381 0.00 0.00 0.00 2.24
3167 3945 2.084546 GAAGGGGCACACATGTAGTTC 58.915 52.381 0.00 0.00 0.00 3.01
3168 3946 0.328258 AGGGGCACACATGTAGTTCC 59.672 55.000 0.00 3.35 0.00 3.62
3169 3947 0.328258 GGGGCACACATGTAGTTCCT 59.672 55.000 0.00 0.00 0.00 3.36
3170 3948 1.679032 GGGGCACACATGTAGTTCCTC 60.679 57.143 0.00 0.00 0.00 3.71
3171 3949 1.679032 GGGCACACATGTAGTTCCTCC 60.679 57.143 0.00 0.00 0.00 4.30
3172 3950 1.003118 GGCACACATGTAGTTCCTCCA 59.997 52.381 0.00 0.00 0.00 3.86
3173 3951 2.552155 GGCACACATGTAGTTCCTCCAA 60.552 50.000 0.00 0.00 0.00 3.53
3174 3952 2.744202 GCACACATGTAGTTCCTCCAAG 59.256 50.000 0.00 0.00 0.00 3.61
3175 3953 3.557054 GCACACATGTAGTTCCTCCAAGA 60.557 47.826 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.869695 TGCTTGTCTCGTTATTACCAGATAA 58.130 36.000 0.00 0.00 0.00 1.75
3 4 4.794278 TGCTTGTCTCGTTATTACCAGA 57.206 40.909 0.00 0.00 0.00 3.86
164 173 8.927675 TCCACATAGTTAAGGTGTTGTTAATT 57.072 30.769 0.00 0.00 0.00 1.40
165 174 7.610305 CCTCCACATAGTTAAGGTGTTGTTAAT 59.390 37.037 0.00 0.00 0.00 1.40
166 175 6.938030 CCTCCACATAGTTAAGGTGTTGTTAA 59.062 38.462 0.00 0.00 0.00 2.01
335 354 4.806225 CGCACATATAAGCAGCGC 57.194 55.556 0.00 0.00 41.95 5.92
424 443 6.686484 TCAGATATGTAAGTGGGCATACAT 57.314 37.500 4.13 4.13 43.30 2.29
449 475 3.731264 CGGGTTCTTCTATGACGACTGAC 60.731 52.174 0.00 0.00 0.00 3.51
518 544 7.015974 CCTGCCTATATATAGCCATGAATGAGA 59.984 40.741 13.49 0.00 0.00 3.27
767 830 5.851720 AGCACATGATGAAGATACTGTAGG 58.148 41.667 0.00 0.00 0.00 3.18
842 917 1.141881 CGAACTGATGGAGGGACGG 59.858 63.158 0.00 0.00 0.00 4.79
877 952 6.914757 GCAACTATCAAATTTATGCTCCAGTC 59.085 38.462 0.00 0.00 0.00 3.51
1710 1879 1.221840 GCCGATGAGCCTCAGGAAA 59.778 57.895 0.00 0.00 0.00 3.13
1744 1913 4.222847 GGCGATCGGGAGGTCCAC 62.223 72.222 18.30 0.00 36.35 4.02
1806 1975 1.344065 TCGGCTTCAGGTAGGTGAAA 58.656 50.000 0.00 0.00 36.01 2.69
1998 2167 4.441634 GGGTCGCTAAAGTACATCATCTGT 60.442 45.833 0.00 0.00 42.13 3.41
2136 2308 4.003788 CCGACCTTGCCCTCACGT 62.004 66.667 0.00 0.00 0.00 4.49
2141 2313 4.016706 CGAACCCGACCTTGCCCT 62.017 66.667 0.00 0.00 38.22 5.19
2142 2314 4.324991 ACGAACCCGACCTTGCCC 62.325 66.667 0.00 0.00 39.50 5.36
2188 2361 3.016474 GCGACGTCCTGCTTTGAGC 62.016 63.158 10.58 0.00 42.82 4.26
2226 2403 2.102578 ACCAACCTTCAATATGCTGCC 58.897 47.619 0.00 0.00 0.00 4.85
2227 2404 3.445096 AGAACCAACCTTCAATATGCTGC 59.555 43.478 0.00 0.00 0.00 5.25
2398 2667 1.589716 AACAAGCAAGATGCCGAGGC 61.590 55.000 7.26 7.26 46.52 4.70
2399 2668 0.883833 AAACAAGCAAGATGCCGAGG 59.116 50.000 0.00 0.00 46.52 4.63
2400 2669 2.030893 TGAAAACAAGCAAGATGCCGAG 60.031 45.455 0.00 0.00 46.52 4.63
2401 2670 1.952990 TGAAAACAAGCAAGATGCCGA 59.047 42.857 0.00 0.00 46.52 5.54
2402 2671 2.322161 CTGAAAACAAGCAAGATGCCG 58.678 47.619 0.00 0.00 46.52 5.69
2403 2672 2.036346 ACCTGAAAACAAGCAAGATGCC 59.964 45.455 0.00 0.00 46.52 4.40
2404 2673 3.054878 CACCTGAAAACAAGCAAGATGC 58.945 45.455 0.00 0.00 45.46 3.91
2405 2674 3.054878 GCACCTGAAAACAAGCAAGATG 58.945 45.455 0.00 0.00 0.00 2.90
2406 2675 2.036346 GGCACCTGAAAACAAGCAAGAT 59.964 45.455 0.00 0.00 0.00 2.40
2407 2676 1.408702 GGCACCTGAAAACAAGCAAGA 59.591 47.619 0.00 0.00 0.00 3.02
2408 2677 1.856802 GGCACCTGAAAACAAGCAAG 58.143 50.000 0.00 0.00 0.00 4.01
2409 2678 0.102120 CGGCACCTGAAAACAAGCAA 59.898 50.000 0.00 0.00 0.00 3.91
2410 2679 1.034838 ACGGCACCTGAAAACAAGCA 61.035 50.000 0.00 0.00 0.00 3.91
2411 2680 0.948678 TACGGCACCTGAAAACAAGC 59.051 50.000 0.00 0.00 0.00 4.01
2412 2681 2.811431 TGATACGGCACCTGAAAACAAG 59.189 45.455 0.00 0.00 0.00 3.16
2413 2682 2.852449 TGATACGGCACCTGAAAACAA 58.148 42.857 0.00 0.00 0.00 2.83
2414 2683 2.550606 GTTGATACGGCACCTGAAAACA 59.449 45.455 0.00 0.00 0.00 2.83
2415 2684 2.095415 GGTTGATACGGCACCTGAAAAC 60.095 50.000 0.00 0.00 0.00 2.43
2416 2685 2.156098 GGTTGATACGGCACCTGAAAA 58.844 47.619 0.00 0.00 0.00 2.29
2417 2686 1.816074 GGTTGATACGGCACCTGAAA 58.184 50.000 0.00 0.00 0.00 2.69
2418 2687 0.390603 CGGTTGATACGGCACCTGAA 60.391 55.000 0.00 0.00 0.00 3.02
2419 2688 1.216977 CGGTTGATACGGCACCTGA 59.783 57.895 0.00 0.00 0.00 3.86
2420 2689 0.179084 ATCGGTTGATACGGCACCTG 60.179 55.000 0.00 0.00 31.44 4.00
2421 2690 1.340248 CTATCGGTTGATACGGCACCT 59.660 52.381 0.00 0.00 35.99 4.00
2422 2691 1.338973 TCTATCGGTTGATACGGCACC 59.661 52.381 0.00 0.00 35.99 5.01
2423 2692 2.391879 GTCTATCGGTTGATACGGCAC 58.608 52.381 0.00 0.00 35.99 5.01
2424 2693 1.338973 GGTCTATCGGTTGATACGGCA 59.661 52.381 0.00 0.00 35.99 5.69
2425 2694 1.338973 TGGTCTATCGGTTGATACGGC 59.661 52.381 0.00 0.00 35.99 5.68
2426 2695 3.378339 GTTGGTCTATCGGTTGATACGG 58.622 50.000 0.00 0.00 35.99 4.02
2427 2696 3.040795 CGTTGGTCTATCGGTTGATACG 58.959 50.000 0.00 0.00 35.99 3.06
2428 2697 3.795101 CACGTTGGTCTATCGGTTGATAC 59.205 47.826 0.00 0.00 35.99 2.24
2429 2698 3.735820 GCACGTTGGTCTATCGGTTGATA 60.736 47.826 0.00 0.00 35.99 2.15
2430 2699 2.888594 CACGTTGGTCTATCGGTTGAT 58.111 47.619 0.00 0.00 38.67 2.57
2431 2700 1.670674 GCACGTTGGTCTATCGGTTGA 60.671 52.381 0.00 0.00 0.00 3.18
2432 2701 0.719465 GCACGTTGGTCTATCGGTTG 59.281 55.000 0.00 0.00 0.00 3.77
2433 2702 0.606604 AGCACGTTGGTCTATCGGTT 59.393 50.000 0.00 0.00 0.00 4.44
2434 2703 0.606604 AAGCACGTTGGTCTATCGGT 59.393 50.000 0.00 0.00 0.00 4.69
2435 2704 0.999406 CAAGCACGTTGGTCTATCGG 59.001 55.000 0.00 0.00 31.82 4.18
2460 2729 9.935241 TGCAATGACCTGCTTTATTTATTTTAA 57.065 25.926 0.00 0.00 43.07 1.52
2461 2730 9.935241 TTGCAATGACCTGCTTTATTTATTTTA 57.065 25.926 0.00 0.00 43.07 1.52
2462 2731 8.845413 TTGCAATGACCTGCTTTATTTATTTT 57.155 26.923 0.00 0.00 43.07 1.82
2463 2732 8.845413 TTTGCAATGACCTGCTTTATTTATTT 57.155 26.923 0.00 0.00 43.07 1.40
2464 2733 9.452287 AATTTGCAATGACCTGCTTTATTTATT 57.548 25.926 0.00 0.00 43.07 1.40
2465 2734 8.885722 CAATTTGCAATGACCTGCTTTATTTAT 58.114 29.630 0.00 0.00 43.07 1.40
2466 2735 7.877097 ACAATTTGCAATGACCTGCTTTATTTA 59.123 29.630 7.04 0.00 43.07 1.40
2467 2736 6.711645 ACAATTTGCAATGACCTGCTTTATTT 59.288 30.769 7.04 0.00 43.07 1.40
2468 2737 6.148150 CACAATTTGCAATGACCTGCTTTATT 59.852 34.615 7.04 0.00 43.07 1.40
2469 2738 5.640357 CACAATTTGCAATGACCTGCTTTAT 59.360 36.000 7.04 0.00 43.07 1.40
2470 2739 4.989797 CACAATTTGCAATGACCTGCTTTA 59.010 37.500 7.04 0.00 43.07 1.85
2471 2740 3.810941 CACAATTTGCAATGACCTGCTTT 59.189 39.130 7.04 0.00 43.07 3.51
2472 2741 3.181463 ACACAATTTGCAATGACCTGCTT 60.181 39.130 7.04 0.00 43.07 3.91
2473 2742 2.366266 ACACAATTTGCAATGACCTGCT 59.634 40.909 7.04 0.00 43.07 4.24
2474 2743 2.758009 ACACAATTTGCAATGACCTGC 58.242 42.857 7.04 0.00 42.95 4.85
2475 2744 4.624015 AGAACACAATTTGCAATGACCTG 58.376 39.130 7.04 0.00 0.00 4.00
2476 2745 4.942761 AGAACACAATTTGCAATGACCT 57.057 36.364 7.04 0.24 0.00 3.85
2477 2746 5.989551 AAAGAACACAATTTGCAATGACC 57.010 34.783 7.04 0.00 0.00 4.02
2478 2747 8.816144 TCTTAAAAGAACACAATTTGCAATGAC 58.184 29.630 7.04 0.63 30.73 3.06
2479 2748 8.939201 TCTTAAAAGAACACAATTTGCAATGA 57.061 26.923 7.04 0.00 30.73 2.57
2509 2778 8.822805 TGTCCTGTTATCTTGGAATAAACTACT 58.177 33.333 0.00 0.00 0.00 2.57
2510 2779 9.614792 ATGTCCTGTTATCTTGGAATAAACTAC 57.385 33.333 0.00 0.00 0.00 2.73
2512 2781 9.178758 GAATGTCCTGTTATCTTGGAATAAACT 57.821 33.333 0.00 0.00 0.00 2.66
2513 2782 8.122952 CGAATGTCCTGTTATCTTGGAATAAAC 58.877 37.037 0.00 0.00 0.00 2.01
2514 2783 8.044309 TCGAATGTCCTGTTATCTTGGAATAAA 58.956 33.333 0.00 0.00 0.00 1.40
2515 2784 7.561251 TCGAATGTCCTGTTATCTTGGAATAA 58.439 34.615 0.00 0.00 0.00 1.40
2516 2785 7.069455 TCTCGAATGTCCTGTTATCTTGGAATA 59.931 37.037 0.00 0.00 0.00 1.75
2517 2786 5.989477 TCGAATGTCCTGTTATCTTGGAAT 58.011 37.500 0.00 0.00 0.00 3.01
2518 2787 5.186992 TCTCGAATGTCCTGTTATCTTGGAA 59.813 40.000 0.00 0.00 0.00 3.53
2519 2788 4.709886 TCTCGAATGTCCTGTTATCTTGGA 59.290 41.667 0.00 0.00 0.00 3.53
2520 2789 5.011090 TCTCGAATGTCCTGTTATCTTGG 57.989 43.478 0.00 0.00 0.00 3.61
2521 2790 5.046529 CCTCTCGAATGTCCTGTTATCTTG 58.953 45.833 0.00 0.00 0.00 3.02
2522 2791 4.442192 GCCTCTCGAATGTCCTGTTATCTT 60.442 45.833 0.00 0.00 0.00 2.40
2523 2792 3.068873 GCCTCTCGAATGTCCTGTTATCT 59.931 47.826 0.00 0.00 0.00 1.98
2524 2793 3.181475 TGCCTCTCGAATGTCCTGTTATC 60.181 47.826 0.00 0.00 0.00 1.75
2525 2794 2.766263 TGCCTCTCGAATGTCCTGTTAT 59.234 45.455 0.00 0.00 0.00 1.89
2526 2795 2.176045 TGCCTCTCGAATGTCCTGTTA 58.824 47.619 0.00 0.00 0.00 2.41
2527 2796 0.976641 TGCCTCTCGAATGTCCTGTT 59.023 50.000 0.00 0.00 0.00 3.16
2528 2797 0.976641 TTGCCTCTCGAATGTCCTGT 59.023 50.000 0.00 0.00 0.00 4.00
2529 2798 1.205655 TCTTGCCTCTCGAATGTCCTG 59.794 52.381 0.00 0.00 0.00 3.86
2530 2799 1.480137 CTCTTGCCTCTCGAATGTCCT 59.520 52.381 0.00 0.00 0.00 3.85
2531 2800 1.478510 TCTCTTGCCTCTCGAATGTCC 59.521 52.381 0.00 0.00 0.00 4.02
2532 2801 2.949451 TCTCTTGCCTCTCGAATGTC 57.051 50.000 0.00 0.00 0.00 3.06
2533 2802 2.102252 GGATCTCTTGCCTCTCGAATGT 59.898 50.000 0.00 0.00 0.00 2.71
2534 2803 2.364970 AGGATCTCTTGCCTCTCGAATG 59.635 50.000 0.00 0.00 0.00 2.67
2535 2804 2.627699 GAGGATCTCTTGCCTCTCGAAT 59.372 50.000 0.00 0.00 45.72 3.34
2536 2805 2.028130 GAGGATCTCTTGCCTCTCGAA 58.972 52.381 0.00 0.00 45.72 3.71
2537 2806 1.686355 GAGGATCTCTTGCCTCTCGA 58.314 55.000 0.00 0.00 45.72 4.04
2542 2811 4.221703 CCGTATATTGAGGATCTCTTGCCT 59.778 45.833 0.00 0.00 37.18 4.75
2543 2812 4.499183 CCGTATATTGAGGATCTCTTGCC 58.501 47.826 0.00 0.00 34.92 4.52
2544 2813 4.499183 CCCGTATATTGAGGATCTCTTGC 58.501 47.826 0.00 0.00 34.92 4.01
2545 2814 4.528596 ACCCCGTATATTGAGGATCTCTTG 59.471 45.833 0.00 0.00 34.92 3.02
2546 2815 4.753186 ACCCCGTATATTGAGGATCTCTT 58.247 43.478 0.00 0.00 34.92 2.85
2547 2816 4.345854 GACCCCGTATATTGAGGATCTCT 58.654 47.826 0.00 0.00 34.92 3.10
2548 2817 3.447944 GGACCCCGTATATTGAGGATCTC 59.552 52.174 0.00 0.00 34.92 2.75
2549 2818 3.077695 AGGACCCCGTATATTGAGGATCT 59.922 47.826 0.00 0.00 34.92 2.75
2550 2819 3.442076 AGGACCCCGTATATTGAGGATC 58.558 50.000 0.00 0.00 0.00 3.36
2551 2820 3.077695 AGAGGACCCCGTATATTGAGGAT 59.922 47.826 0.00 0.00 0.00 3.24
2552 2821 2.449730 AGAGGACCCCGTATATTGAGGA 59.550 50.000 0.00 0.00 0.00 3.71
2553 2822 2.563179 CAGAGGACCCCGTATATTGAGG 59.437 54.545 0.00 0.00 0.00 3.86
2554 2823 3.231818 ACAGAGGACCCCGTATATTGAG 58.768 50.000 0.00 0.00 0.00 3.02
2555 2824 3.228453 GACAGAGGACCCCGTATATTGA 58.772 50.000 0.00 0.00 0.00 2.57
2556 2825 2.030185 CGACAGAGGACCCCGTATATTG 60.030 54.545 0.00 0.00 0.00 1.90
2557 2826 2.158564 TCGACAGAGGACCCCGTATATT 60.159 50.000 0.00 0.00 0.00 1.28
2558 2827 1.422781 TCGACAGAGGACCCCGTATAT 59.577 52.381 0.00 0.00 0.00 0.86
2559 2828 0.839277 TCGACAGAGGACCCCGTATA 59.161 55.000 0.00 0.00 0.00 1.47
2560 2829 0.465824 CTCGACAGAGGACCCCGTAT 60.466 60.000 0.00 0.00 40.75 3.06
2561 2830 1.077930 CTCGACAGAGGACCCCGTA 60.078 63.158 0.00 0.00 40.75 4.02
2562 2831 2.361357 CTCGACAGAGGACCCCGT 60.361 66.667 0.00 0.00 40.75 5.28
2563 2832 3.827898 GCTCGACAGAGGACCCCG 61.828 72.222 0.00 0.00 44.51 5.73
2564 2833 3.462678 GGCTCGACAGAGGACCCC 61.463 72.222 0.00 0.00 44.51 4.95
2565 2834 1.617947 AATGGCTCGACAGAGGACCC 61.618 60.000 0.00 0.00 44.51 4.46
2566 2835 0.250513 AAATGGCTCGACAGAGGACC 59.749 55.000 0.00 0.00 44.51 4.46
2567 2836 1.734465 CAAAATGGCTCGACAGAGGAC 59.266 52.381 0.00 0.00 44.51 3.85
2568 2837 1.945819 GCAAAATGGCTCGACAGAGGA 60.946 52.381 0.00 0.00 44.51 3.71
2569 2838 0.449388 GCAAAATGGCTCGACAGAGG 59.551 55.000 0.00 0.00 44.51 3.69
2570 2839 1.446907 AGCAAAATGGCTCGACAGAG 58.553 50.000 0.00 0.00 41.05 3.35
2571 2840 1.806542 GAAGCAAAATGGCTCGACAGA 59.193 47.619 0.00 0.00 45.07 3.41
2572 2841 1.464687 CGAAGCAAAATGGCTCGACAG 60.465 52.381 0.00 0.00 45.07 3.51
2573 2842 0.516877 CGAAGCAAAATGGCTCGACA 59.483 50.000 0.00 0.00 45.07 4.35
2574 2843 0.517316 ACGAAGCAAAATGGCTCGAC 59.483 50.000 11.73 0.00 45.07 4.20
2575 2844 1.234821 AACGAAGCAAAATGGCTCGA 58.765 45.000 11.73 0.00 45.07 4.04
2576 2845 2.892373 TAACGAAGCAAAATGGCTCG 57.108 45.000 0.00 0.00 45.07 5.03
2577 2846 4.096732 ACATAACGAAGCAAAATGGCTC 57.903 40.909 0.00 0.00 45.07 4.70
2579 2848 4.096732 AGACATAACGAAGCAAAATGGC 57.903 40.909 0.00 0.00 0.00 4.40
2580 2849 5.106555 ACTGAGACATAACGAAGCAAAATGG 60.107 40.000 0.00 0.00 0.00 3.16
2581 2850 5.931532 ACTGAGACATAACGAAGCAAAATG 58.068 37.500 0.00 0.00 0.00 2.32
2582 2851 5.700832 TGACTGAGACATAACGAAGCAAAAT 59.299 36.000 0.00 0.00 0.00 1.82
2583 2852 5.053811 TGACTGAGACATAACGAAGCAAAA 58.946 37.500 0.00 0.00 0.00 2.44
2584 2853 4.627058 TGACTGAGACATAACGAAGCAAA 58.373 39.130 0.00 0.00 0.00 3.68
2585 2854 4.251543 TGACTGAGACATAACGAAGCAA 57.748 40.909 0.00 0.00 0.00 3.91
2586 2855 3.934457 TGACTGAGACATAACGAAGCA 57.066 42.857 0.00 0.00 0.00 3.91
2587 2856 6.037098 AGTATTGACTGAGACATAACGAAGC 58.963 40.000 0.00 0.00 33.41 3.86
2614 2883 9.690913 TGAATCTTCATACAAGATCAAAGGAAT 57.309 29.630 0.00 0.00 36.07 3.01
2615 2884 9.690913 ATGAATCTTCATACAAGATCAAAGGAA 57.309 29.630 3.62 0.00 45.54 3.36
2674 2943 9.416794 GGTCTCATTCAAGTGACACATATATAG 57.583 37.037 8.59 0.00 34.58 1.31
2675 2944 9.147732 AGGTCTCATTCAAGTGACACATATATA 57.852 33.333 8.59 0.00 34.58 0.86
2676 2945 8.027524 AGGTCTCATTCAAGTGACACATATAT 57.972 34.615 8.59 0.00 34.58 0.86
2677 2946 7.423844 AGGTCTCATTCAAGTGACACATATA 57.576 36.000 8.59 0.00 34.58 0.86
2678 2947 6.305272 AGGTCTCATTCAAGTGACACATAT 57.695 37.500 8.59 0.00 34.58 1.78
2679 2948 5.745312 AGGTCTCATTCAAGTGACACATA 57.255 39.130 8.59 0.00 34.58 2.29
2680 2949 4.630644 AGGTCTCATTCAAGTGACACAT 57.369 40.909 8.59 0.00 34.58 3.21
2681 2950 4.588951 ACTAGGTCTCATTCAAGTGACACA 59.411 41.667 8.59 0.00 34.58 3.72
2682 2951 5.140747 ACTAGGTCTCATTCAAGTGACAC 57.859 43.478 0.00 0.00 34.58 3.67
2683 2952 4.832823 TGACTAGGTCTCATTCAAGTGACA 59.167 41.667 0.00 0.00 34.58 3.58
2684 2953 5.164954 GTGACTAGGTCTCATTCAAGTGAC 58.835 45.833 0.00 0.00 33.15 3.67
2685 2954 4.832823 TGTGACTAGGTCTCATTCAAGTGA 59.167 41.667 0.00 0.00 32.30 3.41
2686 2955 4.926238 GTGTGACTAGGTCTCATTCAAGTG 59.074 45.833 5.87 0.00 38.13 3.16
2687 2956 4.021016 GGTGTGACTAGGTCTCATTCAAGT 60.021 45.833 5.87 0.00 38.13 3.16
2688 2957 4.499183 GGTGTGACTAGGTCTCATTCAAG 58.501 47.826 5.87 0.00 38.13 3.02
2689 2958 3.260884 GGGTGTGACTAGGTCTCATTCAA 59.739 47.826 5.87 0.00 38.13 2.69
2690 2959 2.832129 GGGTGTGACTAGGTCTCATTCA 59.168 50.000 5.87 0.00 38.13 2.57
2691 2960 3.100671 AGGGTGTGACTAGGTCTCATTC 58.899 50.000 5.87 3.06 38.13 2.67
2692 2961 3.191888 AGGGTGTGACTAGGTCTCATT 57.808 47.619 5.87 0.00 38.13 2.57
2693 2962 2.930109 AGGGTGTGACTAGGTCTCAT 57.070 50.000 5.87 0.00 38.13 2.90
2694 2963 2.696526 AAGGGTGTGACTAGGTCTCA 57.303 50.000 0.00 0.00 34.38 3.27
2695 2964 3.056465 CAGAAAGGGTGTGACTAGGTCTC 60.056 52.174 0.00 0.00 33.15 3.36
2696 2965 2.900546 CAGAAAGGGTGTGACTAGGTCT 59.099 50.000 0.00 0.00 33.15 3.85
2697 2966 2.633481 ACAGAAAGGGTGTGACTAGGTC 59.367 50.000 0.00 0.00 0.00 3.85
2698 2967 2.690840 ACAGAAAGGGTGTGACTAGGT 58.309 47.619 0.00 0.00 0.00 3.08
2699 2968 3.771577 AACAGAAAGGGTGTGACTAGG 57.228 47.619 0.00 0.00 0.00 3.02
2700 2969 4.631813 GCATAACAGAAAGGGTGTGACTAG 59.368 45.833 0.00 0.00 0.00 2.57
2701 2970 4.286032 AGCATAACAGAAAGGGTGTGACTA 59.714 41.667 0.00 0.00 0.00 2.59
2702 2971 3.073062 AGCATAACAGAAAGGGTGTGACT 59.927 43.478 0.00 0.00 0.00 3.41
2703 2972 3.189287 CAGCATAACAGAAAGGGTGTGAC 59.811 47.826 0.00 0.00 0.00 3.67
2704 2973 3.411446 CAGCATAACAGAAAGGGTGTGA 58.589 45.455 0.00 0.00 0.00 3.58
2705 2974 2.095059 GCAGCATAACAGAAAGGGTGTG 60.095 50.000 0.00 0.00 0.00 3.82
2706 2975 2.162681 GCAGCATAACAGAAAGGGTGT 58.837 47.619 0.00 0.00 0.00 4.16
2707 2976 1.474077 GGCAGCATAACAGAAAGGGTG 59.526 52.381 0.00 0.00 0.00 4.61
2708 2977 1.355720 AGGCAGCATAACAGAAAGGGT 59.644 47.619 0.00 0.00 0.00 4.34
2709 2978 2.019984 GAGGCAGCATAACAGAAAGGG 58.980 52.381 0.00 0.00 0.00 3.95
2710 2979 2.681848 CTGAGGCAGCATAACAGAAAGG 59.318 50.000 0.00 0.00 0.00 3.11
2753 3022 8.241497 AGTTTGGTGTATCGGTAGATATACAA 57.759 34.615 14.27 3.86 46.68 2.41
2762 3031 2.234414 GGTGGAGTTTGGTGTATCGGTA 59.766 50.000 0.00 0.00 0.00 4.02
2785 3058 0.532862 ACAAGTTGCTCGACACCTGG 60.533 55.000 1.81 0.00 0.00 4.45
2846 3623 1.143969 GCTCAAATACGACGACCGGG 61.144 60.000 6.32 0.00 43.93 5.73
2858 3635 0.403271 ACCTGTGCTCCAGCTCAAAT 59.597 50.000 4.95 0.00 42.88 2.32
2993 3770 1.064463 ACAATGTCCGCCCAAGATGAT 60.064 47.619 0.00 0.00 0.00 2.45
3025 3802 2.760650 TGTGCATGGTTGGTGTTGTTTA 59.239 40.909 0.00 0.00 0.00 2.01
3026 3803 1.552337 TGTGCATGGTTGGTGTTGTTT 59.448 42.857 0.00 0.00 0.00 2.83
3048 3826 3.356267 GCACACTGCATCCGCACA 61.356 61.111 0.00 0.00 45.36 4.57
3075 3853 2.821969 GCAATGACCACCATCTCAAAGT 59.178 45.455 0.00 0.00 33.53 2.66
3102 3880 0.319900 CACTCAGGTCGACCCAAGTG 60.320 60.000 34.47 34.47 40.41 3.16
3116 3894 2.359850 GTTCCGCCATGGCACTCA 60.360 61.111 34.93 13.86 42.06 3.41
3138 3916 4.332543 TGCCCCTTCCTCCCGACT 62.333 66.667 0.00 0.00 0.00 4.18
3142 3920 2.616458 ATGTGTGCCCCTTCCTCCC 61.616 63.158 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.