Multiple sequence alignment - TraesCS2D01G315800

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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 TraesCS2D01G315800 chr2D 100.000 3122 0 0 1 3122 405274603 405277724 0.000000e+00 5766.0
1 TraesCS2D01G315800 chr2B 92.796 2471 91 34 1 2416 480411093 480413531 0.000000e+00 3496.0
2 TraesCS2D01G315800 chr2B 89.780 499 29 11 2631 3122 480413529 480414012 1.230000e-173 619.0
3 TraesCS2D01G315800 chr2A 92.536 1956 78 28 513 2416 543307642 543309581 0.000000e+00 2741.0
4 TraesCS2D01G315800 chr2A 89.864 513 24 12 2631 3122 543309579 543310084 4.390000e-178 634.0
5 TraesCS2D01G315800 chr2A 89.928 278 18 6 248 517 543307220 543307495 1.780000e-92 350.0
6 TraesCS2D01G315800 chr2A 88.517 209 21 2 2419 2624 443920915 443921123 1.860000e-62 250.0
7 TraesCS2D01G315800 chr2A 86.463 229 27 2 2405 2629 35678279 35678507 6.690000e-62 248.0
8 TraesCS2D01G315800 chr2A 93.252 163 10 1 1 163 543306843 543307004 4.020000e-59 239.0
9 TraesCS2D01G315800 chr3A 81.674 693 71 36 1166 1854 27543691 27544331 2.760000e-145 525.0
10 TraesCS2D01G315800 chr3A 89.100 211 19 2 2420 2627 651189304 651189513 3.090000e-65 259.0
11 TraesCS2D01G315800 chr3A 88.942 208 18 4 2423 2626 76343837 76343631 5.170000e-63 252.0
12 TraesCS2D01G315800 chr3A 88.462 208 19 3 2423 2627 184272420 184272625 2.400000e-61 246.0
13 TraesCS2D01G315800 chr3D 80.952 693 76 34 1166 1854 19880726 19881366 6.010000e-137 497.0
14 TraesCS2D01G315800 chr3B 85.286 367 35 7 1185 1551 31799301 31799648 8.230000e-96 361.0
15 TraesCS2D01G315800 chr1A 88.263 213 20 3 2419 2627 352839716 352839927 1.860000e-62 250.0
16 TraesCS2D01G315800 chr1A 88.462 208 20 2 2423 2627 454420469 454420263 6.690000e-62 248.0
17 TraesCS2D01G315800 chr5A 88.095 210 21 3 2423 2629 452283233 452283441 2.400000e-61 246.0
18 TraesCS2D01G315800 chr6A 88.038 209 22 3 2423 2628 604910438 604910230 8.650000e-61 244.0
19 TraesCS2D01G315800 chr7D 85.119 168 22 2 1400 1564 629248233 629248400 5.350000e-38 169.0
20 TraesCS2D01G315800 chr7D 77.627 295 43 17 1289 1564 628987361 628987071 1.160000e-34 158.0
21 TraesCS2D01G315800 chr7B 74.935 387 74 19 1196 1563 731243384 731243766 4.170000e-34 156.0
22 TraesCS2D01G315800 chr6D 93.258 89 6 0 1372 1460 374823707 374823619 7.030000e-27 132.0
23 TraesCS2D01G315800 chr1B 100.000 28 0 0 1609 1636 361361834 361361861 6.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G315800 chr2D 405274603 405277724 3121 False 5766.0 5766 100.000 1 3122 1 chr2D.!!$F1 3121
1 TraesCS2D01G315800 chr2B 480411093 480414012 2919 False 2057.5 3496 91.288 1 3122 2 chr2B.!!$F1 3121
2 TraesCS2D01G315800 chr2A 543306843 543310084 3241 False 991.0 2741 91.395 1 3122 4 chr2A.!!$F3 3121
3 TraesCS2D01G315800 chr3A 27543691 27544331 640 False 525.0 525 81.674 1166 1854 1 chr3A.!!$F1 688
4 TraesCS2D01G315800 chr3D 19880726 19881366 640 False 497.0 497 80.952 1166 1854 1 chr3D.!!$F1 688

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
349 523 0.035725 GGTGCCAACTACCCAGGTAC 60.036 60.0 0.0 0.0 37.31 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2710 1.067974 TCGCCAGAGTCAAAGAAACGA 59.932 47.619 0.0 0.0 0.0 3.85 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
136 137 5.504665 GCGTAACTAAGAGCATGCATGATTT 60.505 40.000 30.64 17.12 0.00 2.17
176 178 4.658071 CGGTGTATGTTTATTGGTTGCTC 58.342 43.478 0.00 0.00 0.00 4.26
187 189 1.748879 GGTTGCTCCGCTGCCATAA 60.749 57.895 0.00 0.00 0.00 1.90
348 522 0.178885 AGGTGCCAACTACCCAGGTA 60.179 55.000 0.00 0.00 39.05 3.08
349 523 0.035725 GGTGCCAACTACCCAGGTAC 60.036 60.000 0.00 0.00 37.31 3.34
350 524 0.981943 GTGCCAACTACCCAGGTACT 59.018 55.000 0.00 0.00 43.88 2.73
446 621 1.375523 CGGTACAACTGCTCCACCC 60.376 63.158 0.00 0.00 0.00 4.61
496 675 3.313526 ACACTTCAGCATGTTGTTCTCAC 59.686 43.478 9.54 0.00 37.40 3.51
502 681 0.439985 CATGTTGTTCTCACGCTCCG 59.560 55.000 0.00 0.00 0.00 4.63
505 684 1.005037 TTGTTCTCACGCTCCGCAT 60.005 52.632 0.00 0.00 0.00 4.73
509 688 2.867333 TTCTCACGCTCCGCATCGTC 62.867 60.000 0.00 0.00 36.73 4.20
520 851 2.047274 CATCGTCGGCCAGGTGTT 60.047 61.111 2.24 0.00 0.00 3.32
558 894 4.732065 ACATGATTGTCCATGCCATATGA 58.268 39.130 3.65 0.00 45.79 2.15
873 1226 4.030216 TGCCCAAGAAAGAAAGAAAAGGT 58.970 39.130 0.00 0.00 0.00 3.50
1036 1400 3.311110 TGCGTCCACACCTCCTCC 61.311 66.667 0.00 0.00 0.00 4.30
1037 1401 2.997897 GCGTCCACACCTCCTCCT 60.998 66.667 0.00 0.00 0.00 3.69
1038 1402 2.584391 GCGTCCACACCTCCTCCTT 61.584 63.158 0.00 0.00 0.00 3.36
1047 1411 1.981495 CACCTCCTCCTTGTCCTTCTT 59.019 52.381 0.00 0.00 0.00 2.52
1660 2048 1.456705 CGGGAAGAGGAGGAGGAGG 60.457 68.421 0.00 0.00 0.00 4.30
1661 2049 1.939082 CGGGAAGAGGAGGAGGAGGA 61.939 65.000 0.00 0.00 0.00 3.71
1662 2050 0.105709 GGGAAGAGGAGGAGGAGGAG 60.106 65.000 0.00 0.00 0.00 3.69
2192 2606 6.783892 AAAATGCGTGTAATTTGATTTGCT 57.216 29.167 0.00 0.00 0.00 3.91
2193 2607 6.783892 AAATGCGTGTAATTTGATTTGCTT 57.216 29.167 0.00 0.00 0.00 3.91
2194 2608 7.881643 AAATGCGTGTAATTTGATTTGCTTA 57.118 28.000 0.00 0.00 0.00 3.09
2195 2609 7.881643 AATGCGTGTAATTTGATTTGCTTAA 57.118 28.000 0.00 0.00 0.00 1.85
2270 2690 1.264020 TGAATGTTTGCGTGTGCTCTC 59.736 47.619 0.00 0.00 43.34 3.20
2278 2698 2.653702 GTGTGCTCTCGTGAGGCT 59.346 61.111 15.74 0.00 40.53 4.58
2279 2699 1.735920 GTGTGCTCTCGTGAGGCTG 60.736 63.158 15.74 0.00 40.53 4.85
2280 2700 1.903404 TGTGCTCTCGTGAGGCTGA 60.903 57.895 15.74 0.00 40.53 4.26
2282 2702 0.735632 GTGCTCTCGTGAGGCTGAAG 60.736 60.000 15.74 0.00 40.53 3.02
2283 2703 1.181741 TGCTCTCGTGAGGCTGAAGT 61.182 55.000 15.74 0.00 40.53 3.01
2319 2739 0.784778 GACTCTGGCGAAGTGAAACG 59.215 55.000 0.00 0.00 45.86 3.60
2323 2743 2.011222 TCTGGCGAAGTGAAACGTTTT 58.989 42.857 15.89 0.00 45.86 2.43
2331 2751 4.142364 CGAAGTGAAACGTTTTGTTCGATG 59.858 41.667 29.86 13.87 45.86 3.84
2370 2790 1.253100 TAAAAAGCTTTGGCGAGGGG 58.747 50.000 13.54 0.00 44.37 4.79
2371 2791 2.099652 AAAAAGCTTTGGCGAGGGGC 62.100 55.000 13.54 0.00 44.37 5.80
2400 2820 4.642885 TCGGAATGTTCACTTTTGGACTTT 59.357 37.500 0.00 0.00 32.47 2.66
2401 2821 4.739716 CGGAATGTTCACTTTTGGACTTTG 59.260 41.667 0.00 0.00 30.43 2.77
2402 2822 5.660460 GGAATGTTCACTTTTGGACTTTGT 58.340 37.500 0.00 0.00 30.43 2.83
2403 2823 6.106003 GGAATGTTCACTTTTGGACTTTGTT 58.894 36.000 0.00 0.00 30.43 2.83
2404 2824 6.255670 GGAATGTTCACTTTTGGACTTTGTTC 59.744 38.462 0.00 0.00 30.43 3.18
2405 2825 4.728534 TGTTCACTTTTGGACTTTGTTCG 58.271 39.130 0.00 0.00 31.54 3.95
2409 2829 0.382515 TTTTGGACTTTGTTCGCCGG 59.617 50.000 0.00 0.00 0.00 6.13
2411 2831 3.733960 GGACTTTGTTCGCCGGCC 61.734 66.667 23.46 7.69 0.00 6.13
2412 2832 2.668550 GACTTTGTTCGCCGGCCT 60.669 61.111 23.46 0.00 0.00 5.19
2413 2833 2.203294 ACTTTGTTCGCCGGCCTT 60.203 55.556 23.46 0.00 0.00 4.35
2414 2834 1.792118 GACTTTGTTCGCCGGCCTTT 61.792 55.000 23.46 0.00 0.00 3.11
2415 2835 1.362355 CTTTGTTCGCCGGCCTTTT 59.638 52.632 23.46 0.00 0.00 2.27
2416 2836 0.594110 CTTTGTTCGCCGGCCTTTTA 59.406 50.000 23.46 0.10 0.00 1.52
2417 2837 0.594110 TTTGTTCGCCGGCCTTTTAG 59.406 50.000 23.46 5.48 0.00 1.85
2418 2838 0.535553 TTGTTCGCCGGCCTTTTAGT 60.536 50.000 23.46 0.00 0.00 2.24
2419 2839 0.535553 TGTTCGCCGGCCTTTTAGTT 60.536 50.000 23.46 0.00 0.00 2.24
2420 2840 0.109919 GTTCGCCGGCCTTTTAGTTG 60.110 55.000 23.46 2.86 0.00 3.16
2421 2841 0.250381 TTCGCCGGCCTTTTAGTTGA 60.250 50.000 23.46 5.72 0.00 3.18
2422 2842 0.250381 TCGCCGGCCTTTTAGTTGAA 60.250 50.000 23.46 0.00 0.00 2.69
2423 2843 0.594110 CGCCGGCCTTTTAGTTGAAA 59.406 50.000 23.46 0.00 0.00 2.69
2424 2844 1.001158 CGCCGGCCTTTTAGTTGAAAA 60.001 47.619 23.46 0.00 35.67 2.29
2425 2845 2.544069 CGCCGGCCTTTTAGTTGAAAAA 60.544 45.455 23.46 0.00 36.59 1.94
2426 2846 3.057019 GCCGGCCTTTTAGTTGAAAAAG 58.943 45.455 18.11 2.77 43.19 2.27
2427 2847 3.243602 GCCGGCCTTTTAGTTGAAAAAGA 60.244 43.478 18.11 0.00 45.33 2.52
2428 2848 4.738243 GCCGGCCTTTTAGTTGAAAAAGAA 60.738 41.667 18.11 0.00 45.33 2.52
2429 2849 5.538118 CCGGCCTTTTAGTTGAAAAAGAAT 58.462 37.500 0.00 0.00 45.33 2.40
2430 2850 5.989168 CCGGCCTTTTAGTTGAAAAAGAATT 59.011 36.000 0.00 0.00 45.33 2.17
2431 2851 6.145534 CCGGCCTTTTAGTTGAAAAAGAATTC 59.854 38.462 0.00 0.00 45.33 2.17
2432 2852 6.923508 CGGCCTTTTAGTTGAAAAAGAATTCT 59.076 34.615 0.88 0.88 45.33 2.40
2433 2853 8.079809 CGGCCTTTTAGTTGAAAAAGAATTCTA 58.920 33.333 8.75 0.00 45.33 2.10
2434 2854 9.929180 GGCCTTTTAGTTGAAAAAGAATTCTAT 57.071 29.630 8.75 0.00 45.33 1.98
2441 2861 8.924511 AGTTGAAAAAGAATTCTATGAGACCA 57.075 30.769 8.75 0.00 0.00 4.02
2442 2862 9.007901 AGTTGAAAAAGAATTCTATGAGACCAG 57.992 33.333 8.75 0.00 0.00 4.00
2443 2863 7.928307 TGAAAAAGAATTCTATGAGACCAGG 57.072 36.000 8.75 0.00 0.00 4.45
2444 2864 7.461749 TGAAAAAGAATTCTATGAGACCAGGT 58.538 34.615 8.75 0.00 0.00 4.00
2445 2865 7.607991 TGAAAAAGAATTCTATGAGACCAGGTC 59.392 37.037 12.25 12.25 0.00 3.85
2446 2866 6.882768 AAAGAATTCTATGAGACCAGGTCT 57.117 37.500 23.18 23.18 46.42 3.85
2453 2873 2.282251 AGACCAGGTCTCACGCGA 60.282 61.111 17.31 0.00 38.71 5.87
2454 2874 2.126424 GACCAGGTCTCACGCGAC 60.126 66.667 15.93 0.00 0.00 5.19
2455 2875 2.910479 ACCAGGTCTCACGCGACA 60.910 61.111 15.93 0.00 35.63 4.35
2456 2876 2.430921 CCAGGTCTCACGCGACAC 60.431 66.667 15.93 2.74 35.63 3.67
2457 2877 2.430921 CAGGTCTCACGCGACACC 60.431 66.667 15.93 12.72 35.63 4.16
2458 2878 3.681835 AGGTCTCACGCGACACCC 61.682 66.667 15.93 5.74 30.77 4.61
2459 2879 3.986006 GGTCTCACGCGACACCCA 61.986 66.667 15.93 0.00 35.63 4.51
2460 2880 2.261671 GTCTCACGCGACACCCAT 59.738 61.111 15.93 0.00 34.11 4.00
2461 2881 1.509463 GTCTCACGCGACACCCATA 59.491 57.895 15.93 0.00 34.11 2.74
2462 2882 0.801067 GTCTCACGCGACACCCATAC 60.801 60.000 15.93 0.00 34.11 2.39
2463 2883 0.963856 TCTCACGCGACACCCATACT 60.964 55.000 15.93 0.00 0.00 2.12
2464 2884 0.802222 CTCACGCGACACCCATACTG 60.802 60.000 15.93 0.00 0.00 2.74
2465 2885 1.214325 CACGCGACACCCATACTGA 59.786 57.895 15.93 0.00 0.00 3.41
2466 2886 0.179111 CACGCGACACCCATACTGAT 60.179 55.000 15.93 0.00 0.00 2.90
2467 2887 0.179111 ACGCGACACCCATACTGATG 60.179 55.000 15.93 0.00 0.00 3.07
2480 2900 2.024176 ACTGATGGATAACACGTGGC 57.976 50.000 21.57 5.98 0.00 5.01
2481 2901 1.277842 ACTGATGGATAACACGTGGCA 59.722 47.619 21.57 7.19 0.00 4.92
2482 2902 2.092968 ACTGATGGATAACACGTGGCAT 60.093 45.455 21.57 12.18 0.00 4.40
2483 2903 2.945008 CTGATGGATAACACGTGGCATT 59.055 45.455 21.57 7.84 0.00 3.56
2484 2904 2.942376 TGATGGATAACACGTGGCATTC 59.058 45.455 21.57 11.44 0.00 2.67
2485 2905 2.481289 TGGATAACACGTGGCATTCA 57.519 45.000 21.57 13.97 0.00 2.57
2486 2906 2.080693 TGGATAACACGTGGCATTCAC 58.919 47.619 21.57 4.35 42.74 3.18
2487 2907 2.080693 GGATAACACGTGGCATTCACA 58.919 47.619 21.57 0.00 46.36 3.58
2488 2908 2.486203 GGATAACACGTGGCATTCACAA 59.514 45.455 21.57 0.00 46.36 3.33
2489 2909 3.057876 GGATAACACGTGGCATTCACAAA 60.058 43.478 21.57 0.00 46.36 2.83
2490 2910 2.490328 AACACGTGGCATTCACAAAG 57.510 45.000 21.57 0.00 46.36 2.77
2491 2911 0.030638 ACACGTGGCATTCACAAAGC 59.969 50.000 21.57 0.00 46.36 3.51
2492 2912 0.030504 CACGTGGCATTCACAAAGCA 59.969 50.000 7.95 0.00 46.36 3.91
2493 2913 0.030638 ACGTGGCATTCACAAAGCAC 59.969 50.000 0.00 0.00 46.36 4.40
2494 2914 0.030504 CGTGGCATTCACAAAGCACA 59.969 50.000 0.00 0.00 46.36 4.57
2495 2915 1.490621 GTGGCATTCACAAAGCACAC 58.509 50.000 0.00 0.00 45.39 3.82
2496 2916 1.067516 GTGGCATTCACAAAGCACACT 59.932 47.619 0.00 0.00 45.39 3.55
2497 2917 1.755959 TGGCATTCACAAAGCACACTT 59.244 42.857 0.00 0.00 37.90 3.16
2498 2918 2.129607 GGCATTCACAAAGCACACTTG 58.870 47.619 0.00 0.00 35.85 3.16
2499 2919 2.223782 GGCATTCACAAAGCACACTTGA 60.224 45.455 0.00 0.00 35.85 3.02
2500 2920 2.791004 GCATTCACAAAGCACACTTGAC 59.209 45.455 0.00 0.00 35.85 3.18
2501 2921 3.374745 CATTCACAAAGCACACTTGACC 58.625 45.455 0.00 0.00 35.85 4.02
2502 2922 1.388547 TCACAAAGCACACTTGACCC 58.611 50.000 0.00 0.00 35.85 4.46
2503 2923 1.102154 CACAAAGCACACTTGACCCA 58.898 50.000 0.00 0.00 35.85 4.51
2504 2924 1.102978 ACAAAGCACACTTGACCCAC 58.897 50.000 0.00 0.00 35.85 4.61
2505 2925 0.385390 CAAAGCACACTTGACCCACC 59.615 55.000 0.00 0.00 35.85 4.61
2506 2926 0.755327 AAAGCACACTTGACCCACCC 60.755 55.000 0.00 0.00 35.85 4.61
2507 2927 2.597510 GCACACTTGACCCACCCC 60.598 66.667 0.00 0.00 0.00 4.95
2508 2928 2.115266 CACACTTGACCCACCCCC 59.885 66.667 0.00 0.00 0.00 5.40
2526 2946 4.264373 CCCCCATTTAAAATCAGGGAGA 57.736 45.455 15.86 0.00 42.25 3.71
2527 2947 4.218312 CCCCCATTTAAAATCAGGGAGAG 58.782 47.826 15.86 4.19 42.25 3.20
2528 2948 4.079212 CCCCCATTTAAAATCAGGGAGAGA 60.079 45.833 15.86 0.00 42.25 3.10
2529 2949 5.136105 CCCCATTTAAAATCAGGGAGAGAG 58.864 45.833 15.86 0.95 42.25 3.20
2530 2950 5.103940 CCCCATTTAAAATCAGGGAGAGAGA 60.104 44.000 15.86 0.00 42.25 3.10
2531 2951 6.060788 CCCATTTAAAATCAGGGAGAGAGAG 58.939 44.000 11.05 0.00 42.25 3.20
2532 2952 6.126652 CCCATTTAAAATCAGGGAGAGAGAGA 60.127 42.308 11.05 0.00 42.25 3.10
2533 2953 7.421147 CCCATTTAAAATCAGGGAGAGAGAGAT 60.421 40.741 11.05 0.00 42.25 2.75
2534 2954 7.997803 CCATTTAAAATCAGGGAGAGAGAGATT 59.002 37.037 0.00 0.00 0.00 2.40
2537 2957 9.494055 TTTAAAATCAGGGAGAGAGAGATTAGA 57.506 33.333 0.00 0.00 0.00 2.10
2538 2958 9.667607 TTAAAATCAGGGAGAGAGAGATTAGAT 57.332 33.333 0.00 0.00 0.00 1.98
2539 2959 7.543359 AAATCAGGGAGAGAGAGATTAGATG 57.457 40.000 0.00 0.00 0.00 2.90
2540 2960 4.406456 TCAGGGAGAGAGAGATTAGATGC 58.594 47.826 0.00 0.00 0.00 3.91
2541 2961 4.106179 TCAGGGAGAGAGAGATTAGATGCT 59.894 45.833 0.00 0.00 0.00 3.79
2542 2962 4.834496 CAGGGAGAGAGAGATTAGATGCTT 59.166 45.833 0.00 0.00 0.00 3.91
2543 2963 5.305128 CAGGGAGAGAGAGATTAGATGCTTT 59.695 44.000 0.00 0.00 0.00 3.51
2544 2964 5.305128 AGGGAGAGAGAGATTAGATGCTTTG 59.695 44.000 0.00 0.00 0.00 2.77
2545 2965 5.070313 GGGAGAGAGAGATTAGATGCTTTGT 59.930 44.000 0.00 0.00 0.00 2.83
2546 2966 5.984926 GGAGAGAGAGATTAGATGCTTTGTG 59.015 44.000 0.00 0.00 0.00 3.33
2547 2967 6.183360 GGAGAGAGAGATTAGATGCTTTGTGA 60.183 42.308 0.00 0.00 0.00 3.58
2548 2968 7.364149 AGAGAGAGATTAGATGCTTTGTGAT 57.636 36.000 0.00 0.00 0.00 3.06
2549 2969 7.794041 AGAGAGAGATTAGATGCTTTGTGATT 58.206 34.615 0.00 0.00 0.00 2.57
2550 2970 8.266473 AGAGAGAGATTAGATGCTTTGTGATTT 58.734 33.333 0.00 0.00 0.00 2.17
2551 2971 9.539825 GAGAGAGATTAGATGCTTTGTGATTTA 57.460 33.333 0.00 0.00 0.00 1.40
2559 2979 9.748708 TTAGATGCTTTGTGATTTATAAATGCC 57.251 29.630 15.39 6.16 0.00 4.40
2560 2980 7.784037 AGATGCTTTGTGATTTATAAATGCCA 58.216 30.769 15.39 8.52 0.00 4.92
2561 2981 7.707893 AGATGCTTTGTGATTTATAAATGCCAC 59.292 33.333 15.39 16.49 0.00 5.01
2562 2982 5.804473 TGCTTTGTGATTTATAAATGCCACG 59.196 36.000 15.39 7.08 30.17 4.94
2563 2983 5.804979 GCTTTGTGATTTATAAATGCCACGT 59.195 36.000 15.39 0.00 30.17 4.49
2564 2984 6.237542 GCTTTGTGATTTATAAATGCCACGTG 60.238 38.462 15.39 9.08 30.17 4.49
2565 2985 5.888691 TGTGATTTATAAATGCCACGTGT 57.111 34.783 15.39 0.00 30.17 4.49
2566 2986 5.874831 TGTGATTTATAAATGCCACGTGTC 58.125 37.500 15.39 0.98 30.17 3.67
2567 2987 5.412904 TGTGATTTATAAATGCCACGTGTCA 59.587 36.000 15.39 8.63 30.17 3.58
2568 2988 6.094742 TGTGATTTATAAATGCCACGTGTCAT 59.905 34.615 15.39 11.07 30.17 3.06
2569 2989 6.972328 GTGATTTATAAATGCCACGTGTCATT 59.028 34.615 18.45 18.45 34.66 2.57
2570 2990 7.165812 GTGATTTATAAATGCCACGTGTCATTC 59.834 37.037 23.50 11.05 32.27 2.67
2571 2991 6.502136 TTTATAAATGCCACGTGTCATTCA 57.498 33.333 23.50 11.49 32.27 2.57
2572 2992 6.691754 TTATAAATGCCACGTGTCATTCAT 57.308 33.333 23.50 17.75 32.27 2.57
2573 2993 3.492421 AAATGCCACGTGTCATTCATC 57.508 42.857 23.50 0.00 32.27 2.92
2574 2994 2.112380 ATGCCACGTGTCATTCATCA 57.888 45.000 15.65 0.00 0.00 3.07
2575 2995 1.441738 TGCCACGTGTCATTCATCAG 58.558 50.000 15.65 0.00 0.00 2.90
2576 2996 1.001860 TGCCACGTGTCATTCATCAGA 59.998 47.619 15.65 0.00 0.00 3.27
2577 2997 1.662629 GCCACGTGTCATTCATCAGAG 59.337 52.381 15.65 0.00 0.00 3.35
2578 2998 1.662629 CCACGTGTCATTCATCAGAGC 59.337 52.381 15.65 0.00 0.00 4.09
2579 2999 1.322637 CACGTGTCATTCATCAGAGCG 59.677 52.381 7.58 0.00 0.00 5.03
2580 3000 0.926155 CGTGTCATTCATCAGAGCGG 59.074 55.000 0.00 0.00 0.00 5.52
2581 3001 1.293924 GTGTCATTCATCAGAGCGGG 58.706 55.000 0.00 0.00 0.00 6.13
2582 3002 0.462581 TGTCATTCATCAGAGCGGGC 60.463 55.000 0.00 0.00 0.00 6.13
2583 3003 1.146930 TCATTCATCAGAGCGGGCC 59.853 57.895 0.00 0.00 0.00 5.80
2584 3004 1.147824 CATTCATCAGAGCGGGCCT 59.852 57.895 0.84 0.00 0.00 5.19
2585 3005 0.883814 CATTCATCAGAGCGGGCCTC 60.884 60.000 0.84 0.00 41.07 4.70
2586 3006 1.340399 ATTCATCAGAGCGGGCCTCA 61.340 55.000 0.84 0.00 43.31 3.86
2587 3007 2.202987 CATCAGAGCGGGCCTCAC 60.203 66.667 0.84 0.00 43.31 3.51
2588 3008 3.474570 ATCAGAGCGGGCCTCACC 61.475 66.667 0.84 0.00 43.31 4.02
2589 3009 3.991924 ATCAGAGCGGGCCTCACCT 62.992 63.158 0.84 0.00 43.31 4.00
2595 3015 2.125106 CGGGCCTCACCTGCTAAC 60.125 66.667 0.84 0.00 38.23 2.34
2596 3016 2.272471 GGGCCTCACCTGCTAACC 59.728 66.667 0.84 0.00 39.10 2.85
2597 3017 2.602676 GGGCCTCACCTGCTAACCA 61.603 63.158 0.84 0.00 39.10 3.67
2598 3018 1.609783 GGCCTCACCTGCTAACCAT 59.390 57.895 0.00 0.00 34.51 3.55
2599 3019 0.749454 GGCCTCACCTGCTAACCATG 60.749 60.000 0.00 0.00 34.51 3.66
2600 3020 0.253044 GCCTCACCTGCTAACCATGA 59.747 55.000 0.00 0.00 0.00 3.07
2601 3021 1.745141 GCCTCACCTGCTAACCATGAG 60.745 57.143 0.00 0.00 37.20 2.90
2602 3022 1.833630 CCTCACCTGCTAACCATGAGA 59.166 52.381 0.00 0.00 39.33 3.27
2603 3023 2.419297 CCTCACCTGCTAACCATGAGAC 60.419 54.545 0.00 0.00 39.33 3.36
2604 3024 1.555075 TCACCTGCTAACCATGAGACC 59.445 52.381 0.00 0.00 0.00 3.85
2605 3025 1.556911 CACCTGCTAACCATGAGACCT 59.443 52.381 0.00 0.00 0.00 3.85
2606 3026 1.556911 ACCTGCTAACCATGAGACCTG 59.443 52.381 0.00 0.00 0.00 4.00
2607 3027 1.134280 CCTGCTAACCATGAGACCTGG 60.134 57.143 0.00 0.00 39.80 4.45
2609 3029 1.555075 TGCTAACCATGAGACCTGGTC 59.445 52.381 19.20 19.20 46.29 4.02
2610 3030 1.834263 GCTAACCATGAGACCTGGTCT 59.166 52.381 28.70 28.70 46.29 3.85
2611 3031 2.237392 GCTAACCATGAGACCTGGTCTT 59.763 50.000 28.90 15.21 46.29 3.01
2612 3032 3.451178 GCTAACCATGAGACCTGGTCTTA 59.549 47.826 28.90 25.26 46.29 2.10
2613 3033 4.101741 GCTAACCATGAGACCTGGTCTTAT 59.898 45.833 28.90 26.29 46.29 1.73
2614 3034 5.304614 GCTAACCATGAGACCTGGTCTTATA 59.695 44.000 27.59 18.82 46.29 0.98
2615 3035 6.014156 GCTAACCATGAGACCTGGTCTTATAT 60.014 42.308 27.59 19.95 46.29 0.86
2616 3036 7.178628 GCTAACCATGAGACCTGGTCTTATATA 59.821 40.741 27.59 20.06 46.29 0.86
2617 3037 7.931015 AACCATGAGACCTGGTCTTATATAA 57.069 36.000 27.59 12.73 46.29 0.98
2618 3038 8.511748 AACCATGAGACCTGGTCTTATATAAT 57.488 34.615 27.59 14.88 46.29 1.28
2619 3039 8.511748 ACCATGAGACCTGGTCTTATATAATT 57.488 34.615 27.59 8.70 43.59 1.40
2620 3040 8.949421 ACCATGAGACCTGGTCTTATATAATTT 58.051 33.333 27.59 8.05 43.59 1.82
2621 3041 9.799106 CCATGAGACCTGGTCTTATATAATTTT 57.201 33.333 27.59 7.40 43.53 1.82
2916 3353 3.371285 CGGTCGATCTTCCCTTTTTCTTC 59.629 47.826 0.00 0.00 0.00 2.87
2918 3355 5.004448 GGTCGATCTTCCCTTTTTCTTCTT 58.996 41.667 0.00 0.00 0.00 2.52
2954 3397 5.192522 ACTGTCTCCCTCATGGTCAATTTAT 59.807 40.000 0.00 0.00 34.77 1.40
2960 3403 8.651389 TCTCCCTCATGGTCAATTTATTAGTAG 58.349 37.037 0.00 0.00 34.77 2.57
2962 3405 9.442062 TCCCTCATGGTCAATTTATTAGTAGTA 57.558 33.333 0.00 0.00 34.77 1.82
2999 3442 6.122277 GGAAGGAGGATTCATTCATGTGTAA 58.878 40.000 4.62 0.00 43.93 2.41
3043 3486 4.811024 TGTGCTTAAGAAATCAGCGGATAG 59.189 41.667 6.67 0.00 36.24 2.08
3048 3491 6.677781 TTAAGAAATCAGCGGATAGGTTTG 57.322 37.500 0.00 0.00 32.09 2.93
3051 3494 0.546122 ATCAGCGGATAGGTTTGGCA 59.454 50.000 0.00 0.00 30.03 4.92
3052 3495 0.107703 TCAGCGGATAGGTTTGGCAG 60.108 55.000 0.00 0.00 0.00 4.85
3056 3499 1.134491 GCGGATAGGTTTGGCAGTACT 60.134 52.381 0.00 0.00 0.00 2.73
3057 3500 2.550978 CGGATAGGTTTGGCAGTACTG 58.449 52.381 18.93 18.93 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 6.281405 AGTTACGCTGGACCTGAAAATATAG 58.719 40.000 1.91 0.00 0.00 1.31
176 178 3.272334 GCTCGGTTATGGCAGCGG 61.272 66.667 0.00 0.00 38.23 5.52
187 189 1.167851 CAAATGTGACATGGCTCGGT 58.832 50.000 0.00 0.00 0.00 4.69
307 476 1.204312 GCACGTTCGTTCCTTGCTC 59.796 57.895 0.00 0.00 0.00 4.26
348 522 4.803098 ACTTCAGATTTAGCCGTACAGT 57.197 40.909 0.00 0.00 0.00 3.55
349 523 4.330074 CCAACTTCAGATTTAGCCGTACAG 59.670 45.833 0.00 0.00 0.00 2.74
350 524 4.250464 CCAACTTCAGATTTAGCCGTACA 58.750 43.478 0.00 0.00 0.00 2.90
351 525 4.251268 ACCAACTTCAGATTTAGCCGTAC 58.749 43.478 0.00 0.00 0.00 3.67
352 526 4.546829 ACCAACTTCAGATTTAGCCGTA 57.453 40.909 0.00 0.00 0.00 4.02
446 621 2.106332 GTGATGTCGCCTACCCCG 59.894 66.667 0.00 0.00 0.00 5.73
502 681 4.760047 ACACCTGGCCGACGATGC 62.760 66.667 0.00 0.00 0.00 3.91
505 684 4.980805 GCAACACCTGGCCGACGA 62.981 66.667 0.00 0.00 0.00 4.20
509 688 4.424566 GCATGCAACACCTGGCCG 62.425 66.667 14.21 0.00 0.00 6.13
551 887 2.675844 TCGCGACTGGTTTTTCATATGG 59.324 45.455 3.71 0.00 0.00 2.74
558 894 3.587797 TCTAGATCGCGACTGGTTTTT 57.412 42.857 12.93 0.00 0.00 1.94
873 1226 0.177141 CCGAGGGAAATTCGCACCTA 59.823 55.000 12.54 0.00 36.76 3.08
1036 1400 2.555757 CAAGGAGGCAAAGAAGGACAAG 59.444 50.000 0.00 0.00 0.00 3.16
1037 1401 2.586425 CAAGGAGGCAAAGAAGGACAA 58.414 47.619 0.00 0.00 0.00 3.18
1038 1402 1.202927 CCAAGGAGGCAAAGAAGGACA 60.203 52.381 0.00 0.00 0.00 4.02
1074 1438 2.044946 AAAGACTGCGCCATCCCC 60.045 61.111 4.18 0.00 0.00 4.81
1647 2029 1.930520 GCTCTCCTCCTCCTCCTCT 59.069 63.158 0.00 0.00 0.00 3.69
1660 2048 2.299294 CTGTCGTCCTCGTCGCTCTC 62.299 65.000 0.00 0.00 38.33 3.20
1661 2049 2.358369 TGTCGTCCTCGTCGCTCT 60.358 61.111 0.00 0.00 38.33 4.09
1662 2050 2.098680 CTGTCGTCCTCGTCGCTC 59.901 66.667 0.00 0.00 38.33 5.03
2052 2452 3.664888 TCGTCCCTTCCCCTCCGA 61.665 66.667 0.00 0.00 0.00 4.55
2244 2663 3.547468 GCACACGCAAACATTCATATTCC 59.453 43.478 0.00 0.00 38.36 3.01
2245 2664 4.414852 AGCACACGCAAACATTCATATTC 58.585 39.130 0.00 0.00 42.27 1.75
2247 2666 3.691118 AGAGCACACGCAAACATTCATAT 59.309 39.130 0.00 0.00 42.27 1.78
2250 2669 1.264020 GAGAGCACACGCAAACATTCA 59.736 47.619 0.00 0.00 42.27 2.57
2288 2708 2.755650 GCCAGAGTCAAAGAAACGAGA 58.244 47.619 0.00 0.00 0.00 4.04
2289 2709 1.457303 CGCCAGAGTCAAAGAAACGAG 59.543 52.381 0.00 0.00 0.00 4.18
2290 2710 1.067974 TCGCCAGAGTCAAAGAAACGA 59.932 47.619 0.00 0.00 0.00 3.85
2291 2711 1.497991 TCGCCAGAGTCAAAGAAACG 58.502 50.000 0.00 0.00 0.00 3.60
2292 2712 2.872858 ACTTCGCCAGAGTCAAAGAAAC 59.127 45.455 0.00 0.00 0.00 2.78
2295 2715 1.686587 TCACTTCGCCAGAGTCAAAGA 59.313 47.619 0.00 0.00 0.00 2.52
2319 2739 4.023193 AGGAATCCACACATCGAACAAAAC 60.023 41.667 0.61 0.00 0.00 2.43
2323 2743 2.354704 GGAGGAATCCACACATCGAACA 60.355 50.000 0.61 0.00 0.00 3.18
2347 2767 2.755103 CCTCGCCAAAGCTTTTTATCCT 59.245 45.455 9.53 0.00 36.60 3.24
2348 2768 2.159240 CCCTCGCCAAAGCTTTTTATCC 60.159 50.000 9.53 0.00 36.60 2.59
2370 2790 4.425577 AAGTGAACATTCCGATTCTTGC 57.574 40.909 0.00 0.00 0.00 4.01
2371 2791 5.630680 CCAAAAGTGAACATTCCGATTCTTG 59.369 40.000 0.00 0.00 0.00 3.02
2400 2820 0.535553 AACTAAAAGGCCGGCGAACA 60.536 50.000 22.54 3.05 0.00 3.18
2401 2821 0.109919 CAACTAAAAGGCCGGCGAAC 60.110 55.000 22.54 6.73 0.00 3.95
2402 2822 0.250381 TCAACTAAAAGGCCGGCGAA 60.250 50.000 22.54 2.25 0.00 4.70
2403 2823 0.250381 TTCAACTAAAAGGCCGGCGA 60.250 50.000 22.54 5.45 0.00 5.54
2404 2824 0.594110 TTTCAACTAAAAGGCCGGCG 59.406 50.000 22.54 7.92 0.00 6.46
2405 2825 2.804697 TTTTCAACTAAAAGGCCGGC 57.195 45.000 21.18 21.18 32.05 6.13
2416 2836 8.924511 TGGTCTCATAGAATTCTTTTTCAACT 57.075 30.769 14.36 0.00 0.00 3.16
2417 2837 8.239998 CCTGGTCTCATAGAATTCTTTTTCAAC 58.760 37.037 14.36 5.77 0.00 3.18
2418 2838 7.944554 ACCTGGTCTCATAGAATTCTTTTTCAA 59.055 33.333 14.36 0.00 0.00 2.69
2419 2839 7.461749 ACCTGGTCTCATAGAATTCTTTTTCA 58.538 34.615 14.36 0.00 0.00 2.69
2420 2840 7.826744 AGACCTGGTCTCATAGAATTCTTTTTC 59.173 37.037 23.49 0.51 38.71 2.29
2421 2841 7.694093 AGACCTGGTCTCATAGAATTCTTTTT 58.306 34.615 23.49 0.00 38.71 1.94
2422 2842 7.264294 AGACCTGGTCTCATAGAATTCTTTT 57.736 36.000 23.49 0.00 38.71 2.27
2423 2843 6.882768 AGACCTGGTCTCATAGAATTCTTT 57.117 37.500 23.49 2.41 38.71 2.52
2436 2856 2.282251 TCGCGTGAGACCTGGTCT 60.282 61.111 28.70 28.70 46.42 3.85
2437 2857 2.126424 GTCGCGTGAGACCTGGTC 60.126 66.667 19.20 19.20 35.22 4.02
2438 2858 2.910479 TGTCGCGTGAGACCTGGT 60.910 61.111 5.77 0.00 40.26 4.00
2439 2859 2.430921 GTGTCGCGTGAGACCTGG 60.431 66.667 14.89 0.00 40.26 4.45
2443 2863 0.801067 GTATGGGTGTCGCGTGAGAC 60.801 60.000 17.27 17.27 41.30 3.36
2444 2864 0.963856 AGTATGGGTGTCGCGTGAGA 60.964 55.000 5.77 0.00 0.00 3.27
2445 2865 0.802222 CAGTATGGGTGTCGCGTGAG 60.802 60.000 5.77 0.00 0.00 3.51
2446 2866 1.214325 CAGTATGGGTGTCGCGTGA 59.786 57.895 5.77 0.00 0.00 4.35
2447 2867 0.179111 ATCAGTATGGGTGTCGCGTG 60.179 55.000 5.77 0.00 36.16 5.34
2448 2868 0.179111 CATCAGTATGGGTGTCGCGT 60.179 55.000 5.77 0.00 36.16 6.01
2449 2869 2.593376 CATCAGTATGGGTGTCGCG 58.407 57.895 0.00 0.00 36.16 5.87
2458 2878 3.494626 GCCACGTGTTATCCATCAGTATG 59.505 47.826 15.65 0.00 37.54 2.39
2459 2879 3.133901 TGCCACGTGTTATCCATCAGTAT 59.866 43.478 15.65 0.00 0.00 2.12
2460 2880 2.498078 TGCCACGTGTTATCCATCAGTA 59.502 45.455 15.65 0.00 0.00 2.74
2461 2881 1.277842 TGCCACGTGTTATCCATCAGT 59.722 47.619 15.65 0.00 0.00 3.41
2462 2882 2.022764 TGCCACGTGTTATCCATCAG 57.977 50.000 15.65 0.00 0.00 2.90
2463 2883 2.708216 ATGCCACGTGTTATCCATCA 57.292 45.000 15.65 0.00 0.00 3.07
2464 2884 2.942376 TGAATGCCACGTGTTATCCATC 59.058 45.455 15.65 4.13 0.00 3.51
2465 2885 2.682856 GTGAATGCCACGTGTTATCCAT 59.317 45.455 15.65 6.00 35.86 3.41
2466 2886 2.080693 GTGAATGCCACGTGTTATCCA 58.919 47.619 15.65 4.02 35.86 3.41
2467 2887 2.825086 GTGAATGCCACGTGTTATCC 57.175 50.000 15.65 1.27 35.86 2.59
2476 2896 1.067516 AGTGTGCTTTGTGAATGCCAC 59.932 47.619 0.00 0.00 45.88 5.01
2477 2897 1.401761 AGTGTGCTTTGTGAATGCCA 58.598 45.000 0.00 0.00 0.00 4.92
2478 2898 2.129607 CAAGTGTGCTTTGTGAATGCC 58.870 47.619 0.00 0.00 31.49 4.40
2479 2899 2.791004 GTCAAGTGTGCTTTGTGAATGC 59.209 45.455 0.00 0.00 31.49 3.56
2480 2900 3.374745 GGTCAAGTGTGCTTTGTGAATG 58.625 45.455 0.00 0.00 31.49 2.67
2481 2901 2.362077 GGGTCAAGTGTGCTTTGTGAAT 59.638 45.455 0.00 0.00 31.49 2.57
2482 2902 1.748493 GGGTCAAGTGTGCTTTGTGAA 59.252 47.619 0.00 0.00 31.49 3.18
2483 2903 1.340502 TGGGTCAAGTGTGCTTTGTGA 60.341 47.619 0.00 0.00 31.49 3.58
2484 2904 1.102154 TGGGTCAAGTGTGCTTTGTG 58.898 50.000 0.00 0.00 31.49 3.33
2485 2905 1.102978 GTGGGTCAAGTGTGCTTTGT 58.897 50.000 0.00 0.00 31.49 2.83
2486 2906 0.385390 GGTGGGTCAAGTGTGCTTTG 59.615 55.000 0.00 0.00 31.49 2.77
2487 2907 0.755327 GGGTGGGTCAAGTGTGCTTT 60.755 55.000 0.00 0.00 31.49 3.51
2488 2908 1.152756 GGGTGGGTCAAGTGTGCTT 60.153 57.895 0.00 0.00 34.82 3.91
2489 2909 2.515901 GGGTGGGTCAAGTGTGCT 59.484 61.111 0.00 0.00 0.00 4.40
2490 2910 2.597510 GGGGTGGGTCAAGTGTGC 60.598 66.667 0.00 0.00 0.00 4.57
2491 2911 2.115266 GGGGGTGGGTCAAGTGTG 59.885 66.667 0.00 0.00 0.00 3.82
2505 2925 4.079212 TCTCTCCCTGATTTTAAATGGGGG 60.079 45.833 18.57 16.56 39.73 5.40
2506 2926 5.103940 TCTCTCTCCCTGATTTTAAATGGGG 60.104 44.000 14.96 14.96 38.43 4.96
2507 2927 6.006275 TCTCTCTCCCTGATTTTAAATGGG 57.994 41.667 6.72 6.72 39.22 4.00
2508 2928 6.893583 TCTCTCTCTCCCTGATTTTAAATGG 58.106 40.000 0.00 0.00 0.00 3.16
2509 2929 8.977267 AATCTCTCTCTCCCTGATTTTAAATG 57.023 34.615 0.00 0.00 0.00 2.32
2511 2931 9.494055 TCTAATCTCTCTCTCCCTGATTTTAAA 57.506 33.333 0.00 0.00 0.00 1.52
2512 2932 9.667607 ATCTAATCTCTCTCTCCCTGATTTTAA 57.332 33.333 0.00 0.00 0.00 1.52
2513 2933 9.087871 CATCTAATCTCTCTCTCCCTGATTTTA 57.912 37.037 0.00 0.00 0.00 1.52
2514 2934 7.473228 GCATCTAATCTCTCTCTCCCTGATTTT 60.473 40.741 0.00 0.00 0.00 1.82
2515 2935 6.014327 GCATCTAATCTCTCTCTCCCTGATTT 60.014 42.308 0.00 0.00 0.00 2.17
2516 2936 5.481473 GCATCTAATCTCTCTCTCCCTGATT 59.519 44.000 0.00 0.00 0.00 2.57
2517 2937 5.018809 GCATCTAATCTCTCTCTCCCTGAT 58.981 45.833 0.00 0.00 0.00 2.90
2518 2938 4.106179 AGCATCTAATCTCTCTCTCCCTGA 59.894 45.833 0.00 0.00 0.00 3.86
2519 2939 4.410099 AGCATCTAATCTCTCTCTCCCTG 58.590 47.826 0.00 0.00 0.00 4.45
2520 2940 4.747265 AGCATCTAATCTCTCTCTCCCT 57.253 45.455 0.00 0.00 0.00 4.20
2521 2941 5.070313 ACAAAGCATCTAATCTCTCTCTCCC 59.930 44.000 0.00 0.00 0.00 4.30
2522 2942 5.984926 CACAAAGCATCTAATCTCTCTCTCC 59.015 44.000 0.00 0.00 0.00 3.71
2523 2943 6.804677 TCACAAAGCATCTAATCTCTCTCTC 58.195 40.000 0.00 0.00 0.00 3.20
2524 2944 6.788598 TCACAAAGCATCTAATCTCTCTCT 57.211 37.500 0.00 0.00 0.00 3.10
2525 2945 8.436046 AAATCACAAAGCATCTAATCTCTCTC 57.564 34.615 0.00 0.00 0.00 3.20
2533 2953 9.748708 GGCATTTATAAATCACAAAGCATCTAA 57.251 29.630 7.76 0.00 0.00 2.10
2534 2954 8.911965 TGGCATTTATAAATCACAAAGCATCTA 58.088 29.630 7.76 0.00 0.00 1.98
2535 2955 7.707893 GTGGCATTTATAAATCACAAAGCATCT 59.292 33.333 18.36 0.00 0.00 2.90
2536 2956 7.306167 CGTGGCATTTATAAATCACAAAGCATC 60.306 37.037 21.04 11.62 0.00 3.91
2537 2957 6.476380 CGTGGCATTTATAAATCACAAAGCAT 59.524 34.615 21.04 0.00 0.00 3.79
2538 2958 5.804473 CGTGGCATTTATAAATCACAAAGCA 59.196 36.000 21.04 7.11 0.00 3.91
2539 2959 5.804979 ACGTGGCATTTATAAATCACAAAGC 59.195 36.000 21.04 14.82 0.00 3.51
2540 2960 6.806249 ACACGTGGCATTTATAAATCACAAAG 59.194 34.615 21.57 15.54 0.00 2.77
2541 2961 6.682746 ACACGTGGCATTTATAAATCACAAA 58.317 32.000 21.57 5.26 0.00 2.83
2542 2962 6.072452 TGACACGTGGCATTTATAAATCACAA 60.072 34.615 23.03 0.00 0.00 3.33
2543 2963 5.412904 TGACACGTGGCATTTATAAATCACA 59.587 36.000 23.03 14.76 0.00 3.58
2544 2964 5.874831 TGACACGTGGCATTTATAAATCAC 58.125 37.500 23.03 15.28 0.00 3.06
2545 2965 6.691754 ATGACACGTGGCATTTATAAATCA 57.308 33.333 31.22 14.70 42.08 2.57
2556 2976 1.001860 TCTGATGAATGACACGTGGCA 59.998 47.619 29.28 29.28 37.54 4.92
2557 2977 1.662629 CTCTGATGAATGACACGTGGC 59.337 52.381 21.57 19.24 0.00 5.01
2558 2978 1.662629 GCTCTGATGAATGACACGTGG 59.337 52.381 21.57 1.66 0.00 4.94
2559 2979 1.322637 CGCTCTGATGAATGACACGTG 59.677 52.381 15.48 15.48 0.00 4.49
2560 2980 1.633561 CGCTCTGATGAATGACACGT 58.366 50.000 0.00 0.00 0.00 4.49
2561 2981 0.926155 CCGCTCTGATGAATGACACG 59.074 55.000 0.00 0.00 0.00 4.49
2562 2982 1.293924 CCCGCTCTGATGAATGACAC 58.706 55.000 0.00 0.00 0.00 3.67
2563 2983 0.462581 GCCCGCTCTGATGAATGACA 60.463 55.000 0.00 0.00 0.00 3.58
2564 2984 1.162800 GGCCCGCTCTGATGAATGAC 61.163 60.000 0.00 0.00 0.00 3.06
2565 2985 1.146930 GGCCCGCTCTGATGAATGA 59.853 57.895 0.00 0.00 0.00 2.57
2566 2986 0.883814 GAGGCCCGCTCTGATGAATG 60.884 60.000 0.00 0.00 0.00 2.67
2567 2987 1.340399 TGAGGCCCGCTCTGATGAAT 61.340 55.000 0.00 0.00 0.00 2.57
2568 2988 1.989508 TGAGGCCCGCTCTGATGAA 60.990 57.895 0.00 0.00 0.00 2.57
2569 2989 2.364186 TGAGGCCCGCTCTGATGA 60.364 61.111 0.00 0.00 0.00 2.92
2570 2990 2.202987 GTGAGGCCCGCTCTGATG 60.203 66.667 0.00 0.00 0.00 3.07
2571 2991 3.474570 GGTGAGGCCCGCTCTGAT 61.475 66.667 0.00 0.00 0.00 2.90
2572 2992 4.704103 AGGTGAGGCCCGCTCTGA 62.704 66.667 0.00 0.00 38.26 3.27
2573 2993 4.463879 CAGGTGAGGCCCGCTCTG 62.464 72.222 0.00 0.00 38.26 3.35
2577 2997 4.096003 TTAGCAGGTGAGGCCCGC 62.096 66.667 0.00 0.00 38.26 6.13
2578 2998 2.125106 GTTAGCAGGTGAGGCCCG 60.125 66.667 0.00 0.00 38.26 6.13
2579 2999 1.926426 ATGGTTAGCAGGTGAGGCCC 61.926 60.000 0.00 0.00 38.26 5.80
2580 3000 0.749454 CATGGTTAGCAGGTGAGGCC 60.749 60.000 0.00 0.00 37.58 5.19
2581 3001 0.253044 TCATGGTTAGCAGGTGAGGC 59.747 55.000 0.00 0.00 0.00 4.70
2582 3002 1.833630 TCTCATGGTTAGCAGGTGAGG 59.166 52.381 13.00 0.00 37.49 3.86
2583 3003 2.419297 GGTCTCATGGTTAGCAGGTGAG 60.419 54.545 8.28 8.28 38.07 3.51
2584 3004 1.555075 GGTCTCATGGTTAGCAGGTGA 59.445 52.381 0.00 0.00 0.00 4.02
2585 3005 1.556911 AGGTCTCATGGTTAGCAGGTG 59.443 52.381 0.00 0.00 0.00 4.00
2586 3006 1.556911 CAGGTCTCATGGTTAGCAGGT 59.443 52.381 0.00 0.00 0.00 4.00
2587 3007 1.134280 CCAGGTCTCATGGTTAGCAGG 60.134 57.143 0.00 0.00 32.85 4.85
2588 3008 2.322355 CCAGGTCTCATGGTTAGCAG 57.678 55.000 0.00 0.00 32.85 4.24
2595 3015 9.799106 AAAATTATATAAGACCAGGTCTCATGG 57.201 33.333 23.17 0.00 42.59 3.66
2620 3040 4.121317 TCTGTAAGCGAAACGAGGAAAAA 58.879 39.130 0.00 0.00 0.00 1.94
2621 3041 3.719924 TCTGTAAGCGAAACGAGGAAAA 58.280 40.909 0.00 0.00 0.00 2.29
2622 3042 3.374220 TCTGTAAGCGAAACGAGGAAA 57.626 42.857 0.00 0.00 0.00 3.13
2623 3043 3.057104 TCATCTGTAAGCGAAACGAGGAA 60.057 43.478 0.00 0.00 0.00 3.36
2624 3044 2.490509 TCATCTGTAAGCGAAACGAGGA 59.509 45.455 0.00 0.00 0.00 3.71
2625 3045 2.854777 CTCATCTGTAAGCGAAACGAGG 59.145 50.000 0.00 0.00 0.00 4.63
2626 3046 3.759418 TCTCATCTGTAAGCGAAACGAG 58.241 45.455 0.00 0.00 0.00 4.18
2627 3047 3.842732 TCTCATCTGTAAGCGAAACGA 57.157 42.857 0.00 0.00 0.00 3.85
2628 3048 4.027295 GTCATCTCATCTGTAAGCGAAACG 60.027 45.833 0.00 0.00 0.00 3.60
2629 3049 4.864806 TGTCATCTCATCTGTAAGCGAAAC 59.135 41.667 0.00 0.00 0.00 2.78
2696 3116 8.943002 CCGTCTCTTAACCAAAGTTGTATTATT 58.057 33.333 0.00 0.00 36.68 1.40
2697 3117 8.098912 ACCGTCTCTTAACCAAAGTTGTATTAT 58.901 33.333 0.00 0.00 36.68 1.28
2789 3225 1.293924 CAATCTGCTCTGCCTTACGG 58.706 55.000 0.00 0.00 0.00 4.02
2918 3355 2.158667 GGGAGACAGTGGAGTGGAAAAA 60.159 50.000 0.00 0.00 0.00 1.94
2954 3397 7.093465 CCTTCCAATTCACAGGAGTACTACTAA 60.093 40.741 7.47 0.00 34.91 2.24
2960 3403 4.508662 CTCCTTCCAATTCACAGGAGTAC 58.491 47.826 12.50 0.00 45.25 2.73
2962 3405 3.710209 CTCCTTCCAATTCACAGGAGT 57.290 47.619 12.50 0.00 45.25 3.85
2968 3411 5.653769 TGAATGAATCCTCCTTCCAATTCAC 59.346 40.000 0.00 0.00 40.00 3.18
2999 3442 0.178961 GAGCCTCCCCCAAGTTGTTT 60.179 55.000 1.45 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.