Multiple sequence alignment - TraesCS2A01G117200

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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 TraesCS2A01G117200 chr2A 100.000 2799 0 0 1 2799 67093486 67090688 0.000000e+00 5169.0
1 TraesCS2A01G117200 chr2B 95.364 2049 66 14 1 2039 104081944 104079915 0.000000e+00 3230.0
2 TraesCS2A01G117200 chr2B 91.540 1253 83 9 976 2226 103440339 103441570 0.000000e+00 1705.0
3 TraesCS2A01G117200 chr2B 90.066 453 41 2 2348 2799 103474948 103475397 4.020000e-163 584.0
4 TraesCS2A01G117200 chr2B 87.778 270 22 6 676 936 103440070 103440337 3.500000e-79 305.0
5 TraesCS2A01G117200 chr2B 80.000 200 25 6 2615 2799 104079426 104079227 1.750000e-27 134.0
6 TraesCS2A01G117200 chr2D 92.256 1498 62 15 359 1824 67426422 67427897 0.000000e+00 2074.0
7 TraesCS2A01G117200 chr2D 92.174 460 19 8 1821 2268 67428286 67428740 3.930000e-178 634.0
8 TraesCS2A01G117200 chr2D 95.954 173 6 1 111 282 67426253 67426425 2.120000e-71 279.0
9 TraesCS2A01G117200 chr2D 96.512 86 3 0 281 366 194390226 194390311 2.910000e-30 143.0
10 TraesCS2A01G117200 chr5A 84.557 395 34 13 482 875 56732298 56731930 1.580000e-97 366.0
11 TraesCS2A01G117200 chr5A 79.391 427 57 17 1244 1666 56731598 56731199 3.550000e-69 272.0
12 TraesCS2A01G117200 chr5A 87.952 83 2 2 880 954 56731846 56731764 1.070000e-14 91.6
13 TraesCS2A01G117200 chr5A 89.655 58 2 4 2584 2639 584017572 584017627 1.390000e-08 71.3
14 TraesCS2A01G117200 chr3D 94.565 92 5 0 281 372 8141865 8141774 2.910000e-30 143.0
15 TraesCS2A01G117200 chr1D 96.512 86 3 0 281 366 90754212 90754297 2.910000e-30 143.0
16 TraesCS2A01G117200 chr1D 94.565 92 5 0 281 372 263322586 263322495 2.910000e-30 143.0
17 TraesCS2A01G117200 chr1D 95.349 86 4 0 281 366 295568318 295568403 1.350000e-28 137.0
18 TraesCS2A01G117200 chr1D 95.349 86 4 0 281 366 313916253 313916338 1.350000e-28 137.0
19 TraesCS2A01G117200 chr6D 95.349 86 4 0 281 366 265667801 265667886 1.350000e-28 137.0
20 TraesCS2A01G117200 chr6D 93.478 92 6 0 281 372 379159559 379159468 1.350000e-28 137.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G117200 chr2A 67090688 67093486 2798 True 5169.000000 5169 100.000000 1 2799 1 chr2A.!!$R1 2798
1 TraesCS2A01G117200 chr2B 104079227 104081944 2717 True 1682.000000 3230 87.682000 1 2799 2 chr2B.!!$R1 2798
2 TraesCS2A01G117200 chr2B 103440070 103441570 1500 False 1005.000000 1705 89.659000 676 2226 2 chr2B.!!$F2 1550
3 TraesCS2A01G117200 chr2D 67426253 67428740 2487 False 995.666667 2074 93.461333 111 2268 3 chr2D.!!$F2 2157
4 TraesCS2A01G117200 chr5A 56731199 56732298 1099 True 243.200000 366 83.966667 482 1666 3 chr5A.!!$R1 1184

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
296 299 0.042131 TGGTACTCCCTCCGTTCCAT 59.958 55.0 0.0 0.0 28.53 3.41 F
1403 1557 1.098050 GTCTTGCTATGCCCCTTGTG 58.902 55.0 0.0 0.0 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1564 1718 0.107643 TCGAAAGTGGTGACCATGCA 59.892 50.0 7.94 0.0 35.28 3.96 R
2383 2943 0.036306 TTTTCCTGAGACCGCCTTCC 59.964 55.0 0.00 0.0 0.00 3.46 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
94 96 4.766373 TGATCTGTGCTTTCCATGCTTTTA 59.234 37.500 0.00 0.00 0.00 1.52
132 134 7.673776 GCCAACAAAACAGTTGTAGACAATTTG 60.674 37.037 13.67 13.67 45.66 2.32
199 202 6.036953 TGTGTTCCTGAAAACATGCATTTTTC 59.963 34.615 24.68 24.68 40.96 2.29
263 266 9.469807 CTCCTCTATTGTATGCTAAACAGTTAG 57.530 37.037 0.00 0.00 39.90 2.34
295 298 0.901580 GTGGTACTCCCTCCGTTCCA 60.902 60.000 0.00 0.00 30.66 3.53
296 299 0.042131 TGGTACTCCCTCCGTTCCAT 59.958 55.000 0.00 0.00 28.53 3.41
297 300 1.288633 TGGTACTCCCTCCGTTCCATA 59.711 52.381 0.00 0.00 28.53 2.74
424 432 4.678309 GCCACACTGATGTAAGTCCTCTAC 60.678 50.000 0.00 0.00 36.72 2.59
528 536 9.653287 TTTGTACTCCAGAACATATTTCTGTAG 57.347 33.333 18.28 15.93 43.19 2.74
651 662 8.129211 TCCTAATTCGTATCATGTATATGCTCG 58.871 37.037 0.00 0.52 34.21 5.03
707 718 7.849804 TTTTGAATAATCTGACTAGTCTGCC 57.150 36.000 23.01 8.95 0.00 4.85
849 864 6.942576 AGTGTGTTCTAGGTTATTGAATTGCT 59.057 34.615 0.00 0.00 0.00 3.91
1150 1283 6.664816 TCCTTGTCATTATTCCTGCTGAATTT 59.335 34.615 7.24 0.00 40.92 1.82
1376 1530 3.102972 TCTTGCTATGCCTCTTCTCTGT 58.897 45.455 0.00 0.00 0.00 3.41
1377 1531 3.517100 TCTTGCTATGCCTCTTCTCTGTT 59.483 43.478 0.00 0.00 0.00 3.16
1403 1557 1.098050 GTCTTGCTATGCCCCTTGTG 58.902 55.000 0.00 0.00 0.00 3.33
1458 1612 8.350722 TCTAAATCATACAAGGAGTACATCGTC 58.649 37.037 0.00 0.00 35.05 4.20
1498 1652 3.969312 TCCAGAAGCTGATATCATGGACA 59.031 43.478 17.37 1.49 32.44 4.02
1503 1657 1.532868 GCTGATATCATGGACAACGGC 59.467 52.381 5.72 0.00 0.00 5.68
1564 1718 3.197116 CCTAACTGACTCGGGTAAACCAT 59.803 47.826 0.81 0.00 40.22 3.55
1591 1745 4.223255 TGGTCACCACTTTCGATACCATAA 59.777 41.667 0.00 0.00 30.84 1.90
1598 1752 5.751509 CCACTTTCGATACCATAATTCACGA 59.248 40.000 0.00 0.00 0.00 4.35
1712 1866 3.214696 CCAGGTTGGGATGAGGAATAC 57.785 52.381 0.00 0.00 32.67 1.89
1719 1873 2.171237 TGGGATGAGGAATACACTGCAG 59.829 50.000 13.48 13.48 0.00 4.41
1720 1874 2.486191 GGGATGAGGAATACACTGCAGG 60.486 54.545 19.93 9.66 0.00 4.85
1721 1875 2.216898 GATGAGGAATACACTGCAGGC 58.783 52.381 19.93 0.00 0.00 4.85
1722 1876 0.983467 TGAGGAATACACTGCAGGCA 59.017 50.000 19.93 2.32 0.00 4.75
1996 2542 6.238266 GGATGTCAACGAACACTCAAAAGTTA 60.238 38.462 0.00 0.00 31.71 2.24
2008 2554 5.068198 CACTCAAAAGTTATCATGGGATGGG 59.932 44.000 0.00 0.00 32.05 4.00
2089 2640 8.746751 CATATCGTGTCTAACAGAATAACACAG 58.253 37.037 4.99 0.00 40.10 3.66
2107 2658 3.369147 CACAGAATGGAGAAACACTAGCG 59.631 47.826 0.00 0.00 43.62 4.26
2128 2679 4.326205 CGCATATCGACAAACACTCAAAG 58.674 43.478 0.00 0.00 41.67 2.77
2131 2682 5.554636 CATATCGACAAACACTCAAAGCTC 58.445 41.667 0.00 0.00 0.00 4.09
2135 2686 2.213499 ACAAACACTCAAAGCTCCTCG 58.787 47.619 0.00 0.00 0.00 4.63
2238 2798 0.324368 TGGATACAGGCTCTGACGGT 60.324 55.000 8.91 0.00 46.17 4.83
2268 2828 1.921243 TCGTCATCACAAGGCATACG 58.079 50.000 0.00 0.00 0.00 3.06
2269 2829 1.203758 TCGTCATCACAAGGCATACGT 59.796 47.619 0.00 0.00 0.00 3.57
2270 2830 1.999735 CGTCATCACAAGGCATACGTT 59.000 47.619 0.00 0.00 0.00 3.99
2271 2831 2.222796 CGTCATCACAAGGCATACGTTG 60.223 50.000 0.00 0.00 45.13 4.10
2272 2832 3.000041 GTCATCACAAGGCATACGTTGA 59.000 45.455 5.40 0.00 42.88 3.18
2291 2851 3.541831 CGTGTCGAACGCATCCGG 61.542 66.667 0.00 0.00 46.99 5.14
2293 2853 2.025418 GTGTCGAACGCATCCGGTT 61.025 57.895 0.00 0.00 39.22 4.44
2294 2854 1.301087 TGTCGAACGCATCCGGTTT 60.301 52.632 0.00 0.00 39.22 3.27
2296 2856 1.738830 TCGAACGCATCCGGTTTCC 60.739 57.895 0.00 0.00 39.22 3.13
2297 2857 1.740296 CGAACGCATCCGGTTTCCT 60.740 57.895 0.00 0.00 39.22 3.36
2298 2858 0.458889 CGAACGCATCCGGTTTCCTA 60.459 55.000 0.00 0.00 39.22 2.94
2299 2859 1.287425 GAACGCATCCGGTTTCCTAG 58.713 55.000 0.00 0.00 39.22 3.02
2300 2860 0.899720 AACGCATCCGGTTTCCTAGA 59.100 50.000 0.00 0.00 39.22 2.43
2301 2861 0.899720 ACGCATCCGGTTTCCTAGAA 59.100 50.000 0.00 0.00 39.22 2.10
2302 2862 1.276989 ACGCATCCGGTTTCCTAGAAA 59.723 47.619 0.00 0.00 39.22 2.52
2303 2863 2.289819 ACGCATCCGGTTTCCTAGAAAA 60.290 45.455 0.00 0.00 39.22 2.29
2307 2867 4.398044 GCATCCGGTTTCCTAGAAAAATGA 59.602 41.667 0.00 0.00 0.00 2.57
2308 2868 5.067805 GCATCCGGTTTCCTAGAAAAATGAT 59.932 40.000 0.00 0.00 0.00 2.45
2309 2869 6.729187 CATCCGGTTTCCTAGAAAAATGATC 58.271 40.000 0.00 0.00 0.00 2.92
2310 2870 4.873827 TCCGGTTTCCTAGAAAAATGATCG 59.126 41.667 0.00 0.00 0.00 3.69
2312 2872 4.495844 CGGTTTCCTAGAAAAATGATCGCC 60.496 45.833 0.00 0.00 0.00 5.54
2313 2873 4.398044 GGTTTCCTAGAAAAATGATCGCCA 59.602 41.667 0.00 0.00 0.00 5.69
2314 2874 5.449177 GGTTTCCTAGAAAAATGATCGCCAG 60.449 44.000 0.00 0.00 0.00 4.85
2315 2875 3.206150 TCCTAGAAAAATGATCGCCAGC 58.794 45.455 0.00 0.00 0.00 4.85
2317 2877 3.003068 CCTAGAAAAATGATCGCCAGCTG 59.997 47.826 6.78 6.78 0.00 4.24
2319 2879 1.745087 GAAAAATGATCGCCAGCTGGA 59.255 47.619 37.21 17.52 37.39 3.86
2320 2880 1.838112 AAAATGATCGCCAGCTGGAA 58.162 45.000 37.21 23.08 37.39 3.53
2321 2881 1.098050 AAATGATCGCCAGCTGGAAC 58.902 50.000 37.21 21.64 37.39 3.62
2322 2882 1.091771 AATGATCGCCAGCTGGAACG 61.092 55.000 37.21 28.96 37.39 3.95
2323 2883 1.960040 ATGATCGCCAGCTGGAACGA 61.960 55.000 37.21 32.83 37.39 3.85
2325 2885 2.564553 GATCGCCAGCTGGAACGAGT 62.565 60.000 37.21 22.50 34.21 4.18
2326 2886 2.564553 ATCGCCAGCTGGAACGAGTC 62.565 60.000 37.21 15.41 34.21 3.36
2328 2888 2.651361 CCAGCTGGAACGAGTCGT 59.349 61.111 29.88 13.56 43.97 4.34
2340 2900 3.313012 ACGAGTCGTTGGATCATTCAA 57.687 42.857 13.56 0.00 36.35 2.69
2341 2901 3.861840 ACGAGTCGTTGGATCATTCAAT 58.138 40.909 13.56 0.00 36.35 2.57
2342 2902 4.253685 ACGAGTCGTTGGATCATTCAATT 58.746 39.130 13.56 0.00 36.35 2.32
2345 2905 5.314923 AGTCGTTGGATCATTCAATTTGG 57.685 39.130 0.00 0.00 0.00 3.28
2347 2907 5.653769 AGTCGTTGGATCATTCAATTTGGAT 59.346 36.000 0.00 0.00 0.00 3.41
2348 2908 5.973565 GTCGTTGGATCATTCAATTTGGATC 59.026 40.000 0.00 1.71 36.33 3.36
2349 2909 4.971830 CGTTGGATCATTCAATTTGGATCG 59.028 41.667 0.00 0.00 37.59 3.69
2351 2911 6.563422 GTTGGATCATTCAATTTGGATCGAA 58.437 36.000 0.00 2.80 37.59 3.71
2352 2912 6.964807 TGGATCATTCAATTTGGATCGAAT 57.035 33.333 0.00 0.00 37.59 3.34
2353 2913 6.741109 TGGATCATTCAATTTGGATCGAATG 58.259 36.000 10.71 10.71 43.87 2.67
2354 2914 6.321945 TGGATCATTCAATTTGGATCGAATGT 59.678 34.615 14.48 6.28 43.29 2.71
2355 2915 6.860023 GGATCATTCAATTTGGATCGAATGTC 59.140 38.462 14.48 11.90 43.29 3.06
2356 2916 7.255381 GGATCATTCAATTTGGATCGAATGTCT 60.255 37.037 14.48 7.16 43.29 3.41
2357 2917 7.019774 TCATTCAATTTGGATCGAATGTCTC 57.980 36.000 14.48 0.00 43.29 3.36
2358 2918 5.818136 TTCAATTTGGATCGAATGTCTCC 57.182 39.130 0.00 0.00 0.00 3.71
2360 2920 5.118990 TCAATTTGGATCGAATGTCTCCTC 58.881 41.667 3.79 0.00 0.00 3.71
2361 2921 4.760530 ATTTGGATCGAATGTCTCCTCA 57.239 40.909 3.79 0.00 0.00 3.86
2362 2922 3.526931 TTGGATCGAATGTCTCCTCAC 57.473 47.619 3.79 0.00 0.00 3.51
2363 2923 2.739943 TGGATCGAATGTCTCCTCACT 58.260 47.619 3.79 0.00 0.00 3.41
2364 2924 3.099905 TGGATCGAATGTCTCCTCACTT 58.900 45.455 3.79 0.00 0.00 3.16
2365 2925 3.131223 TGGATCGAATGTCTCCTCACTTC 59.869 47.826 3.79 0.00 0.00 3.01
2367 2927 2.525368 TCGAATGTCTCCTCACTTCCA 58.475 47.619 0.00 0.00 0.00 3.53
2368 2928 3.099905 TCGAATGTCTCCTCACTTCCAT 58.900 45.455 0.00 0.00 0.00 3.41
2369 2929 4.278310 TCGAATGTCTCCTCACTTCCATA 58.722 43.478 0.00 0.00 0.00 2.74
2370 2930 4.098044 TCGAATGTCTCCTCACTTCCATAC 59.902 45.833 0.00 0.00 0.00 2.39
2371 2931 4.098654 CGAATGTCTCCTCACTTCCATACT 59.901 45.833 0.00 0.00 0.00 2.12
2372 2932 5.394663 CGAATGTCTCCTCACTTCCATACTT 60.395 44.000 0.00 0.00 0.00 2.24
2373 2933 6.380079 AATGTCTCCTCACTTCCATACTTT 57.620 37.500 0.00 0.00 0.00 2.66
2374 2934 5.825593 TGTCTCCTCACTTCCATACTTTT 57.174 39.130 0.00 0.00 0.00 2.27
2375 2935 5.551233 TGTCTCCTCACTTCCATACTTTTG 58.449 41.667 0.00 0.00 0.00 2.44
2376 2936 4.393371 GTCTCCTCACTTCCATACTTTTGC 59.607 45.833 0.00 0.00 0.00 3.68
2378 2938 4.579869 TCCTCACTTCCATACTTTTGCTC 58.420 43.478 0.00 0.00 0.00 4.26
2379 2939 3.691609 CCTCACTTCCATACTTTTGCTCC 59.308 47.826 0.00 0.00 0.00 4.70
2380 2940 4.326826 CTCACTTCCATACTTTTGCTCCA 58.673 43.478 0.00 0.00 0.00 3.86
2382 2942 5.136828 TCACTTCCATACTTTTGCTCCAAA 58.863 37.500 0.00 0.00 0.00 3.28
2383 2943 5.241506 TCACTTCCATACTTTTGCTCCAAAG 59.758 40.000 3.04 3.04 34.72 2.77
2384 2944 4.524328 ACTTCCATACTTTTGCTCCAAAGG 59.476 41.667 8.03 0.00 36.67 3.11
2386 2946 4.735369 TCCATACTTTTGCTCCAAAGGAA 58.265 39.130 6.79 0.00 34.71 3.36
2387 2947 4.766891 TCCATACTTTTGCTCCAAAGGAAG 59.233 41.667 6.79 0.00 34.71 3.46
2388 2948 4.082026 CCATACTTTTGCTCCAAAGGAAGG 60.082 45.833 6.79 3.25 34.71 3.46
2389 2949 1.688735 ACTTTTGCTCCAAAGGAAGGC 59.311 47.619 6.79 0.00 34.71 4.35
2390 2950 0.673437 TTTTGCTCCAAAGGAAGGCG 59.327 50.000 0.00 0.00 34.72 5.52
2391 2951 1.178534 TTTGCTCCAAAGGAAGGCGG 61.179 55.000 0.00 0.00 34.04 6.13
2392 2952 2.034221 GCTCCAAAGGAAGGCGGT 59.966 61.111 0.00 0.00 0.00 5.68
2393 2953 2.041115 GCTCCAAAGGAAGGCGGTC 61.041 63.158 0.00 0.00 0.00 4.79
2394 2954 1.679898 CTCCAAAGGAAGGCGGTCT 59.320 57.895 0.00 0.00 0.00 3.85
2395 2955 0.391793 CTCCAAAGGAAGGCGGTCTC 60.392 60.000 0.00 0.00 0.00 3.36
2397 2957 0.674895 CCAAAGGAAGGCGGTCTCAG 60.675 60.000 0.00 0.00 0.00 3.35
2398 2958 0.674895 CAAAGGAAGGCGGTCTCAGG 60.675 60.000 0.00 0.00 0.00 3.86
2412 3132 3.442076 GTCTCAGGAAAACTAGGGAGGA 58.558 50.000 0.00 0.00 0.00 3.71
2435 3155 5.609423 AGCTAACCTCTCACATTCATCATC 58.391 41.667 0.00 0.00 0.00 2.92
2436 3156 5.129980 AGCTAACCTCTCACATTCATCATCA 59.870 40.000 0.00 0.00 0.00 3.07
2437 3157 5.236047 GCTAACCTCTCACATTCATCATCAC 59.764 44.000 0.00 0.00 0.00 3.06
2446 3166 5.105063 CACATTCATCATCACGTACTGACT 58.895 41.667 1.69 0.00 0.00 3.41
2454 3174 0.859232 CACGTACTGACTGTTGCACC 59.141 55.000 0.00 0.00 0.00 5.01
2456 3176 1.139989 CGTACTGACTGTTGCACCAG 58.860 55.000 10.07 10.07 38.45 4.00
2467 3187 0.537143 TTGCACCAGCCGATTTGTCT 60.537 50.000 0.00 0.00 41.13 3.41
2470 3190 1.081892 CACCAGCCGATTTGTCTGAG 58.918 55.000 0.00 0.00 0.00 3.35
2473 3193 1.338105 CCAGCCGATTTGTCTGAGTCA 60.338 52.381 0.00 0.00 0.00 3.41
2517 3238 2.690734 CCCAAACCCTAGCCCTCCC 61.691 68.421 0.00 0.00 0.00 4.30
2518 3239 1.928567 CCAAACCCTAGCCCTCCCA 60.929 63.158 0.00 0.00 0.00 4.37
2519 3240 1.609783 CAAACCCTAGCCCTCCCAG 59.390 63.158 0.00 0.00 0.00 4.45
2520 3241 1.163555 AAACCCTAGCCCTCCCAGT 59.836 57.895 0.00 0.00 0.00 4.00
2521 3242 0.477795 AAACCCTAGCCCTCCCAGTT 60.478 55.000 0.00 0.00 0.00 3.16
2522 3243 1.208165 AACCCTAGCCCTCCCAGTTG 61.208 60.000 0.00 0.00 0.00 3.16
2523 3244 1.616628 CCCTAGCCCTCCCAGTTGT 60.617 63.158 0.00 0.00 0.00 3.32
2524 3245 1.604378 CCTAGCCCTCCCAGTTGTG 59.396 63.158 0.00 0.00 0.00 3.33
2525 3246 1.201429 CCTAGCCCTCCCAGTTGTGT 61.201 60.000 0.00 0.00 0.00 3.72
2526 3247 0.250513 CTAGCCCTCCCAGTTGTGTC 59.749 60.000 0.00 0.00 0.00 3.67
2527 3248 1.198759 TAGCCCTCCCAGTTGTGTCC 61.199 60.000 0.00 0.00 0.00 4.02
2528 3249 2.757077 CCCTCCCAGTTGTGTCCC 59.243 66.667 0.00 0.00 0.00 4.46
2535 3256 3.379452 TCCCAGTTGTGTCCCAATTTTT 58.621 40.909 0.00 0.00 35.02 1.94
2541 3262 2.392662 TGTGTCCCAATTTTTCCAGCA 58.607 42.857 0.00 0.00 0.00 4.41
2546 3267 1.605202 CCCAATTTTTCCAGCACCGTG 60.605 52.381 0.00 0.00 0.00 4.94
2556 3277 2.125269 GCACCGTGCCCGATTAGT 60.125 61.111 12.80 0.00 37.42 2.24
2559 3280 2.108362 CCGTGCCCGATTAGTCCC 59.892 66.667 0.00 0.00 35.63 4.46
2564 3285 3.135814 CCCGATTAGTCCCGGTCC 58.864 66.667 0.00 0.00 43.93 4.46
2569 3290 1.411246 CGATTAGTCCCGGTCCATGAA 59.589 52.381 0.00 0.00 0.00 2.57
2570 3291 2.802057 CGATTAGTCCCGGTCCATGAAC 60.802 54.545 0.00 0.00 0.00 3.18
2571 3292 0.533491 TTAGTCCCGGTCCATGAACG 59.467 55.000 0.00 0.00 42.95 3.95
2576 3297 4.827481 CGGTCCATGAACGGTAGG 57.173 61.111 0.00 0.00 39.28 3.18
2577 3298 1.520787 CGGTCCATGAACGGTAGGC 60.521 63.158 0.00 0.00 39.28 3.93
2578 3299 1.153229 GGTCCATGAACGGTAGGCC 60.153 63.158 0.00 0.00 0.00 5.19
2579 3300 1.600107 GTCCATGAACGGTAGGCCA 59.400 57.895 5.01 0.00 34.09 5.36
2580 3301 0.462047 GTCCATGAACGGTAGGCCAG 60.462 60.000 5.01 0.00 34.09 4.85
2581 3302 1.819632 CCATGAACGGTAGGCCAGC 60.820 63.158 5.01 0.00 34.09 4.85
2582 3303 1.078497 CATGAACGGTAGGCCAGCA 60.078 57.895 5.01 0.00 34.09 4.41
2583 3304 0.464373 CATGAACGGTAGGCCAGCAT 60.464 55.000 5.01 0.00 34.09 3.79
2584 3305 0.464373 ATGAACGGTAGGCCAGCATG 60.464 55.000 5.01 0.00 34.09 4.06
2585 3306 1.220749 GAACGGTAGGCCAGCATGA 59.779 57.895 5.01 0.00 39.69 3.07
2586 3307 0.179045 GAACGGTAGGCCAGCATGAT 60.179 55.000 5.01 0.00 39.69 2.45
2587 3308 0.464373 AACGGTAGGCCAGCATGATG 60.464 55.000 5.01 3.34 39.69 3.07
2588 3309 1.337384 ACGGTAGGCCAGCATGATGA 61.337 55.000 13.69 0.00 39.69 2.92
2589 3310 0.602106 CGGTAGGCCAGCATGATGAG 60.602 60.000 13.69 3.71 39.69 2.90
2590 3311 0.471617 GGTAGGCCAGCATGATGAGT 59.528 55.000 13.69 0.00 39.69 3.41
2591 3312 1.694150 GGTAGGCCAGCATGATGAGTA 59.306 52.381 13.69 0.00 39.69 2.59
2592 3313 2.548920 GGTAGGCCAGCATGATGAGTAC 60.549 54.545 13.69 10.18 39.69 2.73
2593 3314 0.471617 AGGCCAGCATGATGAGTACC 59.528 55.000 13.69 8.26 39.69 3.34
2594 3315 0.536006 GGCCAGCATGATGAGTACCC 60.536 60.000 13.69 0.88 39.69 3.69
2595 3316 0.471617 GCCAGCATGATGAGTACCCT 59.528 55.000 13.69 0.00 39.69 4.34
2596 3317 1.542108 GCCAGCATGATGAGTACCCTC 60.542 57.143 13.69 0.00 39.69 4.30
2597 3318 2.045524 CCAGCATGATGAGTACCCTCT 58.954 52.381 13.69 0.00 39.69 3.69
2598 3319 3.234353 CCAGCATGATGAGTACCCTCTA 58.766 50.000 13.69 0.00 39.69 2.43
2599 3320 3.643320 CCAGCATGATGAGTACCCTCTAA 59.357 47.826 13.69 0.00 39.69 2.10
2600 3321 4.285517 CCAGCATGATGAGTACCCTCTAAT 59.714 45.833 13.69 0.00 39.69 1.73
2601 3322 5.477510 CAGCATGATGAGTACCCTCTAATC 58.522 45.833 4.56 0.00 39.69 1.75
2602 3323 4.530161 AGCATGATGAGTACCCTCTAATCC 59.470 45.833 0.00 0.00 38.61 3.01
2603 3324 4.284490 GCATGATGAGTACCCTCTAATCCA 59.716 45.833 0.00 0.00 38.61 3.41
2604 3325 5.568423 GCATGATGAGTACCCTCTAATCCAG 60.568 48.000 0.00 0.00 38.61 3.86
2605 3326 4.483950 TGATGAGTACCCTCTAATCCAGG 58.516 47.826 0.00 0.00 38.61 4.45
2606 3327 4.170053 TGATGAGTACCCTCTAATCCAGGA 59.830 45.833 0.00 0.00 38.61 3.86
2607 3328 3.912248 TGAGTACCCTCTAATCCAGGAC 58.088 50.000 0.00 0.00 38.61 3.85
2611 3332 0.753262 CCCTCTAATCCAGGACACCG 59.247 60.000 0.00 0.00 31.91 4.94
2613 3334 2.662866 CCTCTAATCCAGGACACCGTA 58.337 52.381 0.00 0.00 31.91 4.02
2618 3339 5.263599 TCTAATCCAGGACACCGTAAGTAA 58.736 41.667 0.00 0.00 0.00 2.24
2620 3341 1.895131 TCCAGGACACCGTAAGTAACC 59.105 52.381 0.00 0.00 0.00 2.85
2624 3345 2.042979 AGGACACCGTAAGTAACCCCTA 59.957 50.000 0.00 0.00 0.00 3.53
2626 3347 3.368427 GGACACCGTAAGTAACCCCTAAC 60.368 52.174 0.00 0.00 0.00 2.34
2632 3353 4.339530 CCGTAAGTAACCCCTAACCTAGTC 59.660 50.000 0.00 0.00 0.00 2.59
2637 3358 5.658474 AGTAACCCCTAACCTAGTCTTCAA 58.342 41.667 0.00 0.00 0.00 2.69
2639 3360 2.838813 ACCCCTAACCTAGTCTTCAAGC 59.161 50.000 0.00 0.00 0.00 4.01
2640 3361 2.170817 CCCCTAACCTAGTCTTCAAGCC 59.829 54.545 0.00 0.00 0.00 4.35
2646 3367 2.035632 CCTAGTCTTCAAGCCGAGGAT 58.964 52.381 0.00 0.00 31.52 3.24
2650 3371 1.066858 GTCTTCAAGCCGAGGATGTCA 60.067 52.381 0.00 0.00 31.52 3.58
2662 3383 3.403936 GATGTCAATCCTTCCCCCG 57.596 57.895 0.00 0.00 0.00 5.73
2663 3384 0.837272 GATGTCAATCCTTCCCCCGA 59.163 55.000 0.00 0.00 0.00 5.14
2669 3390 1.768870 CAATCCTTCCCCCGATGTAGT 59.231 52.381 0.00 0.00 0.00 2.73
2674 3395 0.906775 TTCCCCCGATGTAGTGGTTC 59.093 55.000 0.00 0.00 0.00 3.62
2683 3404 3.367087 CGATGTAGTGGTTCCTTCTTCGT 60.367 47.826 0.00 0.00 30.28 3.85
2686 3407 3.640029 TGTAGTGGTTCCTTCTTCGTTCT 59.360 43.478 0.00 0.00 0.00 3.01
2690 3411 1.459975 GGTTCCTTCTTCGTTCTTCGC 59.540 52.381 0.00 0.00 39.67 4.70
2691 3412 2.405172 GTTCCTTCTTCGTTCTTCGCT 58.595 47.619 0.00 0.00 39.67 4.93
2693 3414 2.673833 TCCTTCTTCGTTCTTCGCTTC 58.326 47.619 0.00 0.00 39.67 3.86
2694 3415 2.035449 TCCTTCTTCGTTCTTCGCTTCA 59.965 45.455 0.00 0.00 39.67 3.02
2725 3447 3.099905 TCCTGACATCTCAGTTCCGAAT 58.900 45.455 0.00 0.00 42.36 3.34
2749 3485 2.612000 TCTTTGGTCCGAGGTCCTTTA 58.388 47.619 6.93 0.00 0.00 1.85
2754 3490 0.539986 GTCCGAGGTCCTTTATGCCA 59.460 55.000 0.00 0.00 0.00 4.92
2761 3497 4.698304 CGAGGTCCTTTATGCCAAAGTTAA 59.302 41.667 0.00 0.00 0.00 2.01
2767 3503 7.310423 GGTCCTTTATGCCAAAGTTAATTCCTT 60.310 37.037 7.03 0.00 0.00 3.36
2768 3504 7.545615 GTCCTTTATGCCAAAGTTAATTCCTTG 59.454 37.037 7.03 0.00 0.00 3.61
2774 3510 3.244976 CAAAGTTAATTCCTTGCAGGCG 58.755 45.455 0.00 0.00 34.61 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 178 5.989551 AAAATGCATGTTTTCAGGAACAC 57.010 34.783 0.00 0.00 41.86 3.32
199 202 5.465390 TCATAGTTGAAGAACCAAACGAGTG 59.535 40.000 0.00 0.00 31.81 3.51
263 266 4.001652 GGAGTACCACTTAACAAAGGCTC 58.998 47.826 0.00 0.00 35.97 4.70
330 333 9.893305 CCGTCCCATAATATAAGAACATTTTTC 57.107 33.333 0.00 0.00 0.00 2.29
354 357 6.651975 AACTGATAATAAGTACTCCCTCCG 57.348 41.667 0.00 0.00 0.00 4.63
484 492 7.840931 AGTACAAATACAGATCATCACACAGA 58.159 34.615 0.00 0.00 33.30 3.41
707 718 6.968131 TTCCAGATTCATCAGTAAACGAAG 57.032 37.500 0.00 0.00 0.00 3.79
849 864 4.508551 ACATCTCATCTACCAAATGGCA 57.491 40.909 0.00 0.00 39.32 4.92
1042 1150 8.356657 CAATTCAAATTAACTGTACCTCAACCA 58.643 33.333 0.00 0.00 0.00 3.67
1403 1557 2.126734 GCATGGACGTTGCAGCAC 60.127 61.111 5.84 0.00 39.90 4.40
1435 1589 7.113658 AGACGATGTACTCCTTGTATGATTT 57.886 36.000 0.00 0.00 33.23 2.17
1436 1590 6.716934 AGACGATGTACTCCTTGTATGATT 57.283 37.500 0.00 0.00 33.23 2.57
1458 1612 0.755686 GAGGTGGCCTCTGGATGTAG 59.244 60.000 3.32 0.00 46.41 2.74
1564 1718 0.107643 TCGAAAGTGGTGACCATGCA 59.892 50.000 7.94 0.00 35.28 3.96
1598 1752 0.320160 GGTTAACCAGGCGACGAAGT 60.320 55.000 20.12 0.00 39.18 3.01
1719 1873 4.256180 CCATAGCCCGACCCTGCC 62.256 72.222 0.00 0.00 0.00 4.85
1720 1874 4.256180 CCCATAGCCCGACCCTGC 62.256 72.222 0.00 0.00 0.00 4.85
1721 1875 2.768344 ACCCATAGCCCGACCCTG 60.768 66.667 0.00 0.00 0.00 4.45
1722 1876 2.768344 CACCCATAGCCCGACCCT 60.768 66.667 0.00 0.00 0.00 4.34
1996 2542 4.220724 CTGTTGAATTCCCATCCCATGAT 58.779 43.478 2.27 0.00 0.00 2.45
2082 2633 5.932303 GCTAGTGTTTCTCCATTCTGTGTTA 59.068 40.000 0.00 0.00 0.00 2.41
2089 2640 2.346803 TGCGCTAGTGTTTCTCCATTC 58.653 47.619 9.73 0.00 0.00 2.67
2107 2658 4.091424 GCTTTGAGTGTTTGTCGATATGC 58.909 43.478 0.00 0.00 0.00 3.14
2128 2679 1.354040 CATCTTGTGTGTCGAGGAGC 58.646 55.000 0.00 0.00 0.00 4.70
2131 2682 2.654749 TAGCATCTTGTGTGTCGAGG 57.345 50.000 0.00 0.00 0.00 4.63
2135 2686 3.931578 AGTCCTTAGCATCTTGTGTGTC 58.068 45.455 0.00 0.00 0.00 3.67
2170 2721 1.340568 TGTCCATGGTTGCACAACATG 59.659 47.619 12.58 15.71 42.85 3.21
2232 2792 1.610038 ACGAACTGTGATGTACCGTCA 59.390 47.619 0.00 0.00 0.00 4.35
2238 2798 4.513198 TGTGATGACGAACTGTGATGTA 57.487 40.909 0.00 0.00 0.00 2.29
2275 2835 1.562575 AAACCGGATGCGTTCGACAC 61.563 55.000 9.46 0.00 0.00 3.67
2276 2836 1.286354 GAAACCGGATGCGTTCGACA 61.286 55.000 9.46 0.00 0.00 4.35
2277 2837 1.418755 GAAACCGGATGCGTTCGAC 59.581 57.895 9.46 0.00 0.00 4.20
2278 2838 1.738830 GGAAACCGGATGCGTTCGA 60.739 57.895 9.46 0.00 0.00 3.71
2279 2839 0.458889 TAGGAAACCGGATGCGTTCG 60.459 55.000 9.46 0.00 0.00 3.95
2281 2841 0.899720 TCTAGGAAACCGGATGCGTT 59.100 50.000 9.46 0.00 0.00 4.84
2283 2843 2.018542 TTTCTAGGAAACCGGATGCG 57.981 50.000 9.46 0.00 0.00 4.73
2284 2844 4.398044 TCATTTTTCTAGGAAACCGGATGC 59.602 41.667 9.46 1.01 0.00 3.91
2286 2846 5.527582 CGATCATTTTTCTAGGAAACCGGAT 59.472 40.000 9.46 0.00 0.00 4.18
2287 2847 4.873827 CGATCATTTTTCTAGGAAACCGGA 59.126 41.667 9.46 0.00 0.00 5.14
2288 2848 4.495844 GCGATCATTTTTCTAGGAAACCGG 60.496 45.833 0.00 0.00 0.00 5.28
2289 2849 4.495844 GGCGATCATTTTTCTAGGAAACCG 60.496 45.833 0.00 0.00 0.00 4.44
2290 2850 4.398044 TGGCGATCATTTTTCTAGGAAACC 59.602 41.667 0.00 0.00 0.00 3.27
2291 2851 5.560966 TGGCGATCATTTTTCTAGGAAAC 57.439 39.130 0.00 0.00 0.00 2.78
2293 2853 3.627577 GCTGGCGATCATTTTTCTAGGAA 59.372 43.478 0.00 0.00 0.00 3.36
2294 2854 3.118261 AGCTGGCGATCATTTTTCTAGGA 60.118 43.478 0.00 0.00 0.00 2.94
2296 2856 3.003068 CCAGCTGGCGATCATTTTTCTAG 59.997 47.826 22.33 0.00 0.00 2.43
2297 2857 2.945008 CCAGCTGGCGATCATTTTTCTA 59.055 45.455 22.33 0.00 0.00 2.10
2298 2858 1.747355 CCAGCTGGCGATCATTTTTCT 59.253 47.619 22.33 0.00 0.00 2.52
2299 2859 1.745087 TCCAGCTGGCGATCATTTTTC 59.255 47.619 28.91 0.00 34.44 2.29
2300 2860 1.838112 TCCAGCTGGCGATCATTTTT 58.162 45.000 28.91 0.00 34.44 1.94
2301 2861 1.474077 GTTCCAGCTGGCGATCATTTT 59.526 47.619 28.91 0.00 34.44 1.82
2302 2862 1.098050 GTTCCAGCTGGCGATCATTT 58.902 50.000 28.91 0.00 34.44 2.32
2303 2863 1.091771 CGTTCCAGCTGGCGATCATT 61.092 55.000 28.91 0.00 34.44 2.57
2307 2867 2.185350 CTCGTTCCAGCTGGCGAT 59.815 61.111 28.34 0.00 31.22 4.58
2308 2868 3.282745 GACTCGTTCCAGCTGGCGA 62.283 63.158 28.91 27.78 34.44 5.54
2309 2869 2.811317 GACTCGTTCCAGCTGGCG 60.811 66.667 28.91 25.23 34.44 5.69
2310 2870 2.811317 CGACTCGTTCCAGCTGGC 60.811 66.667 28.91 14.17 34.44 4.85
2320 2880 3.313012 TTGAATGATCCAACGACTCGT 57.687 42.857 0.00 0.00 43.97 4.18
2321 2881 4.864916 AATTGAATGATCCAACGACTCG 57.135 40.909 0.00 0.00 0.00 4.18
2322 2882 5.123820 TCCAAATTGAATGATCCAACGACTC 59.876 40.000 0.00 0.00 0.00 3.36
2323 2883 5.009631 TCCAAATTGAATGATCCAACGACT 58.990 37.500 0.00 0.00 0.00 4.18
2325 2885 5.220835 CGATCCAAATTGAATGATCCAACGA 60.221 40.000 0.00 0.00 31.94 3.85
2326 2886 4.971830 CGATCCAAATTGAATGATCCAACG 59.028 41.667 0.00 0.00 31.94 4.10
2328 2888 6.772360 TTCGATCCAAATTGAATGATCCAA 57.228 33.333 0.00 0.00 31.52 3.53
2329 2889 6.964807 ATTCGATCCAAATTGAATGATCCA 57.035 33.333 0.00 0.00 42.18 3.41
2335 2895 6.125029 AGGAGACATTCGATCCAAATTGAAT 58.875 36.000 4.88 0.00 43.83 2.57
2336 2896 5.500234 AGGAGACATTCGATCCAAATTGAA 58.500 37.500 4.88 0.00 39.18 2.69
2338 2898 4.877823 TGAGGAGACATTCGATCCAAATTG 59.122 41.667 4.88 0.00 35.45 2.32
2340 2900 4.163078 AGTGAGGAGACATTCGATCCAAAT 59.837 41.667 4.88 0.00 35.45 2.32
2341 2901 3.515502 AGTGAGGAGACATTCGATCCAAA 59.484 43.478 4.88 0.00 35.45 3.28
2342 2902 3.099905 AGTGAGGAGACATTCGATCCAA 58.900 45.455 4.88 0.00 35.45 3.53
2345 2905 3.131223 TGGAAGTGAGGAGACATTCGATC 59.869 47.826 0.00 0.00 0.00 3.69
2347 2907 2.525368 TGGAAGTGAGGAGACATTCGA 58.475 47.619 0.00 0.00 0.00 3.71
2348 2908 3.533606 ATGGAAGTGAGGAGACATTCG 57.466 47.619 0.00 0.00 0.00 3.34
2349 2909 5.606348 AGTATGGAAGTGAGGAGACATTC 57.394 43.478 0.00 0.00 0.00 2.67
2351 2911 6.176183 CAAAAGTATGGAAGTGAGGAGACAT 58.824 40.000 0.00 0.00 0.00 3.06
2352 2912 5.551233 CAAAAGTATGGAAGTGAGGAGACA 58.449 41.667 0.00 0.00 0.00 3.41
2353 2913 4.393371 GCAAAAGTATGGAAGTGAGGAGAC 59.607 45.833 0.00 0.00 0.00 3.36
2354 2914 4.287067 AGCAAAAGTATGGAAGTGAGGAGA 59.713 41.667 0.00 0.00 0.00 3.71
2355 2915 4.583871 AGCAAAAGTATGGAAGTGAGGAG 58.416 43.478 0.00 0.00 0.00 3.69
2356 2916 4.565652 GGAGCAAAAGTATGGAAGTGAGGA 60.566 45.833 0.00 0.00 0.00 3.71
2357 2917 3.691609 GGAGCAAAAGTATGGAAGTGAGG 59.308 47.826 0.00 0.00 0.00 3.86
2358 2918 4.326826 TGGAGCAAAAGTATGGAAGTGAG 58.673 43.478 0.00 0.00 0.00 3.51
2360 2920 5.452078 TTTGGAGCAAAAGTATGGAAGTG 57.548 39.130 0.00 0.00 29.89 3.16
2361 2921 4.524328 CCTTTGGAGCAAAAGTATGGAAGT 59.476 41.667 6.00 0.00 35.73 3.01
2362 2922 4.766891 TCCTTTGGAGCAAAAGTATGGAAG 59.233 41.667 6.00 0.00 35.73 3.46
2363 2923 4.735369 TCCTTTGGAGCAAAAGTATGGAA 58.265 39.130 6.00 0.00 35.73 3.53
2364 2924 4.380843 TCCTTTGGAGCAAAAGTATGGA 57.619 40.909 6.00 0.00 35.73 3.41
2365 2925 4.082026 CCTTCCTTTGGAGCAAAAGTATGG 60.082 45.833 6.00 0.00 35.73 2.74
2367 2927 3.511540 GCCTTCCTTTGGAGCAAAAGTAT 59.488 43.478 6.00 0.00 35.73 2.12
2368 2928 2.890945 GCCTTCCTTTGGAGCAAAAGTA 59.109 45.455 6.00 0.00 35.73 2.24
2369 2929 1.688735 GCCTTCCTTTGGAGCAAAAGT 59.311 47.619 6.00 0.00 35.73 2.66
2370 2930 1.336240 CGCCTTCCTTTGGAGCAAAAG 60.336 52.381 0.00 0.00 36.99 2.27
2371 2931 0.673437 CGCCTTCCTTTGGAGCAAAA 59.327 50.000 0.00 0.00 32.75 2.44
2372 2932 1.178534 CCGCCTTCCTTTGGAGCAAA 61.179 55.000 0.00 0.00 31.21 3.68
2373 2933 1.603455 CCGCCTTCCTTTGGAGCAA 60.603 57.895 0.00 0.00 31.21 3.91
2374 2934 2.034066 CCGCCTTCCTTTGGAGCA 59.966 61.111 0.00 0.00 31.21 4.26
2375 2935 2.034221 ACCGCCTTCCTTTGGAGC 59.966 61.111 0.00 0.00 31.21 4.70
2376 2936 0.391793 GAGACCGCCTTCCTTTGGAG 60.392 60.000 0.00 0.00 31.21 3.86
2378 2938 0.674895 CTGAGACCGCCTTCCTTTGG 60.675 60.000 0.00 0.00 0.00 3.28
2379 2939 0.674895 CCTGAGACCGCCTTCCTTTG 60.675 60.000 0.00 0.00 0.00 2.77
2380 2940 0.836400 TCCTGAGACCGCCTTCCTTT 60.836 55.000 0.00 0.00 0.00 3.11
2382 2942 0.836400 TTTCCTGAGACCGCCTTCCT 60.836 55.000 0.00 0.00 0.00 3.36
2383 2943 0.036306 TTTTCCTGAGACCGCCTTCC 59.964 55.000 0.00 0.00 0.00 3.46
2384 2944 1.157585 GTTTTCCTGAGACCGCCTTC 58.842 55.000 0.00 0.00 0.00 3.46
2386 2946 1.550976 CTAGTTTTCCTGAGACCGCCT 59.449 52.381 0.00 0.00 0.00 5.52
2387 2947 1.405661 CCTAGTTTTCCTGAGACCGCC 60.406 57.143 0.00 0.00 0.00 6.13
2388 2948 1.405661 CCCTAGTTTTCCTGAGACCGC 60.406 57.143 0.00 0.00 0.00 5.68
2389 2949 2.166664 CTCCCTAGTTTTCCTGAGACCG 59.833 54.545 0.00 0.00 0.00 4.79
2390 2950 2.502130 CCTCCCTAGTTTTCCTGAGACC 59.498 54.545 0.00 0.00 0.00 3.85
2391 2951 3.442076 TCCTCCCTAGTTTTCCTGAGAC 58.558 50.000 0.00 0.00 0.00 3.36
2392 2952 3.714144 CTCCTCCCTAGTTTTCCTGAGA 58.286 50.000 0.00 0.00 0.00 3.27
2393 2953 2.169561 GCTCCTCCCTAGTTTTCCTGAG 59.830 54.545 0.00 0.00 0.00 3.35
2394 2954 2.188817 GCTCCTCCCTAGTTTTCCTGA 58.811 52.381 0.00 0.00 0.00 3.86
2395 2955 2.192263 AGCTCCTCCCTAGTTTTCCTG 58.808 52.381 0.00 0.00 0.00 3.86
2397 2957 3.118334 GGTTAGCTCCTCCCTAGTTTTCC 60.118 52.174 0.00 0.00 0.00 3.13
2398 2958 3.775866 AGGTTAGCTCCTCCCTAGTTTTC 59.224 47.826 0.00 0.00 31.32 2.29
2412 3132 5.129980 TGATGATGAATGTGAGAGGTTAGCT 59.870 40.000 0.00 0.00 0.00 3.32
2421 3141 5.230936 GTCAGTACGTGATGATGAATGTGAG 59.769 44.000 0.00 0.00 37.56 3.51
2422 3142 5.102313 GTCAGTACGTGATGATGAATGTGA 58.898 41.667 0.00 0.00 37.56 3.58
2423 3143 5.005107 CAGTCAGTACGTGATGATGAATGTG 59.995 44.000 0.00 0.00 37.56 3.21
2435 3155 0.859232 GGTGCAACAGTCAGTACGTG 59.141 55.000 0.00 0.00 39.98 4.49
2436 3156 0.462375 TGGTGCAACAGTCAGTACGT 59.538 50.000 0.00 0.00 39.98 3.57
2437 3157 1.139989 CTGGTGCAACAGTCAGTACG 58.860 55.000 24.08 0.00 39.98 3.67
2446 3166 1.106351 ACAAATCGGCTGGTGCAACA 61.106 50.000 3.40 3.40 39.98 3.33
2454 3174 2.084610 TGACTCAGACAAATCGGCTG 57.915 50.000 0.00 0.00 0.00 4.85
2456 3176 1.129437 GCTTGACTCAGACAAATCGGC 59.871 52.381 0.00 0.00 0.00 5.54
2467 3187 6.062749 ACTCCGTCTTATATAGCTTGACTCA 58.937 40.000 0.00 0.00 0.00 3.41
2470 3190 5.383958 CGACTCCGTCTTATATAGCTTGAC 58.616 45.833 0.00 0.00 0.00 3.18
2501 3222 1.208165 ACTGGGAGGGCTAGGGTTTG 61.208 60.000 0.00 0.00 0.00 2.93
2517 3238 4.370917 CTGGAAAAATTGGGACACAACTG 58.629 43.478 0.00 0.00 42.94 3.16
2518 3239 3.181466 GCTGGAAAAATTGGGACACAACT 60.181 43.478 0.00 0.00 42.94 3.16
2519 3240 3.130633 GCTGGAAAAATTGGGACACAAC 58.869 45.455 0.00 0.00 42.94 3.32
2520 3241 2.768527 TGCTGGAAAAATTGGGACACAA 59.231 40.909 0.00 0.00 44.54 3.33
2521 3242 2.102252 GTGCTGGAAAAATTGGGACACA 59.898 45.455 0.00 0.00 39.29 3.72
2522 3243 2.547855 GGTGCTGGAAAAATTGGGACAC 60.548 50.000 0.00 0.00 39.29 3.67
2523 3244 1.691434 GGTGCTGGAAAAATTGGGACA 59.309 47.619 0.00 0.00 0.00 4.02
2524 3245 1.336795 CGGTGCTGGAAAAATTGGGAC 60.337 52.381 0.00 0.00 0.00 4.46
2525 3246 0.965439 CGGTGCTGGAAAAATTGGGA 59.035 50.000 0.00 0.00 0.00 4.37
2526 3247 0.678950 ACGGTGCTGGAAAAATTGGG 59.321 50.000 0.00 0.00 0.00 4.12
2527 3248 1.782044 CACGGTGCTGGAAAAATTGG 58.218 50.000 0.00 0.00 0.00 3.16
2528 3249 1.139163 GCACGGTGCTGGAAAAATTG 58.861 50.000 25.08 0.00 40.96 2.32
2541 3262 2.728435 GGGACTAATCGGGCACGGT 61.728 63.158 9.32 0.00 41.39 4.83
2556 3277 1.305129 TACCGTTCATGGACCGGGA 60.305 57.895 18.40 10.45 45.85 5.14
2559 3280 1.520787 GCCTACCGTTCATGGACCG 60.521 63.158 0.00 0.00 0.00 4.79
2564 3285 0.464373 ATGCTGGCCTACCGTTCATG 60.464 55.000 3.32 0.00 39.70 3.07
2569 3290 1.146930 CATCATGCTGGCCTACCGT 59.853 57.895 3.32 0.00 39.70 4.83
2570 3291 0.602106 CTCATCATGCTGGCCTACCG 60.602 60.000 3.32 0.00 39.70 4.02
2571 3292 0.471617 ACTCATCATGCTGGCCTACC 59.528 55.000 3.32 0.00 0.00 3.18
2572 3293 2.548920 GGTACTCATCATGCTGGCCTAC 60.549 54.545 3.32 0.00 0.00 3.18
2573 3294 1.694150 GGTACTCATCATGCTGGCCTA 59.306 52.381 3.32 0.00 0.00 3.93
2574 3295 0.471617 GGTACTCATCATGCTGGCCT 59.528 55.000 3.32 0.00 0.00 5.19
2575 3296 0.536006 GGGTACTCATCATGCTGGCC 60.536 60.000 0.00 0.00 0.00 5.36
2576 3297 0.471617 AGGGTACTCATCATGCTGGC 59.528 55.000 0.00 0.00 0.00 4.85
2577 3298 2.045524 AGAGGGTACTCATCATGCTGG 58.954 52.381 0.00 0.00 46.44 4.85
2578 3299 4.944619 TTAGAGGGTACTCATCATGCTG 57.055 45.455 0.00 0.00 46.44 4.41
2579 3300 4.530161 GGATTAGAGGGTACTCATCATGCT 59.470 45.833 0.00 0.00 46.44 3.79
2580 3301 4.284490 TGGATTAGAGGGTACTCATCATGC 59.716 45.833 0.00 0.00 46.44 4.06
2581 3302 5.046735 CCTGGATTAGAGGGTACTCATCATG 60.047 48.000 0.00 0.00 46.44 3.07
2582 3303 5.090139 CCTGGATTAGAGGGTACTCATCAT 58.910 45.833 0.00 0.00 46.44 2.45
2583 3304 4.170053 TCCTGGATTAGAGGGTACTCATCA 59.830 45.833 0.00 0.00 46.44 3.07
2584 3305 4.525100 GTCCTGGATTAGAGGGTACTCATC 59.475 50.000 0.00 0.00 46.44 2.92
2585 3306 4.078571 TGTCCTGGATTAGAGGGTACTCAT 60.079 45.833 0.00 0.00 46.44 2.90
2586 3307 3.271225 TGTCCTGGATTAGAGGGTACTCA 59.729 47.826 0.00 0.00 46.44 3.41
2587 3308 3.637694 GTGTCCTGGATTAGAGGGTACTC 59.362 52.174 0.00 0.00 44.31 2.59
2588 3309 3.630311 GGTGTCCTGGATTAGAGGGTACT 60.630 52.174 0.00 0.00 0.00 2.73
2589 3310 2.699321 GGTGTCCTGGATTAGAGGGTAC 59.301 54.545 0.00 0.00 0.00 3.34
2590 3311 2.688817 CGGTGTCCTGGATTAGAGGGTA 60.689 54.545 0.00 0.00 0.00 3.69
2591 3312 1.880941 GGTGTCCTGGATTAGAGGGT 58.119 55.000 0.00 0.00 0.00 4.34
2592 3313 0.753262 CGGTGTCCTGGATTAGAGGG 59.247 60.000 0.00 0.00 0.00 4.30
2593 3314 1.486211 ACGGTGTCCTGGATTAGAGG 58.514 55.000 0.00 0.00 0.00 3.69
2594 3315 3.700038 ACTTACGGTGTCCTGGATTAGAG 59.300 47.826 0.00 0.00 0.00 2.43
2595 3316 3.705051 ACTTACGGTGTCCTGGATTAGA 58.295 45.455 0.00 0.00 0.00 2.10
2596 3317 5.346522 GTTACTTACGGTGTCCTGGATTAG 58.653 45.833 0.00 0.00 0.00 1.73
2597 3318 4.160252 GGTTACTTACGGTGTCCTGGATTA 59.840 45.833 0.00 0.00 0.00 1.75
2598 3319 3.055602 GGTTACTTACGGTGTCCTGGATT 60.056 47.826 0.00 0.00 0.00 3.01
2599 3320 2.498885 GGTTACTTACGGTGTCCTGGAT 59.501 50.000 0.00 0.00 0.00 3.41
2600 3321 1.895131 GGTTACTTACGGTGTCCTGGA 59.105 52.381 0.00 0.00 0.00 3.86
2601 3322 1.066645 GGGTTACTTACGGTGTCCTGG 60.067 57.143 0.00 0.00 0.00 4.45
2602 3323 1.066645 GGGGTTACTTACGGTGTCCTG 60.067 57.143 0.00 0.00 0.00 3.86
2603 3324 1.203225 AGGGGTTACTTACGGTGTCCT 60.203 52.381 0.00 0.00 0.00 3.85
2604 3325 1.269958 AGGGGTTACTTACGGTGTCC 58.730 55.000 0.00 0.00 0.00 4.02
2605 3326 3.368427 GGTTAGGGGTTACTTACGGTGTC 60.368 52.174 0.00 0.00 0.00 3.67
2606 3327 2.567169 GGTTAGGGGTTACTTACGGTGT 59.433 50.000 0.00 0.00 0.00 4.16
2607 3328 2.833943 AGGTTAGGGGTTACTTACGGTG 59.166 50.000 0.00 0.00 0.00 4.94
2611 3332 6.665248 TGAAGACTAGGTTAGGGGTTACTTAC 59.335 42.308 0.00 0.00 0.00 2.34
2613 3334 5.658474 TGAAGACTAGGTTAGGGGTTACTT 58.342 41.667 0.00 0.00 0.00 2.24
2618 3339 2.838813 GCTTGAAGACTAGGTTAGGGGT 59.161 50.000 0.00 0.00 0.00 4.95
2620 3341 2.159085 CGGCTTGAAGACTAGGTTAGGG 60.159 54.545 0.00 0.00 0.00 3.53
2624 3345 1.550976 CCTCGGCTTGAAGACTAGGTT 59.449 52.381 10.32 0.00 0.00 3.50
2626 3347 1.475403 TCCTCGGCTTGAAGACTAGG 58.525 55.000 12.19 12.19 0.00 3.02
2632 3353 2.099141 TTGACATCCTCGGCTTGAAG 57.901 50.000 0.00 0.00 0.00 3.02
2646 3367 0.546122 CATCGGGGGAAGGATTGACA 59.454 55.000 0.00 0.00 0.00 3.58
2650 3371 1.768870 CACTACATCGGGGGAAGGATT 59.231 52.381 0.00 0.00 0.00 3.01
2659 3380 1.831736 AGAAGGAACCACTACATCGGG 59.168 52.381 0.00 0.00 0.00 5.14
2662 3383 4.189639 ACGAAGAAGGAACCACTACATC 57.810 45.455 0.00 0.00 0.00 3.06
2663 3384 4.283722 AGAACGAAGAAGGAACCACTACAT 59.716 41.667 0.00 0.00 0.00 2.29
2669 3390 2.750948 CGAAGAACGAAGAAGGAACCA 58.249 47.619 0.00 0.00 45.77 3.67
2674 3395 2.404215 TGAAGCGAAGAACGAAGAAGG 58.596 47.619 0.00 0.00 45.77 3.46
2683 3404 4.495422 GAACTCACCTATGAAGCGAAGAA 58.505 43.478 0.00 0.00 33.30 2.52
2686 3407 2.832129 AGGAACTCACCTATGAAGCGAA 59.168 45.455 0.00 0.00 38.65 4.70
2690 3411 4.808414 TGTCAGGAACTCACCTATGAAG 57.192 45.455 0.00 0.00 38.32 3.02
2691 3412 5.026121 AGATGTCAGGAACTCACCTATGAA 58.974 41.667 0.00 0.00 38.32 2.57
2693 3414 4.403752 TGAGATGTCAGGAACTCACCTATG 59.596 45.833 0.00 0.00 38.32 2.23
2694 3415 4.614475 TGAGATGTCAGGAACTCACCTAT 58.386 43.478 0.00 0.00 38.32 2.57
2725 3447 2.024273 AGGACCTCGGACCAAAGATCTA 60.024 50.000 7.19 0.00 32.53 1.98
2749 3485 4.824289 CTGCAAGGAATTAACTTTGGCAT 58.176 39.130 0.00 0.00 0.00 4.40
2774 3510 1.227497 CCTCGGAGGAGCATGCTTC 60.227 63.158 23.61 21.29 36.27 3.86


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

AutoCloner maintained by Alex Coulton.