Multiple sequence alignment - TraesCS5D01G119000

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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 TraesCS5D01G119000 chr5D 100.000 1233 0 0 1455 2687 160881154 160879922 0.000000e+00 2278
1 TraesCS5D01G119000 chr5D 100.000 1059 0 0 1 1059 160882608 160881550 0.000000e+00 1956
2 TraesCS5D01G119000 chr5D 99.317 732 3 1 1 732 160896117 160895388 0.000000e+00 1323
3 TraesCS5D01G119000 chr5D 94.269 855 34 3 1458 2299 435542429 435541577 0.000000e+00 1293
4 TraesCS5D01G119000 chr5D 98.491 729 8 2 1 729 136568260 136568985 0.000000e+00 1282
5 TraesCS5D01G119000 chr5D 97.665 728 15 1 1 728 154242656 154241931 0.000000e+00 1249
6 TraesCS5D01G119000 chr5D 96.012 326 13 0 728 1053 435542743 435542418 5.090000e-147 531
7 TraesCS5D01G119000 chr7D 94.484 852 31 4 1458 2295 574233068 574233917 0.000000e+00 1299
8 TraesCS5D01G119000 chr7D 97.492 319 8 0 728 1046 574232754 574233072 1.820000e-151 545
9 TraesCS5D01G119000 chr6D 94.471 850 32 3 1461 2297 392885733 392886580 0.000000e+00 1295
10 TraesCS5D01G119000 chr6D 97.771 314 7 0 728 1041 392885416 392885729 2.350000e-150 542
11 TraesCS5D01G119000 chr6D 95.399 326 15 0 728 1053 72195204 72194879 1.100000e-143 520
12 TraesCS5D01G119000 chr2D 94.970 835 27 3 1477 2298 152092128 152092960 0.000000e+00 1295
13 TraesCS5D01G119000 chr2D 98.765 729 6 2 1 729 248425257 248425982 0.000000e+00 1293
14 TraesCS5D01G119000 chr2D 98.361 732 9 2 1 732 248417280 248418008 0.000000e+00 1282
15 TraesCS5D01G119000 chr2D 93.932 857 37 3 1456 2299 468361578 468360724 0.000000e+00 1280
16 TraesCS5D01G119000 chr2D 93.699 857 36 6 1455 2298 607668329 607667478 0.000000e+00 1267
17 TraesCS5D01G119000 chr2D 98.194 720 13 0 12 731 514842198 514841479 0.000000e+00 1258
18 TraesCS5D01G119000 chr2D 97.802 728 12 2 1 728 217434385 217435108 0.000000e+00 1253
19 TraesCS5D01G119000 chr2D 97.802 728 10 5 1 728 373526266 373525545 0.000000e+00 1251
20 TraesCS5D01G119000 chr2D 96.333 300 11 0 728 1027 607669255 607668956 6.680000e-136 494
21 TraesCS5D01G119000 chr1D 97.951 732 13 1 1 732 242219139 242218410 0.000000e+00 1267
22 TraesCS5D01G119000 chr4D 92.541 858 47 5 1455 2299 414509126 414508273 0.000000e+00 1214
23 TraesCS5D01G119000 chr4D 91.566 332 12 5 728 1059 414509439 414509124 6.830000e-121 444
24 TraesCS5D01G119000 chr3D 90.443 858 63 4 1455 2299 189003473 189002622 0.000000e+00 1112
25 TraesCS5D01G119000 chr5A 90.082 857 63 8 1455 2298 599255315 599256162 0.000000e+00 1092
26 TraesCS5D01G119000 chr5A 96.491 399 7 1 2296 2687 259082645 259082247 0.000000e+00 652
27 TraesCS5D01G119000 chr5A 96.988 332 10 0 728 1059 666947789 666947458 2.340000e-155 558
28 TraesCS5D01G119000 chr5A 91.740 339 19 6 728 1059 599254981 599255317 1.880000e-126 462
29 TraesCS5D01G119000 chr5A 89.235 353 23 3 1956 2295 666947428 666947078 6.870000e-116 427
30 TraesCS5D01G119000 chr1A 95.181 332 12 1 728 1059 577043413 577043086 3.070000e-144 521
31 TraesCS5D01G119000 chr1A 94.578 332 14 1 728 1059 485018569 485018242 6.640000e-141 510
32 TraesCS5D01G119000 chrUn 90.141 355 18 5 1956 2295 30435615 30435263 1.900000e-121 446
33 TraesCS5D01G119000 chr2B 81.329 316 41 11 1995 2296 424521190 424520879 9.610000e-60 241


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 TraesCS5D01G119000 chr5D 160879922 160882608 2686 True 2117.0 2278 100.0000 1 2687 2 chr5D.!!$R3 2686
1 TraesCS5D01G119000 chr5D 160895388 160896117 729 True 1323.0 1323 99.3170 1 732 1 chr5D.!!$R2 731
2 TraesCS5D01G119000 chr5D 136568260 136568985 725 False 1282.0 1282 98.4910 1 729 1 chr5D.!!$F1 728
3 TraesCS5D01G119000 chr5D 154241931 154242656 725 True 1249.0 1249 97.6650 1 728 1 chr5D.!!$R1 727
4 TraesCS5D01G119000 chr5D 435541577 435542743 1166 True 912.0 1293 95.1405 728 2299 2 chr5D.!!$R4 1571
5 TraesCS5D01G119000 chr7D 574232754 574233917 1163 False 922.0 1299 95.9880 728 2295 2 chr7D.!!$F1 1567
6 TraesCS5D01G119000 chr6D 392885416 392886580 1164 False 918.5 1295 96.1210 728 2297 2 chr6D.!!$F1 1569
7 TraesCS5D01G119000 chr2D 152092128 152092960 832 False 1295.0 1295 94.9700 1477 2298 1 chr2D.!!$F1 821
8 TraesCS5D01G119000 chr2D 248425257 248425982 725 False 1293.0 1293 98.7650 1 729 1 chr2D.!!$F4 728
9 TraesCS5D01G119000 chr2D 248417280 248418008 728 False 1282.0 1282 98.3610 1 732 1 chr2D.!!$F3 731
10 TraesCS5D01G119000 chr2D 468360724 468361578 854 True 1280.0 1280 93.9320 1456 2299 1 chr2D.!!$R2 843
11 TraesCS5D01G119000 chr2D 514841479 514842198 719 True 1258.0 1258 98.1940 12 731 1 chr2D.!!$R3 719
12 TraesCS5D01G119000 chr2D 217434385 217435108 723 False 1253.0 1253 97.8020 1 728 1 chr2D.!!$F2 727
13 TraesCS5D01G119000 chr2D 373525545 373526266 721 True 1251.0 1251 97.8020 1 728 1 chr2D.!!$R1 727
14 TraesCS5D01G119000 chr2D 607667478 607669255 1777 True 880.5 1267 95.0160 728 2298 2 chr2D.!!$R4 1570
15 TraesCS5D01G119000 chr1D 242218410 242219139 729 True 1267.0 1267 97.9510 1 732 1 chr1D.!!$R1 731
16 TraesCS5D01G119000 chr4D 414508273 414509439 1166 True 829.0 1214 92.0535 728 2299 2 chr4D.!!$R1 1571
17 TraesCS5D01G119000 chr3D 189002622 189003473 851 True 1112.0 1112 90.4430 1455 2299 1 chr3D.!!$R1 844
18 TraesCS5D01G119000 chr5A 599254981 599256162 1181 False 777.0 1092 90.9110 728 2298 2 chr5A.!!$F1 1570
19 TraesCS5D01G119000 chr5A 666947078 666947789 711 True 492.5 558 93.1115 728 2295 2 chr5A.!!$R2 1567

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
274 275 0.534873 GGCCAGGTCAGTTCTCTCTC 59.465 60.0 0.0 0.0 0.0 3.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 2894 1.203523 GGTGTGTTTGGTTGAGCAACA 59.796 47.619 14.55 0.0 42.85 3.33 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
273 274 1.254284 CGGCCAGGTCAGTTCTCTCT 61.254 60.000 2.24 0.00 0.00 3.10
274 275 0.534873 GGCCAGGTCAGTTCTCTCTC 59.465 60.000 0.00 0.00 0.00 3.20
962 972 2.191641 GGTGGAGATCAGGCAGCC 59.808 66.667 1.84 1.84 0.00 4.85
1569 2176 1.809619 GCGCGCTGGAGATACAACA 60.810 57.895 26.67 0.00 0.00 3.33
1696 2303 4.100189 GCTTCTCCCTCTAAAGCTATGTGA 59.900 45.833 0.00 0.00 41.66 3.58
1916 2524 0.605319 ATTGGCCACATGAACGACGT 60.605 50.000 3.88 0.00 0.00 4.34
2164 2780 7.874528 GTGGTTTCATTTTTCATTCCATCTCTT 59.125 33.333 0.00 0.00 0.00 2.85
2178 2794 7.411486 TTCCATCTCTTTAACCAAACACAAA 57.589 32.000 0.00 0.00 0.00 2.83
2190 2806 4.998033 ACCAAACACAAAAACAAAACCGAT 59.002 33.333 0.00 0.00 0.00 4.18
2206 2822 7.013846 ACAAAACCGATCCATTTCACTTTTCTA 59.986 33.333 0.00 0.00 0.00 2.10
2269 2890 0.679960 CCATTCCCTTCCGTTCCACC 60.680 60.000 0.00 0.00 0.00 4.61
2270 2891 0.037590 CATTCCCTTCCGTTCCACCA 59.962 55.000 0.00 0.00 0.00 4.17
2271 2892 0.037734 ATTCCCTTCCGTTCCACCAC 59.962 55.000 0.00 0.00 0.00 4.16
2272 2893 1.057851 TTCCCTTCCGTTCCACCACT 61.058 55.000 0.00 0.00 0.00 4.00
2273 2894 1.057851 TCCCTTCCGTTCCACCACTT 61.058 55.000 0.00 0.00 0.00 3.16
2277 2898 1.333619 CTTCCGTTCCACCACTTGTTG 59.666 52.381 0.00 0.00 0.00 3.33
2299 2920 2.293399 CTCAACCAAACACACCCTAAGC 59.707 50.000 0.00 0.00 0.00 3.09
2300 2921 2.028130 CAACCAAACACACCCTAAGCA 58.972 47.619 0.00 0.00 0.00 3.91
2301 2922 2.428890 CAACCAAACACACCCTAAGCAA 59.571 45.455 0.00 0.00 0.00 3.91
2302 2923 2.028876 ACCAAACACACCCTAAGCAAC 58.971 47.619 0.00 0.00 0.00 4.17
2303 2924 1.339929 CCAAACACACCCTAAGCAACC 59.660 52.381 0.00 0.00 0.00 3.77
2304 2925 2.028130 CAAACACACCCTAAGCAACCA 58.972 47.619 0.00 0.00 0.00 3.67
2305 2926 2.428890 CAAACACACCCTAAGCAACCAA 59.571 45.455 0.00 0.00 0.00 3.67
2306 2927 2.445682 ACACACCCTAAGCAACCAAA 57.554 45.000 0.00 0.00 0.00 3.28
2307 2928 2.741145 ACACACCCTAAGCAACCAAAA 58.259 42.857 0.00 0.00 0.00 2.44
2308 2929 2.429250 ACACACCCTAAGCAACCAAAAC 59.571 45.455 0.00 0.00 0.00 2.43
2309 2930 2.036387 ACACCCTAAGCAACCAAAACC 58.964 47.619 0.00 0.00 0.00 3.27
2310 2931 1.000717 CACCCTAAGCAACCAAAACCG 60.001 52.381 0.00 0.00 0.00 4.44
2311 2932 0.038618 CCCTAAGCAACCAAAACCGC 60.039 55.000 0.00 0.00 0.00 5.68
2312 2933 0.386731 CCTAAGCAACCAAAACCGCG 60.387 55.000 0.00 0.00 0.00 6.46
2313 2934 1.001745 CTAAGCAACCAAAACCGCGC 61.002 55.000 0.00 0.00 0.00 6.86
2314 2935 2.718993 TAAGCAACCAAAACCGCGCG 62.719 55.000 25.67 25.67 0.00 6.86
2315 2936 4.615834 GCAACCAAAACCGCGCGA 62.616 61.111 34.63 0.00 0.00 5.87
2316 2937 2.254051 CAACCAAAACCGCGCGAT 59.746 55.556 34.63 13.37 0.00 4.58
2317 2938 2.080062 CAACCAAAACCGCGCGATG 61.080 57.895 34.63 22.59 0.00 3.84
2318 2939 3.889831 AACCAAAACCGCGCGATGC 62.890 57.895 34.63 0.00 41.47 3.91
2320 2941 4.101790 CAAAACCGCGCGATGCCT 62.102 61.111 34.63 8.59 42.08 4.75
2321 2942 3.799755 AAAACCGCGCGATGCCTC 61.800 61.111 34.63 0.00 42.08 4.70
2326 2947 2.661537 CGCGCGATGCCTCCATTA 60.662 61.111 28.94 0.00 42.08 1.90
2327 2948 2.029288 CGCGCGATGCCTCCATTAT 61.029 57.895 28.94 0.00 42.08 1.28
2328 2949 1.790387 GCGCGATGCCTCCATTATC 59.210 57.895 12.10 0.00 37.76 1.75
2329 2950 1.639298 GCGCGATGCCTCCATTATCC 61.639 60.000 12.10 0.00 37.76 2.59
2330 2951 0.320683 CGCGATGCCTCCATTATCCA 60.321 55.000 0.00 0.00 0.00 3.41
2331 2952 1.446907 GCGATGCCTCCATTATCCAG 58.553 55.000 0.00 0.00 0.00 3.86
2332 2953 1.446907 CGATGCCTCCATTATCCAGC 58.553 55.000 0.00 0.00 0.00 4.85
2333 2954 1.271001 CGATGCCTCCATTATCCAGCA 60.271 52.381 0.00 0.00 34.28 4.41
2334 2955 2.434428 GATGCCTCCATTATCCAGCAG 58.566 52.381 0.00 0.00 33.10 4.24
2335 2956 1.510492 TGCCTCCATTATCCAGCAGA 58.490 50.000 0.00 0.00 0.00 4.26
2336 2957 1.845791 TGCCTCCATTATCCAGCAGAA 59.154 47.619 0.00 0.00 0.00 3.02
2337 2958 2.158711 TGCCTCCATTATCCAGCAGAAG 60.159 50.000 0.00 0.00 0.00 2.85
2338 2959 2.158696 GCCTCCATTATCCAGCAGAAGT 60.159 50.000 0.00 0.00 0.00 3.01
2339 2960 3.071602 GCCTCCATTATCCAGCAGAAGTA 59.928 47.826 0.00 0.00 0.00 2.24
2340 2961 4.444876 GCCTCCATTATCCAGCAGAAGTAA 60.445 45.833 0.00 0.00 0.00 2.24
2341 2962 5.059833 CCTCCATTATCCAGCAGAAGTAAC 58.940 45.833 0.00 0.00 0.00 2.50
2342 2963 4.693283 TCCATTATCCAGCAGAAGTAACG 58.307 43.478 0.00 0.00 0.00 3.18
2343 2964 4.404394 TCCATTATCCAGCAGAAGTAACGA 59.596 41.667 0.00 0.00 0.00 3.85
2344 2965 5.105106 TCCATTATCCAGCAGAAGTAACGAA 60.105 40.000 0.00 0.00 0.00 3.85
2345 2966 5.006746 CCATTATCCAGCAGAAGTAACGAAC 59.993 44.000 0.00 0.00 0.00 3.95
2346 2967 3.678056 ATCCAGCAGAAGTAACGAACA 57.322 42.857 0.00 0.00 0.00 3.18
2347 2968 2.750948 TCCAGCAGAAGTAACGAACAC 58.249 47.619 0.00 0.00 0.00 3.32
2348 2969 1.798813 CCAGCAGAAGTAACGAACACC 59.201 52.381 0.00 0.00 0.00 4.16
2349 2970 1.455786 CAGCAGAAGTAACGAACACCG 59.544 52.381 0.00 0.00 45.44 4.94
2350 2971 0.163146 GCAGAAGTAACGAACACCGC 59.837 55.000 0.00 0.00 43.32 5.68
2351 2972 1.493772 CAGAAGTAACGAACACCGCA 58.506 50.000 0.00 0.00 43.32 5.69
2352 2973 1.191647 CAGAAGTAACGAACACCGCAC 59.808 52.381 0.00 0.00 43.32 5.34
2353 2974 0.509929 GAAGTAACGAACACCGCACC 59.490 55.000 0.00 0.00 43.32 5.01
2354 2975 0.105408 AAGTAACGAACACCGCACCT 59.895 50.000 0.00 0.00 43.32 4.00
2355 2976 0.105408 AGTAACGAACACCGCACCTT 59.895 50.000 0.00 0.00 43.32 3.50
2356 2977 0.509929 GTAACGAACACCGCACCTTC 59.490 55.000 0.00 0.00 43.32 3.46
2357 2978 0.600782 TAACGAACACCGCACCTTCC 60.601 55.000 0.00 0.00 43.32 3.46
2358 2979 2.030562 CGAACACCGCACCTTCCT 59.969 61.111 0.00 0.00 0.00 3.36
2359 2980 2.027625 CGAACACCGCACCTTCCTC 61.028 63.158 0.00 0.00 0.00 3.71
2360 2981 2.027625 GAACACCGCACCTTCCTCG 61.028 63.158 0.00 0.00 0.00 4.63
2361 2982 4.681978 ACACCGCACCTTCCTCGC 62.682 66.667 0.00 0.00 0.00 5.03
2364 2985 4.821589 CCGCACCTTCCTCGCCTC 62.822 72.222 0.00 0.00 0.00 4.70
2365 2986 4.069232 CGCACCTTCCTCGCCTCA 62.069 66.667 0.00 0.00 0.00 3.86
2366 2987 2.125350 GCACCTTCCTCGCCTCAG 60.125 66.667 0.00 0.00 0.00 3.35
2367 2988 2.948720 GCACCTTCCTCGCCTCAGT 61.949 63.158 0.00 0.00 0.00 3.41
2368 2989 1.216710 CACCTTCCTCGCCTCAGTC 59.783 63.158 0.00 0.00 0.00 3.51
2369 2990 1.228894 ACCTTCCTCGCCTCAGTCA 60.229 57.895 0.00 0.00 0.00 3.41
2370 2991 1.216710 CCTTCCTCGCCTCAGTCAC 59.783 63.158 0.00 0.00 0.00 3.67
2371 2992 1.216710 CTTCCTCGCCTCAGTCACC 59.783 63.158 0.00 0.00 0.00 4.02
2372 2993 2.549611 CTTCCTCGCCTCAGTCACCG 62.550 65.000 0.00 0.00 0.00 4.94
2373 2994 4.803426 CCTCGCCTCAGTCACCGC 62.803 72.222 0.00 0.00 0.00 5.68
2374 2995 4.803426 CTCGCCTCAGTCACCGCC 62.803 72.222 0.00 0.00 0.00 6.13
2400 3021 4.867599 CGGCGCTCTCCGGTTACC 62.868 72.222 7.64 0.00 45.38 2.85
2401 3022 4.525949 GGCGCTCTCCGGTTACCC 62.526 72.222 7.64 0.00 37.44 3.69
2414 3035 2.349590 GGTTACCCGTACAACATGACC 58.650 52.381 0.00 0.00 0.00 4.02
2415 3036 2.349590 GTTACCCGTACAACATGACCC 58.650 52.381 0.00 0.00 0.00 4.46
2416 3037 0.903942 TACCCGTACAACATGACCCC 59.096 55.000 0.00 0.00 0.00 4.95
2417 3038 1.448893 CCCGTACAACATGACCCCG 60.449 63.158 0.00 0.00 0.00 5.73
2418 3039 1.294138 CCGTACAACATGACCCCGT 59.706 57.895 0.00 0.00 0.00 5.28
2419 3040 0.738412 CCGTACAACATGACCCCGTC 60.738 60.000 0.00 0.00 0.00 4.79
2420 3041 0.245539 CGTACAACATGACCCCGTCT 59.754 55.000 0.00 0.00 33.15 4.18
2421 3042 1.734707 CGTACAACATGACCCCGTCTC 60.735 57.143 0.00 0.00 33.15 3.36
2422 3043 0.899720 TACAACATGACCCCGTCTCC 59.100 55.000 0.00 0.00 33.15 3.71
2423 3044 1.078426 CAACATGACCCCGTCTCCC 60.078 63.158 0.00 0.00 33.15 4.30
2424 3045 2.656069 AACATGACCCCGTCTCCCG 61.656 63.158 0.00 0.00 33.15 5.14
2425 3046 4.530857 CATGACCCCGTCTCCCGC 62.531 72.222 0.00 0.00 33.15 6.13
2426 3047 4.779733 ATGACCCCGTCTCCCGCT 62.780 66.667 0.00 0.00 33.15 5.52
2431 3052 3.528370 CCCGTCTCCCGCTCGAAT 61.528 66.667 0.00 0.00 34.38 3.34
2432 3053 2.026301 CCGTCTCCCGCTCGAATC 59.974 66.667 0.00 0.00 34.38 2.52
2433 3054 2.026301 CGTCTCCCGCTCGAATCC 59.974 66.667 0.00 0.00 0.00 3.01
2434 3055 2.482333 CGTCTCCCGCTCGAATCCT 61.482 63.158 0.00 0.00 0.00 3.24
2435 3056 1.360911 GTCTCCCGCTCGAATCCTC 59.639 63.158 0.00 0.00 0.00 3.71
2436 3057 1.076995 TCTCCCGCTCGAATCCTCA 60.077 57.895 0.00 0.00 0.00 3.86
2437 3058 0.468214 TCTCCCGCTCGAATCCTCAT 60.468 55.000 0.00 0.00 0.00 2.90
2438 3059 0.038709 CTCCCGCTCGAATCCTCATC 60.039 60.000 0.00 0.00 0.00 2.92
2439 3060 0.468214 TCCCGCTCGAATCCTCATCT 60.468 55.000 0.00 0.00 0.00 2.90
2440 3061 0.390860 CCCGCTCGAATCCTCATCTT 59.609 55.000 0.00 0.00 0.00 2.40
2441 3062 1.604185 CCCGCTCGAATCCTCATCTTC 60.604 57.143 0.00 0.00 0.00 2.87
2442 3063 1.604185 CCGCTCGAATCCTCATCTTCC 60.604 57.143 0.00 0.00 0.00 3.46
2443 3064 1.339610 CGCTCGAATCCTCATCTTCCT 59.660 52.381 0.00 0.00 0.00 3.36
2444 3065 2.606795 CGCTCGAATCCTCATCTTCCTC 60.607 54.545 0.00 0.00 0.00 3.71
2445 3066 2.288763 GCTCGAATCCTCATCTTCCTCC 60.289 54.545 0.00 0.00 0.00 4.30
2446 3067 3.230134 CTCGAATCCTCATCTTCCTCCT 58.770 50.000 0.00 0.00 0.00 3.69
2447 3068 4.402829 CTCGAATCCTCATCTTCCTCCTA 58.597 47.826 0.00 0.00 0.00 2.94
2448 3069 4.145807 TCGAATCCTCATCTTCCTCCTAC 58.854 47.826 0.00 0.00 0.00 3.18
2449 3070 3.257127 CGAATCCTCATCTTCCTCCTACC 59.743 52.174 0.00 0.00 0.00 3.18
2450 3071 2.777459 TCCTCATCTTCCTCCTACCC 57.223 55.000 0.00 0.00 0.00 3.69
2451 3072 1.937350 TCCTCATCTTCCTCCTACCCA 59.063 52.381 0.00 0.00 0.00 4.51
2452 3073 2.043227 CCTCATCTTCCTCCTACCCAC 58.957 57.143 0.00 0.00 0.00 4.61
2453 3074 2.043227 CTCATCTTCCTCCTACCCACC 58.957 57.143 0.00 0.00 0.00 4.61
2454 3075 1.132500 CATCTTCCTCCTACCCACCC 58.868 60.000 0.00 0.00 0.00 4.61
2455 3076 0.029989 ATCTTCCTCCTACCCACCCC 60.030 60.000 0.00 0.00 0.00 4.95
2456 3077 1.082206 CTTCCTCCTACCCACCCCA 59.918 63.158 0.00 0.00 0.00 4.96
2457 3078 0.549169 CTTCCTCCTACCCACCCCAA 60.549 60.000 0.00 0.00 0.00 4.12
2458 3079 0.549169 TTCCTCCTACCCACCCCAAG 60.549 60.000 0.00 0.00 0.00 3.61
2459 3080 1.229853 CCTCCTACCCACCCCAAGT 60.230 63.158 0.00 0.00 0.00 3.16
2460 3081 1.272554 CCTCCTACCCACCCCAAGTC 61.273 65.000 0.00 0.00 0.00 3.01
2461 3082 0.252742 CTCCTACCCACCCCAAGTCT 60.253 60.000 0.00 0.00 0.00 3.24
2462 3083 0.252558 TCCTACCCACCCCAAGTCTC 60.253 60.000 0.00 0.00 0.00 3.36
2463 3084 0.546747 CCTACCCACCCCAAGTCTCA 60.547 60.000 0.00 0.00 0.00 3.27
2464 3085 1.584724 CTACCCACCCCAAGTCTCAT 58.415 55.000 0.00 0.00 0.00 2.90
2465 3086 2.628559 CCTACCCACCCCAAGTCTCATA 60.629 54.545 0.00 0.00 0.00 2.15
2466 3087 1.286248 ACCCACCCCAAGTCTCATAC 58.714 55.000 0.00 0.00 0.00 2.39
2467 3088 0.546598 CCCACCCCAAGTCTCATACC 59.453 60.000 0.00 0.00 0.00 2.73
2468 3089 0.546598 CCACCCCAAGTCTCATACCC 59.453 60.000 0.00 0.00 0.00 3.69
2469 3090 0.546598 CACCCCAAGTCTCATACCCC 59.453 60.000 0.00 0.00 0.00 4.95
2470 3091 0.623617 ACCCCAAGTCTCATACCCCC 60.624 60.000 0.00 0.00 0.00 5.40
2471 3092 1.696097 CCCCAAGTCTCATACCCCCG 61.696 65.000 0.00 0.00 0.00 5.73
2472 3093 1.146263 CCAAGTCTCATACCCCCGC 59.854 63.158 0.00 0.00 0.00 6.13
2473 3094 1.146263 CAAGTCTCATACCCCCGCC 59.854 63.158 0.00 0.00 0.00 6.13
2474 3095 1.306654 AAGTCTCATACCCCCGCCA 60.307 57.895 0.00 0.00 0.00 5.69
2475 3096 1.623542 AAGTCTCATACCCCCGCCAC 61.624 60.000 0.00 0.00 0.00 5.01
2476 3097 2.766651 TCTCATACCCCCGCCACC 60.767 66.667 0.00 0.00 0.00 4.61
2477 3098 3.873812 CTCATACCCCCGCCACCC 61.874 72.222 0.00 0.00 0.00 4.61
2507 3128 4.020617 CACAGAGCCTTGGCCGGA 62.021 66.667 5.05 0.00 0.00 5.14
2508 3129 3.249189 ACAGAGCCTTGGCCGGAA 61.249 61.111 5.05 0.00 0.00 4.30
2509 3130 2.747855 CAGAGCCTTGGCCGGAAC 60.748 66.667 5.05 0.00 0.00 3.62
2510 3131 4.035102 AGAGCCTTGGCCGGAACC 62.035 66.667 5.05 0.00 0.00 3.62
2557 3178 4.143333 CGGGGGCTTCGTCGTCAT 62.143 66.667 0.00 0.00 0.00 3.06
2558 3179 2.267961 GGGGGCTTCGTCGTCATT 59.732 61.111 0.00 0.00 0.00 2.57
2559 3180 2.106683 GGGGGCTTCGTCGTCATTG 61.107 63.158 0.00 0.00 0.00 2.82
2560 3181 1.079405 GGGGCTTCGTCGTCATTGA 60.079 57.895 0.00 0.00 0.00 2.57
2561 3182 1.084370 GGGGCTTCGTCGTCATTGAG 61.084 60.000 0.00 0.00 0.00 3.02
2562 3183 1.084370 GGGCTTCGTCGTCATTGAGG 61.084 60.000 0.00 0.00 0.00 3.86
2563 3184 0.108804 GGCTTCGTCGTCATTGAGGA 60.109 55.000 4.98 4.98 0.00 3.71
2564 3185 0.992802 GCTTCGTCGTCATTGAGGAC 59.007 55.000 23.28 23.28 41.98 3.85
2577 3198 4.329831 AGGACGACCTCTCTGAGC 57.670 61.111 0.00 0.00 44.13 4.26
2578 3199 1.688811 AGGACGACCTCTCTGAGCT 59.311 57.895 0.00 0.00 44.13 4.09
2579 3200 0.039035 AGGACGACCTCTCTGAGCTT 59.961 55.000 0.00 0.00 44.13 3.74
2580 3201 0.454196 GGACGACCTCTCTGAGCTTC 59.546 60.000 0.00 0.00 0.00 3.86
2581 3202 1.459450 GACGACCTCTCTGAGCTTCT 58.541 55.000 0.00 0.00 0.00 2.85
2582 3203 1.132262 GACGACCTCTCTGAGCTTCTG 59.868 57.143 0.00 0.00 0.00 3.02
2583 3204 0.179140 CGACCTCTCTGAGCTTCTGC 60.179 60.000 0.00 0.00 40.05 4.26
2584 3205 0.894141 GACCTCTCTGAGCTTCTGCA 59.106 55.000 0.00 0.00 42.74 4.41
2585 3206 0.896923 ACCTCTCTGAGCTTCTGCAG 59.103 55.000 7.63 7.63 42.74 4.41
2586 3207 0.176219 CCTCTCTGAGCTTCTGCAGG 59.824 60.000 15.13 0.00 42.74 4.85
2587 3208 0.896923 CTCTCTGAGCTTCTGCAGGT 59.103 55.000 15.13 0.00 42.74 4.00
2592 3213 3.566130 GAGCTTCTGCAGGTCCATT 57.434 52.632 15.13 0.00 43.33 3.16
2593 3214 1.831580 GAGCTTCTGCAGGTCCATTT 58.168 50.000 15.13 0.00 43.33 2.32
2594 3215 2.165998 GAGCTTCTGCAGGTCCATTTT 58.834 47.619 15.13 0.00 43.33 1.82
2595 3216 2.560105 GAGCTTCTGCAGGTCCATTTTT 59.440 45.455 15.13 0.00 43.33 1.94
2596 3217 2.560105 AGCTTCTGCAGGTCCATTTTTC 59.440 45.455 15.13 0.00 42.74 2.29
2597 3218 2.560105 GCTTCTGCAGGTCCATTTTTCT 59.440 45.455 15.13 0.00 39.41 2.52
2598 3219 3.006217 GCTTCTGCAGGTCCATTTTTCTT 59.994 43.478 15.13 0.00 39.41 2.52
2599 3220 4.502087 GCTTCTGCAGGTCCATTTTTCTTT 60.502 41.667 15.13 0.00 39.41 2.52
2600 3221 4.853924 TCTGCAGGTCCATTTTTCTTTC 57.146 40.909 15.13 0.00 0.00 2.62
2601 3222 3.253188 TCTGCAGGTCCATTTTTCTTTCG 59.747 43.478 15.13 0.00 0.00 3.46
2602 3223 3.218453 TGCAGGTCCATTTTTCTTTCGA 58.782 40.909 0.00 0.00 0.00 3.71
2603 3224 3.826157 TGCAGGTCCATTTTTCTTTCGAT 59.174 39.130 0.00 0.00 0.00 3.59
2604 3225 4.280677 TGCAGGTCCATTTTTCTTTCGATT 59.719 37.500 0.00 0.00 0.00 3.34
2605 3226 4.859245 GCAGGTCCATTTTTCTTTCGATTC 59.141 41.667 0.00 0.00 0.00 2.52
2606 3227 5.335976 GCAGGTCCATTTTTCTTTCGATTCT 60.336 40.000 0.00 0.00 0.00 2.40
2607 3228 6.681777 CAGGTCCATTTTTCTTTCGATTCTT 58.318 36.000 0.00 0.00 0.00 2.52
2608 3229 7.147976 CAGGTCCATTTTTCTTTCGATTCTTT 58.852 34.615 0.00 0.00 0.00 2.52
2609 3230 8.296713 CAGGTCCATTTTTCTTTCGATTCTTTA 58.703 33.333 0.00 0.00 0.00 1.85
2610 3231 8.297426 AGGTCCATTTTTCTTTCGATTCTTTAC 58.703 33.333 0.00 0.00 0.00 2.01
2611 3232 7.541091 GGTCCATTTTTCTTTCGATTCTTTACC 59.459 37.037 0.00 0.00 0.00 2.85
2612 3233 7.541091 GTCCATTTTTCTTTCGATTCTTTACCC 59.459 37.037 0.00 0.00 0.00 3.69
2613 3234 6.811665 CCATTTTTCTTTCGATTCTTTACCCC 59.188 38.462 0.00 0.00 0.00 4.95
2614 3235 7.309805 CCATTTTTCTTTCGATTCTTTACCCCT 60.310 37.037 0.00 0.00 0.00 4.79
2615 3236 7.591421 TTTTTCTTTCGATTCTTTACCCCTT 57.409 32.000 0.00 0.00 0.00 3.95
2616 3237 7.591421 TTTTCTTTCGATTCTTTACCCCTTT 57.409 32.000 0.00 0.00 0.00 3.11
2617 3238 7.591421 TTTCTTTCGATTCTTTACCCCTTTT 57.409 32.000 0.00 0.00 0.00 2.27
2618 3239 8.694581 TTTCTTTCGATTCTTTACCCCTTTTA 57.305 30.769 0.00 0.00 0.00 1.52
2619 3240 8.694581 TTCTTTCGATTCTTTACCCCTTTTAA 57.305 30.769 0.00 0.00 0.00 1.52
2620 3241 8.102800 TCTTTCGATTCTTTACCCCTTTTAAC 57.897 34.615 0.00 0.00 0.00 2.01
2621 3242 6.822667 TTCGATTCTTTACCCCTTTTAACC 57.177 37.500 0.00 0.00 0.00 2.85
2622 3243 6.130692 TCGATTCTTTACCCCTTTTAACCT 57.869 37.500 0.00 0.00 0.00 3.50
2623 3244 5.941647 TCGATTCTTTACCCCTTTTAACCTG 59.058 40.000 0.00 0.00 0.00 4.00
2624 3245 5.392703 CGATTCTTTACCCCTTTTAACCTGC 60.393 44.000 0.00 0.00 0.00 4.85
2625 3246 4.734843 TCTTTACCCCTTTTAACCTGCT 57.265 40.909 0.00 0.00 0.00 4.24
2626 3247 5.846528 TCTTTACCCCTTTTAACCTGCTA 57.153 39.130 0.00 0.00 0.00 3.49
2627 3248 5.812286 TCTTTACCCCTTTTAACCTGCTAG 58.188 41.667 0.00 0.00 0.00 3.42
2628 3249 5.311385 TCTTTACCCCTTTTAACCTGCTAGT 59.689 40.000 0.00 0.00 0.00 2.57
2629 3250 5.587760 TTACCCCTTTTAACCTGCTAGTT 57.412 39.130 0.00 0.00 0.00 2.24
2630 3251 6.700845 TTACCCCTTTTAACCTGCTAGTTA 57.299 37.500 0.00 0.00 0.00 2.24
2631 3252 5.587760 ACCCCTTTTAACCTGCTAGTTAA 57.412 39.130 7.52 7.52 39.76 2.01
2632 3253 6.148735 ACCCCTTTTAACCTGCTAGTTAAT 57.851 37.500 11.14 0.00 40.80 1.40
2633 3254 6.558498 ACCCCTTTTAACCTGCTAGTTAATT 58.442 36.000 11.14 0.00 40.80 1.40
2634 3255 7.014449 ACCCCTTTTAACCTGCTAGTTAATTT 58.986 34.615 11.14 0.00 40.80 1.82
2635 3256 7.177921 ACCCCTTTTAACCTGCTAGTTAATTTC 59.822 37.037 11.14 0.00 40.80 2.17
2636 3257 7.363530 CCCCTTTTAACCTGCTAGTTAATTTCC 60.364 40.741 11.14 0.00 40.80 3.13
2637 3258 7.396339 CCCTTTTAACCTGCTAGTTAATTTCCT 59.604 37.037 11.14 0.00 40.80 3.36
2638 3259 8.459635 CCTTTTAACCTGCTAGTTAATTTCCTC 58.540 37.037 11.14 0.00 40.80 3.71
2639 3260 9.232473 CTTTTAACCTGCTAGTTAATTTCCTCT 57.768 33.333 11.14 0.00 40.80 3.69
2643 3264 8.966069 AACCTGCTAGTTAATTTCCTCTATTC 57.034 34.615 0.00 0.00 0.00 1.75
2644 3265 7.510407 ACCTGCTAGTTAATTTCCTCTATTCC 58.490 38.462 0.00 0.00 0.00 3.01
2645 3266 7.127339 ACCTGCTAGTTAATTTCCTCTATTCCA 59.873 37.037 0.00 0.00 0.00 3.53
2646 3267 7.442666 CCTGCTAGTTAATTTCCTCTATTCCAC 59.557 40.741 0.00 0.00 0.00 4.02
2647 3268 8.090788 TGCTAGTTAATTTCCTCTATTCCACT 57.909 34.615 0.00 0.00 0.00 4.00
2648 3269 7.987458 TGCTAGTTAATTTCCTCTATTCCACTG 59.013 37.037 0.00 0.00 0.00 3.66
2649 3270 8.204836 GCTAGTTAATTTCCTCTATTCCACTGA 58.795 37.037 0.00 0.00 0.00 3.41
2652 3273 9.981460 AGTTAATTTCCTCTATTCCACTGAAAT 57.019 29.630 0.00 0.00 34.79 2.17
2661 3282 8.787852 CCTCTATTCCACTGAAATAATTAAGGC 58.212 37.037 0.00 0.00 33.32 4.35
2662 3283 8.691661 TCTATTCCACTGAAATAATTAAGGCC 57.308 34.615 0.00 0.00 33.32 5.19
2663 3284 6.731292 ATTCCACTGAAATAATTAAGGCCC 57.269 37.500 0.00 0.00 33.32 5.80
2664 3285 5.466127 TCCACTGAAATAATTAAGGCCCT 57.534 39.130 0.00 0.00 0.00 5.19
2665 3286 5.445964 TCCACTGAAATAATTAAGGCCCTC 58.554 41.667 0.00 0.00 0.00 4.30
2666 3287 5.193728 TCCACTGAAATAATTAAGGCCCTCT 59.806 40.000 0.00 0.00 0.00 3.69
2667 3288 5.893824 CCACTGAAATAATTAAGGCCCTCTT 59.106 40.000 0.00 0.00 39.40 2.85
2668 3289 6.381133 CCACTGAAATAATTAAGGCCCTCTTT 59.619 38.462 0.00 0.00 36.93 2.52
2669 3290 7.260603 CACTGAAATAATTAAGGCCCTCTTTG 58.739 38.462 0.00 0.00 36.93 2.77
2670 3291 6.954102 ACTGAAATAATTAAGGCCCTCTTTGT 59.046 34.615 0.00 0.00 36.93 2.83
2671 3292 7.454694 ACTGAAATAATTAAGGCCCTCTTTGTT 59.545 33.333 0.00 0.00 36.93 2.83
2672 3293 8.201242 TGAAATAATTAAGGCCCTCTTTGTTT 57.799 30.769 0.00 0.00 36.93 2.83
2673 3294 8.093927 TGAAATAATTAAGGCCCTCTTTGTTTG 58.906 33.333 0.00 0.00 36.93 2.93
2674 3295 4.890158 AATTAAGGCCCTCTTTGTTTGG 57.110 40.909 0.00 0.00 36.93 3.28
2675 3296 2.302587 TAAGGCCCTCTTTGTTTGGG 57.697 50.000 0.00 0.00 43.62 4.12
2676 3297 0.264657 AAGGCCCTCTTTGTTTGGGT 59.735 50.000 0.00 0.00 42.77 4.51
2677 3298 0.264657 AGGCCCTCTTTGTTTGGGTT 59.735 50.000 0.00 0.00 42.77 4.11
2678 3299 0.392706 GGCCCTCTTTGTTTGGGTTG 59.607 55.000 0.00 0.00 42.77 3.77
2679 3300 0.392706 GCCCTCTTTGTTTGGGTTGG 59.607 55.000 0.00 0.00 42.77 3.77
2680 3301 2.032151 GCCCTCTTTGTTTGGGTTGGA 61.032 52.381 0.00 0.00 42.77 3.53
2681 3302 1.963515 CCCTCTTTGTTTGGGTTGGAG 59.036 52.381 0.00 0.00 36.32 3.86
2682 3303 1.341209 CCTCTTTGTTTGGGTTGGAGC 59.659 52.381 0.00 0.00 0.00 4.70
2683 3304 2.310538 CTCTTTGTTTGGGTTGGAGCT 58.689 47.619 0.00 0.00 0.00 4.09
2684 3305 2.695147 CTCTTTGTTTGGGTTGGAGCTT 59.305 45.455 0.00 0.00 0.00 3.74
2685 3306 3.103742 TCTTTGTTTGGGTTGGAGCTTT 58.896 40.909 0.00 0.00 0.00 3.51
2686 3307 4.282496 TCTTTGTTTGGGTTGGAGCTTTA 58.718 39.130 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
814 824 3.083997 GAGATGCGGGAGGGTGGT 61.084 66.667 0.00 0.00 0.00 4.16
1496 2103 4.704833 AGCGAGTTGGCGTGCCAT 62.705 61.111 15.40 0.00 46.64 4.40
2164 2780 6.480981 TCGGTTTTGTTTTTGTGTTTGGTTAA 59.519 30.769 0.00 0.00 0.00 2.01
2178 2794 5.529581 AGTGAAATGGATCGGTTTTGTTT 57.470 34.783 0.00 0.00 0.00 2.83
2206 2822 6.723298 TCCATTCCTGTGTTTGTTACAAAT 57.277 33.333 13.84 0.00 38.80 2.32
2213 2829 1.953686 CCGTTCCATTCCTGTGTTTGT 59.046 47.619 0.00 0.00 0.00 2.83
2257 2878 1.333619 CAACAAGTGGTGGAACGGAAG 59.666 52.381 0.00 0.00 38.12 3.46
2269 2890 2.923020 GTGTTTGGTTGAGCAACAAGTG 59.077 45.455 14.55 0.00 42.85 3.16
2270 2891 2.560542 TGTGTTTGGTTGAGCAACAAGT 59.439 40.909 14.55 0.00 42.85 3.16
2271 2892 2.923020 GTGTGTTTGGTTGAGCAACAAG 59.077 45.455 14.55 0.00 42.85 3.16
2272 2893 2.353208 GGTGTGTTTGGTTGAGCAACAA 60.353 45.455 14.55 0.89 42.85 2.83
2273 2894 1.203523 GGTGTGTTTGGTTGAGCAACA 59.796 47.619 14.55 0.00 42.85 3.33
2277 2898 1.975660 TAGGGTGTGTTTGGTTGAGC 58.024 50.000 0.00 0.00 0.00 4.26
2299 2920 2.080062 CATCGCGCGGTTTTGGTTG 61.080 57.895 31.69 4.65 0.00 3.77
2300 2921 2.254051 CATCGCGCGGTTTTGGTT 59.746 55.556 31.69 1.79 0.00 3.67
2301 2922 4.398598 GCATCGCGCGGTTTTGGT 62.399 61.111 31.69 4.55 0.00 3.67
2303 2924 4.101790 AGGCATCGCGCGGTTTTG 62.102 61.111 31.69 21.83 43.84 2.44
2304 2925 3.799755 GAGGCATCGCGCGGTTTT 61.800 61.111 31.69 10.54 43.84 2.43
2309 2930 1.959899 GATAATGGAGGCATCGCGCG 61.960 60.000 26.76 26.76 43.84 6.86
2310 2931 1.639298 GGATAATGGAGGCATCGCGC 61.639 60.000 0.00 0.00 41.28 6.86
2311 2932 0.320683 TGGATAATGGAGGCATCGCG 60.321 55.000 0.00 0.00 0.00 5.87
2312 2933 1.446907 CTGGATAATGGAGGCATCGC 58.553 55.000 0.00 0.00 0.00 4.58
2313 2934 1.271001 TGCTGGATAATGGAGGCATCG 60.271 52.381 0.00 0.00 0.00 3.84
2314 2935 2.039480 TCTGCTGGATAATGGAGGCATC 59.961 50.000 0.00 0.00 0.00 3.91
2315 2936 2.060275 TCTGCTGGATAATGGAGGCAT 58.940 47.619 0.00 0.00 0.00 4.40
2316 2937 1.510492 TCTGCTGGATAATGGAGGCA 58.490 50.000 0.00 0.00 0.00 4.75
2317 2938 2.158696 ACTTCTGCTGGATAATGGAGGC 60.159 50.000 0.00 0.00 0.00 4.70
2318 2939 3.853355 ACTTCTGCTGGATAATGGAGG 57.147 47.619 0.00 0.00 0.00 4.30
2319 2940 4.747108 CGTTACTTCTGCTGGATAATGGAG 59.253 45.833 0.00 0.00 0.00 3.86
2320 2941 4.404394 TCGTTACTTCTGCTGGATAATGGA 59.596 41.667 0.00 0.00 0.00 3.41
2321 2942 4.693283 TCGTTACTTCTGCTGGATAATGG 58.307 43.478 0.00 0.00 0.00 3.16
2322 2943 5.580691 TGTTCGTTACTTCTGCTGGATAATG 59.419 40.000 0.00 0.00 0.00 1.90
2323 2944 5.581085 GTGTTCGTTACTTCTGCTGGATAAT 59.419 40.000 0.00 0.00 0.00 1.28
2324 2945 4.927425 GTGTTCGTTACTTCTGCTGGATAA 59.073 41.667 0.00 0.00 0.00 1.75
2325 2946 4.491676 GTGTTCGTTACTTCTGCTGGATA 58.508 43.478 0.00 0.00 0.00 2.59
2326 2947 3.326747 GTGTTCGTTACTTCTGCTGGAT 58.673 45.455 0.00 0.00 0.00 3.41
2327 2948 2.547218 GGTGTTCGTTACTTCTGCTGGA 60.547 50.000 0.00 0.00 0.00 3.86
2328 2949 1.798813 GGTGTTCGTTACTTCTGCTGG 59.201 52.381 0.00 0.00 0.00 4.85
2329 2950 1.455786 CGGTGTTCGTTACTTCTGCTG 59.544 52.381 0.00 0.00 0.00 4.41
2330 2951 1.779569 CGGTGTTCGTTACTTCTGCT 58.220 50.000 0.00 0.00 0.00 4.24
2331 2952 0.163146 GCGGTGTTCGTTACTTCTGC 59.837 55.000 0.00 0.00 41.72 4.26
2332 2953 1.191647 GTGCGGTGTTCGTTACTTCTG 59.808 52.381 0.00 0.00 41.72 3.02
2333 2954 1.494824 GTGCGGTGTTCGTTACTTCT 58.505 50.000 0.00 0.00 41.72 2.85
2334 2955 0.509929 GGTGCGGTGTTCGTTACTTC 59.490 55.000 0.00 0.00 41.72 3.01
2335 2956 0.105408 AGGTGCGGTGTTCGTTACTT 59.895 50.000 0.00 0.00 41.72 2.24
2336 2957 0.105408 AAGGTGCGGTGTTCGTTACT 59.895 50.000 0.00 0.00 41.72 2.24
2337 2958 0.509929 GAAGGTGCGGTGTTCGTTAC 59.490 55.000 0.00 0.00 41.72 2.50
2338 2959 0.600782 GGAAGGTGCGGTGTTCGTTA 60.601 55.000 0.00 0.00 41.72 3.18
2339 2960 1.890510 GGAAGGTGCGGTGTTCGTT 60.891 57.895 0.00 0.00 41.72 3.85
2340 2961 2.280592 GGAAGGTGCGGTGTTCGT 60.281 61.111 0.00 0.00 41.72 3.85
2341 2962 2.027625 GAGGAAGGTGCGGTGTTCG 61.028 63.158 0.00 0.00 42.76 3.95
2342 2963 2.027625 CGAGGAAGGTGCGGTGTTC 61.028 63.158 0.00 0.00 0.00 3.18
2343 2964 2.030562 CGAGGAAGGTGCGGTGTT 59.969 61.111 0.00 0.00 0.00 3.32
2344 2965 4.681978 GCGAGGAAGGTGCGGTGT 62.682 66.667 0.00 0.00 0.00 4.16
2347 2968 4.821589 GAGGCGAGGAAGGTGCGG 62.822 72.222 0.00 0.00 0.00 5.69
2348 2969 3.997064 CTGAGGCGAGGAAGGTGCG 62.997 68.421 0.00 0.00 0.00 5.34
2349 2970 2.125350 CTGAGGCGAGGAAGGTGC 60.125 66.667 0.00 0.00 0.00 5.01
2350 2971 1.216710 GACTGAGGCGAGGAAGGTG 59.783 63.158 0.00 0.00 0.00 4.00
2351 2972 1.228894 TGACTGAGGCGAGGAAGGT 60.229 57.895 0.00 0.00 0.00 3.50
2352 2973 1.216710 GTGACTGAGGCGAGGAAGG 59.783 63.158 0.00 0.00 0.00 3.46
2353 2974 1.216710 GGTGACTGAGGCGAGGAAG 59.783 63.158 0.00 0.00 0.00 3.46
2354 2975 2.636412 CGGTGACTGAGGCGAGGAA 61.636 63.158 0.00 0.00 0.00 3.36
2355 2976 3.062466 CGGTGACTGAGGCGAGGA 61.062 66.667 0.00 0.00 0.00 3.71
2356 2977 4.803426 GCGGTGACTGAGGCGAGG 62.803 72.222 0.00 0.00 0.00 4.63
2357 2978 4.803426 GGCGGTGACTGAGGCGAG 62.803 72.222 0.00 0.00 0.00 5.03
2395 3016 2.349590 GGGTCATGTTGTACGGGTAAC 58.650 52.381 0.00 0.00 0.00 2.50
2396 3017 1.278699 GGGGTCATGTTGTACGGGTAA 59.721 52.381 0.00 0.00 0.00 2.85
2397 3018 0.903942 GGGGTCATGTTGTACGGGTA 59.096 55.000 0.00 0.00 0.00 3.69
2398 3019 1.681076 GGGGTCATGTTGTACGGGT 59.319 57.895 0.00 0.00 0.00 5.28
2399 3020 1.448893 CGGGGTCATGTTGTACGGG 60.449 63.158 0.00 0.00 0.00 5.28
2400 3021 0.738412 GACGGGGTCATGTTGTACGG 60.738 60.000 0.00 0.00 32.09 4.02
2401 3022 0.245539 AGACGGGGTCATGTTGTACG 59.754 55.000 0.00 0.00 34.60 3.67
2402 3023 1.405121 GGAGACGGGGTCATGTTGTAC 60.405 57.143 0.00 0.00 34.60 2.90
2403 3024 0.899720 GGAGACGGGGTCATGTTGTA 59.100 55.000 0.00 0.00 34.60 2.41
2404 3025 1.677552 GGAGACGGGGTCATGTTGT 59.322 57.895 0.00 0.00 34.60 3.32
2405 3026 1.078426 GGGAGACGGGGTCATGTTG 60.078 63.158 0.00 0.00 34.60 3.33
2406 3027 2.656069 CGGGAGACGGGGTCATGTT 61.656 63.158 0.00 0.00 39.42 2.71
2407 3028 3.075005 CGGGAGACGGGGTCATGT 61.075 66.667 0.00 0.00 39.42 3.21
2408 3029 4.530857 GCGGGAGACGGGGTCATG 62.531 72.222 0.00 0.00 44.51 3.07
2409 3030 4.779733 AGCGGGAGACGGGGTCAT 62.780 66.667 0.00 0.00 44.51 3.06
2414 3035 3.486252 GATTCGAGCGGGAGACGGG 62.486 68.421 0.00 0.00 44.51 5.28
2415 3036 2.026301 GATTCGAGCGGGAGACGG 59.974 66.667 0.00 0.00 44.51 4.79
2417 3038 1.360911 GAGGATTCGAGCGGGAGAC 59.639 63.158 0.00 0.00 0.00 3.36
2418 3039 0.468214 ATGAGGATTCGAGCGGGAGA 60.468 55.000 0.00 0.00 0.00 3.71
2419 3040 0.038709 GATGAGGATTCGAGCGGGAG 60.039 60.000 0.00 0.00 0.00 4.30
2420 3041 0.468214 AGATGAGGATTCGAGCGGGA 60.468 55.000 0.00 0.00 0.00 5.14
2421 3042 0.390860 AAGATGAGGATTCGAGCGGG 59.609 55.000 0.00 0.00 0.00 6.13
2422 3043 1.604185 GGAAGATGAGGATTCGAGCGG 60.604 57.143 0.00 0.00 0.00 5.52
2423 3044 1.339610 AGGAAGATGAGGATTCGAGCG 59.660 52.381 0.00 0.00 0.00 5.03
2424 3045 2.288763 GGAGGAAGATGAGGATTCGAGC 60.289 54.545 0.00 0.00 0.00 5.03
2425 3046 3.230134 AGGAGGAAGATGAGGATTCGAG 58.770 50.000 0.00 0.00 0.00 4.04
2426 3047 3.320610 AGGAGGAAGATGAGGATTCGA 57.679 47.619 0.00 0.00 0.00 3.71
2427 3048 3.257127 GGTAGGAGGAAGATGAGGATTCG 59.743 52.174 0.00 0.00 0.00 3.34
2428 3049 3.580895 GGGTAGGAGGAAGATGAGGATTC 59.419 52.174 0.00 0.00 0.00 2.52
2429 3050 3.051032 TGGGTAGGAGGAAGATGAGGATT 60.051 47.826 0.00 0.00 0.00 3.01
2430 3051 2.524440 TGGGTAGGAGGAAGATGAGGAT 59.476 50.000 0.00 0.00 0.00 3.24
2431 3052 1.937350 TGGGTAGGAGGAAGATGAGGA 59.063 52.381 0.00 0.00 0.00 3.71
2432 3053 2.043227 GTGGGTAGGAGGAAGATGAGG 58.957 57.143 0.00 0.00 0.00 3.86
2433 3054 2.043227 GGTGGGTAGGAGGAAGATGAG 58.957 57.143 0.00 0.00 0.00 2.90
2434 3055 1.344087 GGGTGGGTAGGAGGAAGATGA 60.344 57.143 0.00 0.00 0.00 2.92
2435 3056 1.132500 GGGTGGGTAGGAGGAAGATG 58.868 60.000 0.00 0.00 0.00 2.90
2436 3057 0.029989 GGGGTGGGTAGGAGGAAGAT 60.030 60.000 0.00 0.00 0.00 2.40
2437 3058 1.394963 GGGGTGGGTAGGAGGAAGA 59.605 63.158 0.00 0.00 0.00 2.87
2438 3059 0.549169 TTGGGGTGGGTAGGAGGAAG 60.549 60.000 0.00 0.00 0.00 3.46
2439 3060 0.549169 CTTGGGGTGGGTAGGAGGAA 60.549 60.000 0.00 0.00 0.00 3.36
2440 3061 1.082206 CTTGGGGTGGGTAGGAGGA 59.918 63.158 0.00 0.00 0.00 3.71
2441 3062 1.229853 ACTTGGGGTGGGTAGGAGG 60.230 63.158 0.00 0.00 0.00 4.30
2442 3063 0.252742 AGACTTGGGGTGGGTAGGAG 60.253 60.000 0.00 0.00 0.00 3.69
2443 3064 0.252558 GAGACTTGGGGTGGGTAGGA 60.253 60.000 0.00 0.00 0.00 2.94
2444 3065 0.546747 TGAGACTTGGGGTGGGTAGG 60.547 60.000 0.00 0.00 0.00 3.18
2445 3066 1.584724 ATGAGACTTGGGGTGGGTAG 58.415 55.000 0.00 0.00 0.00 3.18
2446 3067 2.474112 GTATGAGACTTGGGGTGGGTA 58.526 52.381 0.00 0.00 0.00 3.69
2447 3068 1.286248 GTATGAGACTTGGGGTGGGT 58.714 55.000 0.00 0.00 0.00 4.51
2448 3069 0.546598 GGTATGAGACTTGGGGTGGG 59.453 60.000 0.00 0.00 0.00 4.61
2449 3070 0.546598 GGGTATGAGACTTGGGGTGG 59.453 60.000 0.00 0.00 0.00 4.61
2450 3071 0.546598 GGGGTATGAGACTTGGGGTG 59.453 60.000 0.00 0.00 0.00 4.61
2451 3072 0.623617 GGGGGTATGAGACTTGGGGT 60.624 60.000 0.00 0.00 0.00 4.95
2452 3073 1.696097 CGGGGGTATGAGACTTGGGG 61.696 65.000 0.00 0.00 0.00 4.96
2453 3074 1.830145 CGGGGGTATGAGACTTGGG 59.170 63.158 0.00 0.00 0.00 4.12
2454 3075 1.146263 GCGGGGGTATGAGACTTGG 59.854 63.158 0.00 0.00 0.00 3.61
2455 3076 1.146263 GGCGGGGGTATGAGACTTG 59.854 63.158 0.00 0.00 0.00 3.16
2456 3077 1.306654 TGGCGGGGGTATGAGACTT 60.307 57.895 0.00 0.00 0.00 3.01
2457 3078 2.064581 GTGGCGGGGGTATGAGACT 61.065 63.158 0.00 0.00 0.00 3.24
2458 3079 2.504519 GTGGCGGGGGTATGAGAC 59.495 66.667 0.00 0.00 0.00 3.36
2459 3080 2.766651 GGTGGCGGGGGTATGAGA 60.767 66.667 0.00 0.00 0.00 3.27
2460 3081 3.873812 GGGTGGCGGGGGTATGAG 61.874 72.222 0.00 0.00 0.00 2.90
2490 3111 3.551496 TTCCGGCCAAGGCTCTGTG 62.551 63.158 11.40 0.00 41.60 3.66
2491 3112 3.249189 TTCCGGCCAAGGCTCTGT 61.249 61.111 11.40 0.00 41.60 3.41
2492 3113 2.747855 GTTCCGGCCAAGGCTCTG 60.748 66.667 11.40 1.54 41.60 3.35
2493 3114 4.035102 GGTTCCGGCCAAGGCTCT 62.035 66.667 11.40 0.00 41.60 4.09
2540 3161 3.659089 AATGACGACGAAGCCCCCG 62.659 63.158 0.00 0.00 0.00 5.73
2541 3162 2.106683 CAATGACGACGAAGCCCCC 61.107 63.158 0.00 0.00 0.00 5.40
2542 3163 1.079405 TCAATGACGACGAAGCCCC 60.079 57.895 0.00 0.00 0.00 5.80
2543 3164 1.084370 CCTCAATGACGACGAAGCCC 61.084 60.000 0.00 0.00 0.00 5.19
2544 3165 0.108804 TCCTCAATGACGACGAAGCC 60.109 55.000 0.00 0.00 0.00 4.35
2545 3166 0.992802 GTCCTCAATGACGACGAAGC 59.007 55.000 0.00 0.00 0.00 3.86
2561 3182 0.454196 GAAGCTCAGAGAGGTCGTCC 59.546 60.000 0.00 0.00 39.62 4.79
2562 3183 1.132262 CAGAAGCTCAGAGAGGTCGTC 59.868 57.143 0.00 0.00 39.62 4.20
2563 3184 1.173043 CAGAAGCTCAGAGAGGTCGT 58.827 55.000 0.00 0.00 39.62 4.34
2564 3185 0.179140 GCAGAAGCTCAGAGAGGTCG 60.179 60.000 0.00 0.00 39.62 4.79
2565 3186 0.894141 TGCAGAAGCTCAGAGAGGTC 59.106 55.000 0.00 0.00 39.62 3.85
2566 3187 0.896923 CTGCAGAAGCTCAGAGAGGT 59.103 55.000 8.42 0.00 42.52 3.85
2567 3188 0.176219 CCTGCAGAAGCTCAGAGAGG 59.824 60.000 17.39 0.00 42.74 3.69
2568 3189 0.896923 ACCTGCAGAAGCTCAGAGAG 59.103 55.000 17.39 0.00 42.74 3.20
2569 3190 0.894141 GACCTGCAGAAGCTCAGAGA 59.106 55.000 17.39 0.00 42.74 3.10
2570 3191 0.108233 GGACCTGCAGAAGCTCAGAG 60.108 60.000 17.39 0.00 42.74 3.35
2571 3192 0.833409 TGGACCTGCAGAAGCTCAGA 60.833 55.000 17.39 0.00 42.74 3.27
2572 3193 0.252479 ATGGACCTGCAGAAGCTCAG 59.748 55.000 17.39 0.00 42.74 3.35
2573 3194 0.694771 AATGGACCTGCAGAAGCTCA 59.305 50.000 17.39 6.48 42.74 4.26
2574 3195 1.831580 AAATGGACCTGCAGAAGCTC 58.168 50.000 17.39 3.72 42.74 4.09
2575 3196 2.299326 AAAATGGACCTGCAGAAGCT 57.701 45.000 17.39 0.00 42.74 3.74
2576 3197 2.560105 AGAAAAATGGACCTGCAGAAGC 59.440 45.455 17.39 3.42 42.57 3.86
2577 3198 4.861102 AAGAAAAATGGACCTGCAGAAG 57.139 40.909 17.39 1.02 0.00 2.85
2578 3199 4.261572 CGAAAGAAAAATGGACCTGCAGAA 60.262 41.667 17.39 0.00 0.00 3.02
2579 3200 3.253188 CGAAAGAAAAATGGACCTGCAGA 59.747 43.478 17.39 0.00 0.00 4.26
2580 3201 3.253188 TCGAAAGAAAAATGGACCTGCAG 59.747 43.478 6.78 6.78 37.03 4.41
2581 3202 3.218453 TCGAAAGAAAAATGGACCTGCA 58.782 40.909 0.00 0.00 37.03 4.41
2582 3203 3.915437 TCGAAAGAAAAATGGACCTGC 57.085 42.857 0.00 0.00 37.03 4.85
2596 3217 7.176165 AGGTTAAAAGGGGTAAAGAATCGAAAG 59.824 37.037 0.00 0.00 0.00 2.62
2597 3218 7.005902 AGGTTAAAAGGGGTAAAGAATCGAAA 58.994 34.615 0.00 0.00 0.00 3.46
2598 3219 6.431852 CAGGTTAAAAGGGGTAAAGAATCGAA 59.568 38.462 0.00 0.00 0.00 3.71
2599 3220 5.941647 CAGGTTAAAAGGGGTAAAGAATCGA 59.058 40.000 0.00 0.00 0.00 3.59
2600 3221 5.392703 GCAGGTTAAAAGGGGTAAAGAATCG 60.393 44.000 0.00 0.00 0.00 3.34
2601 3222 5.715279 AGCAGGTTAAAAGGGGTAAAGAATC 59.285 40.000 0.00 0.00 0.00 2.52
2602 3223 5.651303 AGCAGGTTAAAAGGGGTAAAGAAT 58.349 37.500 0.00 0.00 0.00 2.40
2603 3224 5.069518 AGCAGGTTAAAAGGGGTAAAGAA 57.930 39.130 0.00 0.00 0.00 2.52
2604 3225 4.734843 AGCAGGTTAAAAGGGGTAAAGA 57.265 40.909 0.00 0.00 0.00 2.52
2605 3226 5.567430 ACTAGCAGGTTAAAAGGGGTAAAG 58.433 41.667 0.00 0.00 0.00 1.85
2606 3227 5.587760 ACTAGCAGGTTAAAAGGGGTAAA 57.412 39.130 0.00 0.00 0.00 2.01
2607 3228 5.587760 AACTAGCAGGTTAAAAGGGGTAA 57.412 39.130 0.00 0.00 0.00 2.85
2608 3229 6.700845 TTAACTAGCAGGTTAAAAGGGGTA 57.299 37.500 10.44 0.00 38.30 3.69
2609 3230 5.587760 TTAACTAGCAGGTTAAAAGGGGT 57.412 39.130 10.44 0.00 38.30 4.95
2610 3231 7.363530 GGAAATTAACTAGCAGGTTAAAAGGGG 60.364 40.741 14.88 0.00 42.46 4.79
2611 3232 7.396339 AGGAAATTAACTAGCAGGTTAAAAGGG 59.604 37.037 14.88 0.00 42.46 3.95
2612 3233 8.349568 AGGAAATTAACTAGCAGGTTAAAAGG 57.650 34.615 14.88 0.00 42.46 3.11
2613 3234 9.232473 AGAGGAAATTAACTAGCAGGTTAAAAG 57.768 33.333 14.88 0.00 42.46 2.27
2618 3239 7.993758 GGAATAGAGGAAATTAACTAGCAGGTT 59.006 37.037 0.00 0.00 0.00 3.50
2619 3240 7.127339 TGGAATAGAGGAAATTAACTAGCAGGT 59.873 37.037 0.00 0.00 0.00 4.00
2620 3241 7.442666 GTGGAATAGAGGAAATTAACTAGCAGG 59.557 40.741 0.00 0.00 0.00 4.85
2621 3242 8.207545 AGTGGAATAGAGGAAATTAACTAGCAG 58.792 37.037 0.00 0.00 0.00 4.24
2622 3243 7.987458 CAGTGGAATAGAGGAAATTAACTAGCA 59.013 37.037 0.00 0.00 0.00 3.49
2623 3244 8.204836 TCAGTGGAATAGAGGAAATTAACTAGC 58.795 37.037 0.00 0.00 0.00 3.42
2626 3247 9.981460 ATTTCAGTGGAATAGAGGAAATTAACT 57.019 29.630 0.00 0.00 32.71 2.24
2635 3256 8.787852 GCCTTAATTATTTCAGTGGAATAGAGG 58.212 37.037 14.59 14.59 31.93 3.69
2636 3257 8.787852 GGCCTTAATTATTTCAGTGGAATAGAG 58.212 37.037 4.05 2.65 31.93 2.43
2637 3258 7.724061 GGGCCTTAATTATTTCAGTGGAATAGA 59.276 37.037 0.84 0.00 31.93 1.98
2638 3259 7.725844 AGGGCCTTAATTATTTCAGTGGAATAG 59.274 37.037 0.00 0.00 31.93 1.73
2639 3260 7.591821 AGGGCCTTAATTATTTCAGTGGAATA 58.408 34.615 0.00 0.00 31.93 1.75
2640 3261 6.443832 AGGGCCTTAATTATTTCAGTGGAAT 58.556 36.000 0.00 1.38 31.93 3.01
2641 3262 5.837829 AGGGCCTTAATTATTTCAGTGGAA 58.162 37.500 0.00 0.00 0.00 3.53
2642 3263 5.193728 AGAGGGCCTTAATTATTTCAGTGGA 59.806 40.000 7.89 0.00 0.00 4.02
2643 3264 5.449553 AGAGGGCCTTAATTATTTCAGTGG 58.550 41.667 7.89 0.00 0.00 4.00
2644 3265 7.093771 ACAAAGAGGGCCTTAATTATTTCAGTG 60.094 37.037 7.89 0.00 34.00 3.66
2645 3266 6.954102 ACAAAGAGGGCCTTAATTATTTCAGT 59.046 34.615 7.89 0.00 34.00 3.41
2646 3267 7.410120 ACAAAGAGGGCCTTAATTATTTCAG 57.590 36.000 7.89 0.00 34.00 3.02
2647 3268 7.790782 AACAAAGAGGGCCTTAATTATTTCA 57.209 32.000 7.89 0.00 34.00 2.69
2648 3269 7.549134 CCAAACAAAGAGGGCCTTAATTATTTC 59.451 37.037 7.89 0.00 34.00 2.17
2649 3270 7.394016 CCAAACAAAGAGGGCCTTAATTATTT 58.606 34.615 7.89 2.37 34.00 1.40
2650 3271 6.070251 CCCAAACAAAGAGGGCCTTAATTATT 60.070 38.462 7.89 0.00 35.44 1.40
2651 3272 5.425217 CCCAAACAAAGAGGGCCTTAATTAT 59.575 40.000 7.89 0.00 35.44 1.28
2652 3273 4.775253 CCCAAACAAAGAGGGCCTTAATTA 59.225 41.667 7.89 0.00 35.44 1.40
2653 3274 3.582647 CCCAAACAAAGAGGGCCTTAATT 59.417 43.478 7.89 0.00 35.44 1.40
2654 3275 3.173151 CCCAAACAAAGAGGGCCTTAAT 58.827 45.455 7.89 0.00 35.44 1.40
2655 3276 2.090999 ACCCAAACAAAGAGGGCCTTAA 60.091 45.455 7.89 0.00 46.88 1.85
2656 3277 1.501604 ACCCAAACAAAGAGGGCCTTA 59.498 47.619 7.89 0.00 46.88 2.69
2657 3278 0.264657 ACCCAAACAAAGAGGGCCTT 59.735 50.000 7.89 0.00 46.88 4.35
2658 3279 0.264657 AACCCAAACAAAGAGGGCCT 59.735 50.000 5.25 5.25 46.88 5.19
2659 3280 0.392706 CAACCCAAACAAAGAGGGCC 59.607 55.000 0.00 0.00 46.88 5.80
2660 3281 0.392706 CCAACCCAAACAAAGAGGGC 59.607 55.000 0.00 0.00 46.88 5.19
2662 3283 1.341209 GCTCCAACCCAAACAAAGAGG 59.659 52.381 0.00 0.00 0.00 3.69
2663 3284 2.310538 AGCTCCAACCCAAACAAAGAG 58.689 47.619 0.00 0.00 0.00 2.85
2664 3285 2.452600 AGCTCCAACCCAAACAAAGA 57.547 45.000 0.00 0.00 0.00 2.52
2665 3286 3.541996 AAAGCTCCAACCCAAACAAAG 57.458 42.857 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.