Multiple sequence alignment - TraesCS1A01G381700

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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 TraesCS1A01G381700 chr1A 100.000 2619 0 0 1 2619 552203378 552200760 0.000000e+00 4837
1 TraesCS1A01G381700 chr1A 94.245 1668 68 10 1 1656 552182942 552181291 0.000000e+00 2523
2 TraesCS1A01G381700 chr1A 87.739 628 41 6 1654 2247 552211641 552211016 0.000000e+00 701
3 TraesCS1A01G381700 chr1D 94.881 1680 62 8 1 1656 461118557 461116878 0.000000e+00 2604
4 TraesCS1A01G381700 chr1D 85.304 626 55 14 1654 2246 461138811 461138190 1.720000e-171 612
5 TraesCS1A01G381700 chr1D 80.000 245 43 6 1 241 371219989 371220231 2.680000e-40 176
6 TraesCS1A01G381700 chr1D 89.024 82 7 2 286 366 461118701 461118621 1.660000e-17 100
7 TraesCS1A01G381700 chr1B 93.789 950 58 1 1 949 633321927 633320978 0.000000e+00 1426
8 TraesCS1A01G381700 chr1B 94.708 718 27 4 949 1656 633320938 633320222 0.000000e+00 1105
9 TraesCS1A01G381700 chr1B 83.094 627 50 27 1654 2227 633331100 633330477 1.070000e-143 520
10 TraesCS1A01G381700 chr1B 77.812 329 50 15 89 409 288406761 288407074 5.760000e-42 182
11 TraesCS1A01G381700 chr1B 90.598 117 9 2 1654 1769 549465613 549465728 1.260000e-33 154
12 TraesCS1A01G381700 chr1B 77.099 262 48 12 9 266 408655091 408654838 9.770000e-30 141
13 TraesCS1A01G381700 chr1B 82.051 117 19 2 2038 2153 619401727 619401842 5.970000e-17 99
14 TraesCS1A01G381700 chr3A 97.855 373 8 0 2247 2619 508695866 508695494 0.000000e+00 645
15 TraesCS1A01G381700 chr3A 97.594 374 9 0 2246 2619 26698293 26698666 2.200000e-180 641
16 TraesCS1A01G381700 chr3A 97.581 372 9 0 2248 2619 34214837 34214466 2.840000e-179 638
17 TraesCS1A01G381700 chr3A 97.074 376 11 0 2244 2619 749742394 749742019 3.680000e-178 634
18 TraesCS1A01G381700 chr3A 81.395 129 19 5 2012 2136 487453949 487453822 1.660000e-17 100
19 TraesCS1A01G381700 chr4A 97.849 372 8 0 2248 2619 606724360 606724731 0.000000e+00 643
20 TraesCS1A01G381700 chr4A 97.581 372 9 0 2248 2619 606787847 606788218 2.840000e-179 638
21 TraesCS1A01G381700 chr4A 97.074 376 11 0 2244 2619 611615705 611615330 3.680000e-178 634
22 TraesCS1A01G381700 chr4A 75.484 465 75 28 1 450 615224351 615224791 9.570000e-45 191
23 TraesCS1A01G381700 chr4A 76.015 271 53 11 137 402 656932453 656932716 2.120000e-26 130
24 TraesCS1A01G381700 chr4A 81.295 139 18 8 2044 2177 552510593 552510728 3.560000e-19 106
25 TraesCS1A01G381700 chr2A 97.600 375 9 0 2245 2619 96942239 96942613 0.000000e+00 643
26 TraesCS1A01G381700 chr2A 80.309 259 41 9 1 253 680101611 680101865 1.240000e-43 187
27 TraesCS1A01G381700 chr5A 96.632 386 12 1 2235 2619 514880984 514881369 7.900000e-180 640
28 TraesCS1A01G381700 chrUn 86.911 191 24 1 2038 2227 61003344 61003154 2.040000e-51 213
29 TraesCS1A01G381700 chr5B 81.633 245 38 5 10 253 692280627 692280865 2.060000e-46 196
30 TraesCS1A01G381700 chr5B 81.159 138 20 6 315 449 491240464 491240330 3.560000e-19 106
31 TraesCS1A01G381700 chr7B 90.598 117 9 2 1654 1769 64765159 64765274 1.260000e-33 154
32 TraesCS1A01G381700 chr6B 88.889 117 11 2 1654 1769 655258244 655258129 2.720000e-30 143
33 TraesCS1A01G381700 chr6B 88.034 117 12 2 1654 1769 30364883 30364998 1.260000e-28 137
34 TraesCS1A01G381700 chr6B 83.333 138 17 6 2044 2177 624612896 624612761 3.540000e-24 122
35 TraesCS1A01G381700 chr5D 88.793 116 13 0 1654 1769 556407880 556407995 2.720000e-30 143
36 TraesCS1A01G381700 chr3B 87.179 117 13 2 1654 1769 769345318 769345203 5.880000e-27 132
37 TraesCS1A01G381700 chr7D 85.841 113 11 5 267 375 285229381 285229492 5.920000e-22 115
38 TraesCS1A01G381700 chr7A 85.841 113 11 5 267 375 323434387 323434498 5.920000e-22 115
39 TraesCS1A01G381700 chr6A 81.560 141 24 2 2038 2177 143485764 143485903 5.920000e-22 115
40 TraesCS1A01G381700 chr6A 85.455 110 16 0 2038 2147 461979528 461979637 5.920000e-22 115


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 TraesCS1A01G381700 chr1A 552200760 552203378 2618 True 4837.0 4837 100.0000 1 2619 1 chr1A.!!$R2 2618
1 TraesCS1A01G381700 chr1A 552181291 552182942 1651 True 2523.0 2523 94.2450 1 1656 1 chr1A.!!$R1 1655
2 TraesCS1A01G381700 chr1A 552211016 552211641 625 True 701.0 701 87.7390 1654 2247 1 chr1A.!!$R3 593
3 TraesCS1A01G381700 chr1D 461116878 461118701 1823 True 1352.0 2604 91.9525 1 1656 2 chr1D.!!$R2 1655
4 TraesCS1A01G381700 chr1D 461138190 461138811 621 True 612.0 612 85.3040 1654 2246 1 chr1D.!!$R1 592
5 TraesCS1A01G381700 chr1B 633320222 633321927 1705 True 1265.5 1426 94.2485 1 1656 2 chr1B.!!$R3 1655
6 TraesCS1A01G381700 chr1B 633330477 633331100 623 True 520.0 520 83.0940 1654 2227 1 chr1B.!!$R2 573

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
949 1097 3.709653 GGTACCTCTCTCTCTCTCTCTCA 59.29 52.174 4.06 0.0 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2537 0.03467 CTGCTGCTAGCCTTTTCCCT 60.035 55.0 13.29 0.0 41.51 4.2 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
61 206 7.045126 TCATATCCAACATATACGTCACACA 57.955 36.000 0.00 0.00 0.00 3.72
63 208 8.147704 TCATATCCAACATATACGTCACACATT 58.852 33.333 0.00 0.00 0.00 2.71
282 427 9.434420 TGTGAATTTGAGAAAAACACTGATTTT 57.566 25.926 0.00 0.00 34.24 1.82
631 778 9.593134 CATAATTATCTTCTACTCCATACCAGC 57.407 37.037 0.00 0.00 0.00 4.85
638 785 5.340891 TCTACTCCATACCAGCCTTCTAT 57.659 43.478 0.00 0.00 0.00 1.98
854 1002 5.657826 AGATCAGATCCTCATTCCATACG 57.342 43.478 6.80 0.00 0.00 3.06
856 1004 6.249192 AGATCAGATCCTCATTCCATACGTA 58.751 40.000 6.80 0.00 0.00 3.57
925 1073 6.209192 TCCTTTCTTGCTTGCATTATTCTTCA 59.791 34.615 0.00 0.00 0.00 3.02
949 1097 3.709653 GGTACCTCTCTCTCTCTCTCTCA 59.290 52.174 4.06 0.00 0.00 3.27
952 1100 6.042781 GGTACCTCTCTCTCTCTCTCTCAATA 59.957 46.154 4.06 0.00 0.00 1.90
953 1101 6.575244 ACCTCTCTCTCTCTCTCTCAATAA 57.425 41.667 0.00 0.00 0.00 1.40
959 1147 9.645128 TCTCTCTCTCTCTCTCAATAAATCAAT 57.355 33.333 0.00 0.00 0.00 2.57
1059 1249 9.316730 GAATCATACAAACCGGTATGTTTACTA 57.683 33.333 8.00 0.00 46.78 1.82
1111 1301 5.516339 GCAAATAAGTCGCAAGCATTATGTT 59.484 36.000 0.00 0.00 31.13 2.71
1335 1533 2.003301 GCGAGGAAAGACATGGAACTC 58.997 52.381 0.00 0.00 0.00 3.01
1445 1644 1.811965 CACGATGAACAGAATGCCCAA 59.188 47.619 0.00 0.00 42.53 4.12
1645 1844 1.069765 CAAGTCGTGTGTGGCCTCT 59.930 57.895 3.32 0.00 0.00 3.69
1713 1912 2.029666 CCGAGCAGGATTAGGGCG 59.970 66.667 0.00 0.00 45.00 6.13
1717 1916 4.547367 GCAGGATTAGGGCGGCGT 62.547 66.667 9.37 9.74 0.00 5.68
1718 1917 2.280186 CAGGATTAGGGCGGCGTC 60.280 66.667 7.70 5.57 0.00 5.19
1719 1918 2.444140 AGGATTAGGGCGGCGTCT 60.444 61.111 12.73 10.78 0.00 4.18
1722 1921 1.887707 GATTAGGGCGGCGTCTTGG 60.888 63.158 12.73 0.00 0.00 3.61
1724 1923 2.588856 ATTAGGGCGGCGTCTTGGAC 62.589 60.000 12.73 0.00 0.00 4.02
1728 1927 4.681978 GCGGCGTCTTGGACTGGT 62.682 66.667 9.37 0.00 0.00 4.00
1735 1935 2.936993 GCGTCTTGGACTGGTGATTCAT 60.937 50.000 0.00 0.00 0.00 2.57
1740 1940 0.830648 GGACTGGTGATTCATCGGGA 59.169 55.000 10.46 0.00 0.00 5.14
1770 1970 0.608640 AGGGTGTTCGTGATGGTCTC 59.391 55.000 0.00 0.00 0.00 3.36
1783 1983 3.749064 GTCTCGAGGTGCGGCTGA 61.749 66.667 13.56 0.00 41.33 4.26
1837 2037 3.572682 CCGCCTTTTTACCTCCTTTCTTT 59.427 43.478 0.00 0.00 0.00 2.52
1849 2049 0.109132 CTTTCTTTGACATGGCGGCC 60.109 55.000 13.32 13.32 0.00 6.13
1965 2196 2.265739 GCCGCCTGATGTCAGTCA 59.734 61.111 9.03 0.00 42.27 3.41
1985 2218 4.900747 GTCATTTCGATGCGCTTTAAGATC 59.099 41.667 9.73 0.31 0.00 2.75
2109 2392 5.284079 ACGTCGAACTGCTTCTAAAACTTA 58.716 37.500 0.00 0.00 0.00 2.24
2118 2401 7.716612 ACTGCTTCTAAAACTTAGCACAAATT 58.283 30.769 0.00 0.00 38.61 1.82
2185 2468 4.786068 CACGTGGCACTGTATTTTTAATCG 59.214 41.667 16.72 0.00 0.00 3.34
2204 2487 1.154169 GCATGCACACGTGACATGG 60.154 57.895 34.96 24.75 41.22 3.66
2247 2530 9.833917 ATGGCTTACTTTATAAAAGTCTCTACC 57.166 33.333 8.24 5.91 0.00 3.18
2248 2531 8.818860 TGGCTTACTTTATAAAAGTCTCTACCA 58.181 33.333 8.24 7.98 0.00 3.25
2249 2532 9.096160 GGCTTACTTTATAAAAGTCTCTACCAC 57.904 37.037 8.24 0.00 0.00 4.16
2250 2533 9.872721 GCTTACTTTATAAAAGTCTCTACCACT 57.127 33.333 8.24 0.00 0.00 4.00
2257 2540 9.638176 TTATAAAAGTCTCTACCACTACTAGGG 57.362 37.037 0.00 0.00 0.00 3.53
2258 2541 5.793034 AAAGTCTCTACCACTACTAGGGA 57.207 43.478 0.00 0.00 0.00 4.20
2259 2542 5.793034 AAGTCTCTACCACTACTAGGGAA 57.207 43.478 0.00 0.00 0.00 3.97
2260 2543 5.793034 AGTCTCTACCACTACTAGGGAAA 57.207 43.478 0.00 0.00 0.00 3.13
2261 2544 6.150034 AGTCTCTACCACTACTAGGGAAAA 57.850 41.667 0.00 0.00 0.00 2.29
2262 2545 6.189133 AGTCTCTACCACTACTAGGGAAAAG 58.811 44.000 0.00 0.00 0.00 2.27
2263 2546 5.360429 GTCTCTACCACTACTAGGGAAAAGG 59.640 48.000 0.00 0.00 0.00 3.11
2264 2547 4.028825 TCTACCACTACTAGGGAAAAGGC 58.971 47.826 0.00 0.00 0.00 4.35
2265 2548 2.917205 ACCACTACTAGGGAAAAGGCT 58.083 47.619 0.00 0.00 0.00 4.58
2266 2549 4.070681 ACCACTACTAGGGAAAAGGCTA 57.929 45.455 0.00 0.00 0.00 3.93
2267 2550 4.031611 ACCACTACTAGGGAAAAGGCTAG 58.968 47.826 0.00 0.00 0.00 3.42
2268 2551 3.181464 CCACTACTAGGGAAAAGGCTAGC 60.181 52.174 6.04 6.04 0.00 3.42
2269 2552 3.451178 CACTACTAGGGAAAAGGCTAGCA 59.549 47.826 18.24 0.00 0.00 3.49
2270 2553 3.707102 ACTACTAGGGAAAAGGCTAGCAG 59.293 47.826 18.24 4.16 0.00 4.24
2271 2554 1.210722 ACTAGGGAAAAGGCTAGCAGC 59.789 52.381 18.24 0.00 41.46 5.25
2272 2555 1.210478 CTAGGGAAAAGGCTAGCAGCA 59.790 52.381 18.24 0.00 44.75 4.41
2273 2556 0.034670 AGGGAAAAGGCTAGCAGCAG 60.035 55.000 18.24 0.00 44.75 4.24
2274 2557 1.661498 GGGAAAAGGCTAGCAGCAGC 61.661 60.000 18.24 7.98 44.75 5.25
2275 2558 1.427020 GAAAAGGCTAGCAGCAGCG 59.573 57.895 18.24 0.00 44.75 5.18
2276 2559 2.589636 GAAAAGGCTAGCAGCAGCGC 62.590 60.000 18.24 0.00 44.75 5.92
2284 2567 3.732892 GCAGCAGCGCGGGTTTTA 61.733 61.111 10.16 0.00 0.00 1.52
2285 2568 2.480555 CAGCAGCGCGGGTTTTAG 59.519 61.111 10.16 0.00 0.00 1.85
2286 2569 2.032634 CAGCAGCGCGGGTTTTAGA 61.033 57.895 10.16 0.00 0.00 2.10
2287 2570 2.033194 AGCAGCGCGGGTTTTAGAC 61.033 57.895 8.83 0.00 0.00 2.59
2300 2583 4.049869 GGTTTTAGACCTATCAGTAGCGC 58.950 47.826 0.00 0.00 45.55 5.92
2301 2584 3.620929 TTTAGACCTATCAGTAGCGCG 57.379 47.619 0.00 0.00 0.00 6.86
2302 2585 1.520494 TAGACCTATCAGTAGCGCGG 58.480 55.000 8.83 0.00 0.00 6.46
2303 2586 1.173444 AGACCTATCAGTAGCGCGGG 61.173 60.000 8.83 0.00 0.00 6.13
2304 2587 2.143594 GACCTATCAGTAGCGCGGGG 62.144 65.000 8.83 0.00 0.00 5.73
2305 2588 2.201022 CCTATCAGTAGCGCGGGGT 61.201 63.158 8.83 9.74 0.00 4.95
2306 2589 1.007271 CTATCAGTAGCGCGGGGTG 60.007 63.158 15.06 0.00 0.00 4.61
2307 2590 2.421877 CTATCAGTAGCGCGGGGTGG 62.422 65.000 15.06 4.08 0.00 4.61
2309 2592 3.454573 CAGTAGCGCGGGGTGGTA 61.455 66.667 15.06 0.00 0.00 3.25
2310 2593 3.455469 AGTAGCGCGGGGTGGTAC 61.455 66.667 15.06 9.74 44.20 3.34
2311 2594 4.860261 GTAGCGCGGGGTGGTACG 62.860 72.222 15.06 0.00 37.30 3.67
2317 2600 2.493030 CGGGGTGGTACGCTACTG 59.507 66.667 0.00 0.00 39.78 2.74
2318 2601 2.048023 CGGGGTGGTACGCTACTGA 61.048 63.158 0.00 0.00 39.78 3.41
2319 2602 1.597797 CGGGGTGGTACGCTACTGAA 61.598 60.000 0.00 0.00 39.78 3.02
2320 2603 0.609662 GGGGTGGTACGCTACTGAAA 59.390 55.000 0.00 0.00 39.78 2.69
2321 2604 1.002315 GGGGTGGTACGCTACTGAAAA 59.998 52.381 0.00 0.00 39.78 2.29
2322 2605 2.344025 GGGTGGTACGCTACTGAAAAG 58.656 52.381 0.00 0.00 39.78 2.27
2323 2606 2.344025 GGTGGTACGCTACTGAAAAGG 58.656 52.381 0.00 0.00 39.78 3.11
2324 2607 1.730612 GTGGTACGCTACTGAAAAGGC 59.269 52.381 0.00 0.00 35.02 4.35
2327 2610 3.876300 CGCTACTGAAAAGGCGCT 58.124 55.556 7.64 0.00 41.08 5.92
2328 2611 3.044809 CGCTACTGAAAAGGCGCTA 57.955 52.632 7.64 0.00 41.08 4.26
2329 2612 0.645868 CGCTACTGAAAAGGCGCTAC 59.354 55.000 7.64 0.00 41.08 3.58
2330 2613 1.722011 GCTACTGAAAAGGCGCTACA 58.278 50.000 7.64 0.00 0.00 2.74
2331 2614 1.661112 GCTACTGAAAAGGCGCTACAG 59.339 52.381 7.64 12.10 35.14 2.74
2332 2615 1.661112 CTACTGAAAAGGCGCTACAGC 59.339 52.381 7.64 0.00 37.78 4.40
2333 2616 0.035458 ACTGAAAAGGCGCTACAGCT 59.965 50.000 7.64 0.00 39.32 4.24
2334 2617 1.275291 ACTGAAAAGGCGCTACAGCTA 59.725 47.619 7.64 0.00 39.32 3.32
2335 2618 2.289444 ACTGAAAAGGCGCTACAGCTAA 60.289 45.455 7.64 0.00 39.32 3.09
2336 2619 2.073816 TGAAAAGGCGCTACAGCTAAC 58.926 47.619 7.64 0.00 39.32 2.34
2337 2620 2.073816 GAAAAGGCGCTACAGCTAACA 58.926 47.619 7.64 0.00 39.32 2.41
2338 2621 2.178912 AAAGGCGCTACAGCTAACAA 57.821 45.000 7.64 0.00 39.32 2.83
2339 2622 2.178912 AAGGCGCTACAGCTAACAAA 57.821 45.000 7.64 0.00 39.32 2.83
2340 2623 2.403252 AGGCGCTACAGCTAACAAAT 57.597 45.000 7.64 0.00 39.32 2.32
2341 2624 3.536956 AGGCGCTACAGCTAACAAATA 57.463 42.857 7.64 0.00 39.32 1.40
2342 2625 3.458189 AGGCGCTACAGCTAACAAATAG 58.542 45.455 7.64 0.00 39.32 1.73
2359 2642 2.815647 GCAGTAGCGTGCCTCCAC 60.816 66.667 0.00 0.00 37.49 4.02
2360 2643 2.125512 CAGTAGCGTGCCTCCACC 60.126 66.667 0.00 0.00 38.79 4.61
2361 2644 3.391382 AGTAGCGTGCCTCCACCC 61.391 66.667 0.00 0.00 38.79 4.61
2362 2645 3.702048 GTAGCGTGCCTCCACCCA 61.702 66.667 0.00 0.00 38.79 4.51
2363 2646 3.702048 TAGCGTGCCTCCACCCAC 61.702 66.667 0.00 0.00 38.79 4.61
2367 2650 3.702048 GTGCCTCCACCCACGCTA 61.702 66.667 0.00 0.00 35.92 4.26
2368 2651 3.702048 TGCCTCCACCCACGCTAC 61.702 66.667 0.00 0.00 0.00 3.58
2369 2652 4.814294 GCCTCCACCCACGCTACG 62.814 72.222 0.00 0.00 0.00 3.51
2370 2653 4.143333 CCTCCACCCACGCTACGG 62.143 72.222 0.00 0.00 0.00 4.02
2371 2654 4.814294 CTCCACCCACGCTACGGC 62.814 72.222 0.00 0.00 0.00 5.68
2373 2656 3.454573 CCACCCACGCTACGGCTA 61.455 66.667 0.00 0.00 36.09 3.93
2374 2657 2.574929 CACCCACGCTACGGCTAA 59.425 61.111 0.00 0.00 36.09 3.09
2375 2658 1.079681 CACCCACGCTACGGCTAAA 60.080 57.895 0.00 0.00 36.09 1.85
2376 2659 0.461339 CACCCACGCTACGGCTAAAT 60.461 55.000 0.00 0.00 36.09 1.40
2377 2660 0.179092 ACCCACGCTACGGCTAAATC 60.179 55.000 0.00 0.00 36.09 2.17
2378 2661 1.213094 CCCACGCTACGGCTAAATCG 61.213 60.000 0.00 0.00 36.09 3.34
2379 2662 0.248743 CCACGCTACGGCTAAATCGA 60.249 55.000 0.00 0.00 36.09 3.59
2380 2663 1.602165 CCACGCTACGGCTAAATCGAT 60.602 52.381 0.00 0.00 36.09 3.59
2381 2664 2.124903 CACGCTACGGCTAAATCGATT 58.875 47.619 4.39 4.39 36.09 3.34
2382 2665 2.538449 CACGCTACGGCTAAATCGATTT 59.462 45.455 25.48 25.48 36.09 2.17
2383 2666 3.732219 CACGCTACGGCTAAATCGATTTA 59.268 43.478 25.03 25.03 36.09 1.40
2385 2668 3.979495 CGCTACGGCTAAATCGATTTAGT 59.021 43.478 38.75 29.20 46.78 2.24
2386 2669 5.149273 CGCTACGGCTAAATCGATTTAGTA 58.851 41.667 38.75 28.89 46.78 1.82
2387 2670 5.283247 CGCTACGGCTAAATCGATTTAGTAG 59.717 44.000 38.75 33.75 46.78 2.57
2388 2671 5.060693 GCTACGGCTAAATCGATTTAGTAGC 59.939 44.000 35.10 35.10 46.78 3.58
2389 2672 4.940463 ACGGCTAAATCGATTTAGTAGCA 58.060 39.130 38.75 19.42 46.78 3.49
2390 2673 4.982916 ACGGCTAAATCGATTTAGTAGCAG 59.017 41.667 38.75 33.18 46.78 4.24
2391 2674 4.143305 CGGCTAAATCGATTTAGTAGCAGC 60.143 45.833 38.75 31.46 46.78 5.25
2392 2675 4.143305 GGCTAAATCGATTTAGTAGCAGCG 60.143 45.833 38.75 23.46 46.78 5.18
2393 2676 4.680110 GCTAAATCGATTTAGTAGCAGCGA 59.320 41.667 38.75 17.10 46.78 4.93
2394 2677 5.164138 GCTAAATCGATTTAGTAGCAGCGAG 60.164 44.000 38.75 23.89 46.78 5.03
2395 2678 3.992260 ATCGATTTAGTAGCAGCGAGT 57.008 42.857 0.00 0.00 0.00 4.18
2396 2679 3.777465 TCGATTTAGTAGCAGCGAGTT 57.223 42.857 0.00 0.00 0.00 3.01
2397 2680 4.106029 TCGATTTAGTAGCAGCGAGTTT 57.894 40.909 0.00 0.00 0.00 2.66
2398 2681 4.103357 TCGATTTAGTAGCAGCGAGTTTC 58.897 43.478 0.00 0.00 0.00 2.78
2399 2682 3.857665 CGATTTAGTAGCAGCGAGTTTCA 59.142 43.478 0.00 0.00 0.00 2.69
2400 2683 4.027295 CGATTTAGTAGCAGCGAGTTTCAG 60.027 45.833 0.00 0.00 0.00 3.02
2401 2684 2.941453 TAGTAGCAGCGAGTTTCAGG 57.059 50.000 0.00 0.00 0.00 3.86
2402 2685 1.257743 AGTAGCAGCGAGTTTCAGGA 58.742 50.000 0.00 0.00 0.00 3.86
2403 2686 1.203523 AGTAGCAGCGAGTTTCAGGAG 59.796 52.381 0.00 0.00 0.00 3.69
2404 2687 0.532573 TAGCAGCGAGTTTCAGGAGG 59.467 55.000 0.00 0.00 0.00 4.30
2405 2688 1.188219 AGCAGCGAGTTTCAGGAGGA 61.188 55.000 0.00 0.00 0.00 3.71
2406 2689 0.739112 GCAGCGAGTTTCAGGAGGAG 60.739 60.000 0.00 0.00 0.00 3.69
2407 2690 0.739112 CAGCGAGTTTCAGGAGGAGC 60.739 60.000 0.00 0.00 0.00 4.70
2408 2691 1.188219 AGCGAGTTTCAGGAGGAGCA 61.188 55.000 0.00 0.00 0.00 4.26
2409 2692 1.016653 GCGAGTTTCAGGAGGAGCAC 61.017 60.000 0.00 0.00 0.00 4.40
2410 2693 0.605589 CGAGTTTCAGGAGGAGCACT 59.394 55.000 0.00 0.00 0.00 4.40
2411 2694 1.671261 CGAGTTTCAGGAGGAGCACTG 60.671 57.143 0.00 0.00 36.07 3.66
2412 2695 0.036022 AGTTTCAGGAGGAGCACTGC 59.964 55.000 0.00 0.00 37.90 4.40
2417 2700 3.713650 GGAGGAGCACTGCTGGTA 58.286 61.111 8.69 0.00 39.88 3.25
2418 2701 1.983224 GGAGGAGCACTGCTGGTAA 59.017 57.895 8.69 0.00 39.88 2.85
2419 2702 0.543749 GGAGGAGCACTGCTGGTAAT 59.456 55.000 8.69 0.00 39.88 1.89
2420 2703 1.065126 GGAGGAGCACTGCTGGTAATT 60.065 52.381 8.69 0.00 39.88 1.40
2421 2704 2.170607 GGAGGAGCACTGCTGGTAATTA 59.829 50.000 8.69 0.00 39.88 1.40
2422 2705 3.462021 GAGGAGCACTGCTGGTAATTAG 58.538 50.000 8.69 0.00 39.88 1.73
2423 2706 2.840651 AGGAGCACTGCTGGTAATTAGT 59.159 45.455 8.69 0.00 39.88 2.24
2424 2707 4.030913 AGGAGCACTGCTGGTAATTAGTA 58.969 43.478 8.69 0.00 39.88 1.82
2425 2708 4.100189 AGGAGCACTGCTGGTAATTAGTAG 59.900 45.833 8.69 0.00 39.88 2.57
2426 2709 4.141914 GGAGCACTGCTGGTAATTAGTAGT 60.142 45.833 8.69 0.00 39.88 2.73
2427 2710 5.068723 GGAGCACTGCTGGTAATTAGTAGTA 59.931 44.000 8.69 0.00 39.88 1.82
2428 2711 6.150396 AGCACTGCTGGTAATTAGTAGTAG 57.850 41.667 1.67 10.53 38.75 2.57
2429 2712 4.745620 GCACTGCTGGTAATTAGTAGTAGC 59.254 45.833 11.50 7.99 38.75 3.58
2430 2713 4.976731 CACTGCTGGTAATTAGTAGTAGCG 59.023 45.833 11.50 2.51 38.75 4.26
2431 2714 3.973657 TGCTGGTAATTAGTAGTAGCGC 58.026 45.455 0.00 0.00 32.66 5.92
2432 2715 3.635373 TGCTGGTAATTAGTAGTAGCGCT 59.365 43.478 17.26 17.26 32.66 5.92
2433 2716 4.098960 TGCTGGTAATTAGTAGTAGCGCTT 59.901 41.667 18.68 0.00 32.66 4.68
2434 2717 4.680567 GCTGGTAATTAGTAGTAGCGCTTC 59.319 45.833 18.68 11.64 0.00 3.86
2435 2718 5.507650 GCTGGTAATTAGTAGTAGCGCTTCT 60.508 44.000 18.68 19.91 0.00 2.85
2436 2719 6.069684 TGGTAATTAGTAGTAGCGCTTCTC 57.930 41.667 20.53 11.82 0.00 2.87
2437 2720 5.826737 TGGTAATTAGTAGTAGCGCTTCTCT 59.173 40.000 20.53 17.70 0.00 3.10
2438 2721 6.017275 TGGTAATTAGTAGTAGCGCTTCTCTC 60.017 42.308 20.53 14.18 0.00 3.20
2439 2722 6.205270 GGTAATTAGTAGTAGCGCTTCTCTCT 59.795 42.308 20.53 19.79 0.00 3.10
2440 2723 5.682943 ATTAGTAGTAGCGCTTCTCTCTG 57.317 43.478 20.53 0.00 0.00 3.35
2441 2724 1.673920 AGTAGTAGCGCTTCTCTCTGC 59.326 52.381 20.53 11.85 0.00 4.26
2442 2725 1.025812 TAGTAGCGCTTCTCTCTGCC 58.974 55.000 20.53 0.00 0.00 4.85
2443 2726 1.227118 GTAGCGCTTCTCTCTGCCC 60.227 63.158 18.68 0.00 0.00 5.36
2444 2727 2.775856 TAGCGCTTCTCTCTGCCCG 61.776 63.158 18.68 0.00 0.00 6.13
2448 2731 4.140599 CTTCTCTCTGCCCGCGCT 62.141 66.667 5.56 0.00 35.36 5.92
2449 2732 4.441695 TTCTCTCTGCCCGCGCTG 62.442 66.667 5.56 0.00 35.36 5.18
2455 2738 4.207281 CTGCCCGCGCTGCTACTA 62.207 66.667 17.83 0.00 35.36 1.82
2456 2739 3.506059 CTGCCCGCGCTGCTACTAT 62.506 63.158 17.83 0.00 35.36 2.12
2457 2740 2.280186 GCCCGCGCTGCTACTATT 60.280 61.111 5.56 0.00 0.00 1.73
2458 2741 1.006571 GCCCGCGCTGCTACTATTA 60.007 57.895 5.56 0.00 0.00 0.98
2459 2742 0.389948 GCCCGCGCTGCTACTATTAT 60.390 55.000 5.56 0.00 0.00 1.28
2460 2743 1.939838 GCCCGCGCTGCTACTATTATT 60.940 52.381 5.56 0.00 0.00 1.40
2461 2744 2.413837 CCCGCGCTGCTACTATTATTT 58.586 47.619 5.56 0.00 0.00 1.40
2462 2745 2.412089 CCCGCGCTGCTACTATTATTTC 59.588 50.000 5.56 0.00 0.00 2.17
2463 2746 2.090658 CCGCGCTGCTACTATTATTTCG 59.909 50.000 5.56 0.00 0.00 3.46
2464 2747 2.724690 CGCGCTGCTACTATTATTTCGT 59.275 45.455 5.56 0.00 0.00 3.85
2465 2748 3.910170 CGCGCTGCTACTATTATTTCGTA 59.090 43.478 5.56 0.00 0.00 3.43
2466 2749 4.557690 CGCGCTGCTACTATTATTTCGTAT 59.442 41.667 5.56 0.00 0.00 3.06
2467 2750 5.060569 CGCGCTGCTACTATTATTTCGTATT 59.939 40.000 5.56 0.00 0.00 1.89
2468 2751 6.399669 CGCGCTGCTACTATTATTTCGTATTT 60.400 38.462 5.56 0.00 0.00 1.40
2469 2752 7.288672 GCGCTGCTACTATTATTTCGTATTTT 58.711 34.615 0.00 0.00 0.00 1.82
2470 2753 8.430063 GCGCTGCTACTATTATTTCGTATTTTA 58.570 33.333 0.00 0.00 0.00 1.52
2503 2786 9.828852 TTTTATTTCATGTTGTATTCGTACACC 57.171 29.630 0.00 0.00 0.00 4.16
2504 2787 8.780846 TTATTTCATGTTGTATTCGTACACCT 57.219 30.769 0.00 0.00 0.00 4.00
2505 2788 7.681939 ATTTCATGTTGTATTCGTACACCTT 57.318 32.000 0.00 0.00 0.00 3.50
2506 2789 7.499321 TTTCATGTTGTATTCGTACACCTTT 57.501 32.000 0.00 0.00 0.00 3.11
2507 2790 8.604640 TTTCATGTTGTATTCGTACACCTTTA 57.395 30.769 0.00 0.00 0.00 1.85
2508 2791 7.585286 TCATGTTGTATTCGTACACCTTTAC 57.415 36.000 0.00 0.00 0.00 2.01
2509 2792 7.153315 TCATGTTGTATTCGTACACCTTTACA 58.847 34.615 0.00 0.00 0.00 2.41
2510 2793 6.768029 TGTTGTATTCGTACACCTTTACAC 57.232 37.500 0.00 0.00 0.00 2.90
2511 2794 6.279123 TGTTGTATTCGTACACCTTTACACA 58.721 36.000 0.00 0.00 0.00 3.72
2512 2795 6.760298 TGTTGTATTCGTACACCTTTACACAA 59.240 34.615 0.00 0.00 0.00 3.33
2513 2796 7.279536 TGTTGTATTCGTACACCTTTACACAAA 59.720 33.333 0.00 0.00 0.00 2.83
2514 2797 7.966246 TGTATTCGTACACCTTTACACAAAT 57.034 32.000 0.00 0.00 0.00 2.32
2515 2798 8.380743 TGTATTCGTACACCTTTACACAAATT 57.619 30.769 0.00 0.00 0.00 1.82
2516 2799 8.838365 TGTATTCGTACACCTTTACACAAATTT 58.162 29.630 0.00 0.00 0.00 1.82
2517 2800 9.667989 GTATTCGTACACCTTTACACAAATTTT 57.332 29.630 0.00 0.00 0.00 1.82
2518 2801 8.791355 ATTCGTACACCTTTACACAAATTTTC 57.209 30.769 0.00 0.00 0.00 2.29
2519 2802 7.317842 TCGTACACCTTTACACAAATTTTCA 57.682 32.000 0.00 0.00 0.00 2.69
2520 2803 7.932335 TCGTACACCTTTACACAAATTTTCAT 58.068 30.769 0.00 0.00 0.00 2.57
2521 2804 9.053840 TCGTACACCTTTACACAAATTTTCATA 57.946 29.630 0.00 0.00 0.00 2.15
2522 2805 9.109533 CGTACACCTTTACACAAATTTTCATAC 57.890 33.333 0.00 0.00 0.00 2.39
2523 2806 9.953697 GTACACCTTTACACAAATTTTCATACA 57.046 29.630 0.00 0.00 0.00 2.29
2525 2808 9.308318 ACACCTTTACACAAATTTTCATACAAC 57.692 29.630 0.00 0.00 0.00 3.32
2526 2809 9.307121 CACCTTTACACAAATTTTCATACAACA 57.693 29.630 0.00 0.00 0.00 3.33
2527 2810 9.528018 ACCTTTACACAAATTTTCATACAACAG 57.472 29.630 0.00 0.00 0.00 3.16
2528 2811 8.977505 CCTTTACACAAATTTTCATACAACAGG 58.022 33.333 0.00 0.00 0.00 4.00
2529 2812 9.743057 CTTTACACAAATTTTCATACAACAGGA 57.257 29.630 0.00 0.00 0.00 3.86
2533 2816 9.612066 ACACAAATTTTCATACAACAGGAATTT 57.388 25.926 0.00 0.00 0.00 1.82
2573 2856 9.208022 ACATCATAATGAGTTATTACATCACGG 57.792 33.333 0.00 0.00 34.22 4.94
2574 2857 8.659491 CATCATAATGAGTTATTACATCACGGG 58.341 37.037 0.00 0.00 34.22 5.28
2575 2858 7.158697 TCATAATGAGTTATTACATCACGGGG 58.841 38.462 0.00 0.00 34.22 5.73
2576 2859 5.367945 AATGAGTTATTACATCACGGGGT 57.632 39.130 0.00 0.00 0.00 4.95
2577 2860 4.131649 TGAGTTATTACATCACGGGGTG 57.868 45.455 0.00 0.00 34.45 4.61
2578 2861 3.770388 TGAGTTATTACATCACGGGGTGA 59.230 43.478 4.05 0.38 46.90 4.02
2579 2862 4.223255 TGAGTTATTACATCACGGGGTGAA 59.777 41.667 4.05 0.00 45.96 3.18
2580 2863 5.168647 AGTTATTACATCACGGGGTGAAA 57.831 39.130 4.05 0.00 45.96 2.69
2581 2864 5.562635 AGTTATTACATCACGGGGTGAAAA 58.437 37.500 4.05 0.00 45.96 2.29
2582 2865 6.005198 AGTTATTACATCACGGGGTGAAAAA 58.995 36.000 4.05 0.00 45.96 1.94
2600 2883 4.888038 AAAAACCGTGTGGACTAGTTTC 57.112 40.909 0.00 0.00 39.21 2.78
2601 2884 3.547054 AAACCGTGTGGACTAGTTTCA 57.453 42.857 0.00 0.00 39.21 2.69
2602 2885 3.547054 AACCGTGTGGACTAGTTTCAA 57.453 42.857 0.00 0.00 39.21 2.69
2603 2886 3.107642 ACCGTGTGGACTAGTTTCAAG 57.892 47.619 0.00 0.00 39.21 3.02
2604 2887 2.433239 ACCGTGTGGACTAGTTTCAAGT 59.567 45.455 0.00 0.00 39.21 3.16
2605 2888 2.800544 CCGTGTGGACTAGTTTCAAGTG 59.199 50.000 0.00 0.00 37.49 3.16
2606 2889 2.800544 CGTGTGGACTAGTTTCAAGTGG 59.199 50.000 0.00 0.00 0.00 4.00
2607 2890 3.491964 CGTGTGGACTAGTTTCAAGTGGA 60.492 47.826 0.00 0.00 0.00 4.02
2608 2891 3.808174 GTGTGGACTAGTTTCAAGTGGAC 59.192 47.826 0.00 0.00 0.00 4.02
2609 2892 3.057734 GTGGACTAGTTTCAAGTGGACG 58.942 50.000 0.00 0.00 0.00 4.79
2610 2893 2.036733 TGGACTAGTTTCAAGTGGACGG 59.963 50.000 0.00 0.00 0.00 4.79
2611 2894 2.298163 GGACTAGTTTCAAGTGGACGGA 59.702 50.000 0.00 0.00 0.00 4.69
2612 2895 3.315418 GACTAGTTTCAAGTGGACGGAC 58.685 50.000 0.00 0.00 0.00 4.79
2613 2896 2.696707 ACTAGTTTCAAGTGGACGGACA 59.303 45.455 0.00 0.00 0.00 4.02
2614 2897 2.930826 AGTTTCAAGTGGACGGACAT 57.069 45.000 0.00 0.00 0.00 3.06
2615 2898 2.767505 AGTTTCAAGTGGACGGACATC 58.232 47.619 0.00 0.00 0.00 3.06
2616 2899 1.804748 GTTTCAAGTGGACGGACATCC 59.195 52.381 0.00 0.00 39.45 3.51
2617 2900 1.052617 TTCAAGTGGACGGACATCCA 58.947 50.000 0.00 0.00 46.92 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
308 453 7.287229 CCGCACAAAATAAAAACCAATGTAAG 58.713 34.615 0.00 0.00 0.00 2.34
359 506 2.816672 CCTGCTCTCCTTGGTTTTCTTC 59.183 50.000 0.00 0.00 0.00 2.87
404 551 3.695060 TGGTAGATTCTCTTCACGTCCTC 59.305 47.826 0.00 0.00 0.00 3.71
559 706 6.147656 TGCGATATATTTGACATGCAACTAGG 59.852 38.462 0.00 0.00 35.91 3.02
820 968 8.767341 TGAGGATCTGATCTTGGGGAAACCTA 62.767 46.154 16.61 0.00 44.39 3.08
854 1002 3.629398 AGCCATGCTTCTTAGTTGCATAC 59.371 43.478 12.23 9.04 44.39 2.39
856 1004 2.731572 AGCCATGCTTCTTAGTTGCAT 58.268 42.857 8.31 8.31 46.74 3.96
882 1030 0.874390 GAATGGAAAGAGTGCGTGCA 59.126 50.000 0.00 0.00 0.00 4.57
925 1073 4.307259 AGAGAGAGAGAGAGAGGTACCAT 58.693 47.826 15.94 1.21 0.00 3.55
959 1147 8.642432 TGGTTAAACATACATTTCCATCAACAA 58.358 29.630 0.00 0.00 0.00 2.83
972 1160 6.641169 TTGCAACTCATGGTTAAACATACA 57.359 33.333 5.49 0.00 36.23 2.29
973 1161 7.312154 TGATTGCAACTCATGGTTAAACATAC 58.688 34.615 5.49 0.00 36.23 2.39
1059 1249 3.882888 CACCAACGCCATGGAAATAGTAT 59.117 43.478 18.40 0.00 43.54 2.12
1111 1301 9.729023 CAAAATCAGTGTTTTGATACAAGTACA 57.271 29.630 18.33 0.00 46.78 2.90
1404 1602 8.621921 TCGTGCGCAACATATTAAAAATAAAT 57.378 26.923 14.00 0.00 0.00 1.40
1445 1644 3.155093 GCAACGGATCTTGCATTTCAT 57.845 42.857 13.27 0.00 45.07 2.57
1645 1844 5.520288 GCTCTCGCAGATGATGTAAAACTTA 59.480 40.000 0.00 0.00 33.89 2.24
1670 1869 1.001406 CCTCGTTTGACTTGCTCTCCT 59.999 52.381 0.00 0.00 0.00 3.69
1713 1912 0.321653 AATCACCAGTCCAAGACGCC 60.322 55.000 0.00 0.00 37.67 5.68
1717 1916 2.093500 CCGATGAATCACCAGTCCAAGA 60.093 50.000 0.00 0.00 0.00 3.02
1718 1917 2.283298 CCGATGAATCACCAGTCCAAG 58.717 52.381 0.00 0.00 0.00 3.61
1719 1918 1.065491 CCCGATGAATCACCAGTCCAA 60.065 52.381 0.00 0.00 0.00 3.53
1722 1921 2.280628 GTTCCCGATGAATCACCAGTC 58.719 52.381 0.00 0.00 34.90 3.51
1724 1923 1.210478 AGGTTCCCGATGAATCACCAG 59.790 52.381 0.00 0.00 36.48 4.00
1725 1924 1.285280 AGGTTCCCGATGAATCACCA 58.715 50.000 0.00 0.00 36.48 4.17
1726 1925 2.484947 GGTAGGTTCCCGATGAATCACC 60.485 54.545 0.00 3.50 36.48 4.02
1728 1927 2.434336 CAGGTAGGTTCCCGATGAATCA 59.566 50.000 1.59 0.00 36.48 2.57
1735 1935 1.001248 CCTCCAGGTAGGTTCCCGA 59.999 63.158 0.00 0.00 39.02 5.14
1758 1958 1.934220 GCACCTCGAGACCATCACGA 61.934 60.000 15.71 0.00 37.16 4.35
1770 1970 3.589654 TTCCTTCAGCCGCACCTCG 62.590 63.158 0.00 0.00 38.08 4.63
1783 1983 2.665603 GAGCTGTCCCGCTTCCTT 59.334 61.111 0.00 0.00 41.08 3.36
1812 2012 0.331616 AGGAGGTAAAAAGGCGGCAT 59.668 50.000 13.08 0.00 0.00 4.40
1813 2013 0.111639 AAGGAGGTAAAAAGGCGGCA 59.888 50.000 13.08 0.00 0.00 5.69
1816 2016 4.277423 TCAAAGAAAGGAGGTAAAAAGGCG 59.723 41.667 0.00 0.00 0.00 5.52
1965 2196 3.059597 CGGATCTTAAAGCGCATCGAAAT 60.060 43.478 11.47 0.00 0.00 2.17
1985 2218 2.815647 GGCGAGAAGGAAGCACGG 60.816 66.667 0.00 0.00 0.00 4.94
2109 2392 9.900710 TTATCAACGTATTTACAAATTTGTGCT 57.099 25.926 29.72 17.40 42.31 4.40
2118 2401 8.041919 TGGATGAGGTTATCAACGTATTTACAA 58.958 33.333 0.00 0.00 42.53 2.41
2185 2468 1.154169 CATGTCACGTGTGCATGCC 60.154 57.895 28.21 7.25 37.84 4.40
2204 2487 4.781934 AGCCATCTGTTATAAGTGGGTTC 58.218 43.478 5.48 0.00 37.38 3.62
2247 2530 3.451178 TGCTAGCCTTTTCCCTAGTAGTG 59.549 47.826 13.29 0.00 34.81 2.74
2248 2531 3.707102 CTGCTAGCCTTTTCCCTAGTAGT 59.293 47.826 13.29 0.00 38.66 2.73
2249 2532 3.493524 GCTGCTAGCCTTTTCCCTAGTAG 60.494 52.174 13.29 7.97 43.15 2.57
2250 2533 2.434702 GCTGCTAGCCTTTTCCCTAGTA 59.565 50.000 13.29 0.00 34.48 1.82
2251 2534 1.210722 GCTGCTAGCCTTTTCCCTAGT 59.789 52.381 13.29 0.00 34.48 2.57
2252 2535 1.210478 TGCTGCTAGCCTTTTCCCTAG 59.790 52.381 13.29 0.00 41.51 3.02
2253 2536 1.210478 CTGCTGCTAGCCTTTTCCCTA 59.790 52.381 13.29 0.00 41.51 3.53
2254 2537 0.034670 CTGCTGCTAGCCTTTTCCCT 60.035 55.000 13.29 0.00 41.51 4.20
2255 2538 1.661498 GCTGCTGCTAGCCTTTTCCC 61.661 60.000 13.29 0.00 41.51 3.97
2256 2539 1.805910 GCTGCTGCTAGCCTTTTCC 59.194 57.895 13.29 0.00 41.51 3.13
2257 2540 1.427020 CGCTGCTGCTAGCCTTTTC 59.573 57.895 13.29 0.00 41.51 2.29
2258 2541 2.694760 GCGCTGCTGCTAGCCTTTT 61.695 57.895 13.29 0.00 41.51 2.27
2259 2542 3.130160 GCGCTGCTGCTAGCCTTT 61.130 61.111 13.29 0.00 41.51 3.11
2265 2548 2.789845 TAAAACCCGCGCTGCTGCTA 62.790 55.000 14.03 0.00 36.97 3.49
2267 2550 3.667429 CTAAAACCCGCGCTGCTGC 62.667 63.158 5.56 5.34 0.00 5.25
2268 2551 2.032634 TCTAAAACCCGCGCTGCTG 61.033 57.895 5.56 0.00 0.00 4.41
2269 2552 2.033194 GTCTAAAACCCGCGCTGCT 61.033 57.895 5.56 0.00 0.00 4.24
2270 2553 2.479198 GTCTAAAACCCGCGCTGC 59.521 61.111 5.56 0.00 0.00 5.25
2271 2554 3.174788 GGTCTAAAACCCGCGCTG 58.825 61.111 5.56 0.00 42.85 5.18
2279 2562 3.729716 CGCGCTACTGATAGGTCTAAAAC 59.270 47.826 5.56 0.00 0.00 2.43
2280 2563 3.243301 CCGCGCTACTGATAGGTCTAAAA 60.243 47.826 5.56 0.00 0.00 1.52
2281 2564 2.292569 CCGCGCTACTGATAGGTCTAAA 59.707 50.000 5.56 0.00 0.00 1.85
2282 2565 1.878088 CCGCGCTACTGATAGGTCTAA 59.122 52.381 5.56 0.00 0.00 2.10
2283 2566 1.520494 CCGCGCTACTGATAGGTCTA 58.480 55.000 5.56 0.00 0.00 2.59
2284 2567 1.173444 CCCGCGCTACTGATAGGTCT 61.173 60.000 5.56 0.00 0.00 3.85
2285 2568 1.286260 CCCGCGCTACTGATAGGTC 59.714 63.158 5.56 0.00 0.00 3.85
2286 2569 2.201022 CCCCGCGCTACTGATAGGT 61.201 63.158 5.56 0.00 0.00 3.08
2287 2570 2.201022 ACCCCGCGCTACTGATAGG 61.201 63.158 5.56 0.00 0.00 2.57
2288 2571 1.007271 CACCCCGCGCTACTGATAG 60.007 63.158 5.56 0.00 0.00 2.08
2289 2572 2.495409 CCACCCCGCGCTACTGATA 61.495 63.158 5.56 0.00 0.00 2.15
2290 2573 3.849951 CCACCCCGCGCTACTGAT 61.850 66.667 5.56 0.00 0.00 2.90
2291 2574 3.942377 TACCACCCCGCGCTACTGA 62.942 63.158 5.56 0.00 0.00 3.41
2292 2575 3.454573 TACCACCCCGCGCTACTG 61.455 66.667 5.56 0.00 0.00 2.74
2293 2576 3.455469 GTACCACCCCGCGCTACT 61.455 66.667 5.56 0.00 0.00 2.57
2294 2577 4.860261 CGTACCACCCCGCGCTAC 62.860 72.222 5.56 0.00 0.00 3.58
2300 2583 1.597797 TTCAGTAGCGTACCACCCCG 61.598 60.000 0.00 0.00 0.00 5.73
2301 2584 0.609662 TTTCAGTAGCGTACCACCCC 59.390 55.000 0.00 0.00 0.00 4.95
2302 2585 2.344025 CTTTTCAGTAGCGTACCACCC 58.656 52.381 0.00 0.00 0.00 4.61
2303 2586 2.344025 CCTTTTCAGTAGCGTACCACC 58.656 52.381 0.00 0.00 0.00 4.61
2304 2587 1.730612 GCCTTTTCAGTAGCGTACCAC 59.269 52.381 0.00 0.00 0.00 4.16
2305 2588 1.670674 CGCCTTTTCAGTAGCGTACCA 60.671 52.381 0.00 0.00 43.45 3.25
2306 2589 0.997196 CGCCTTTTCAGTAGCGTACC 59.003 55.000 0.00 0.00 43.45 3.34
2311 2594 1.661112 CTGTAGCGCCTTTTCAGTAGC 59.339 52.381 2.29 0.00 0.00 3.58
2312 2595 1.661112 GCTGTAGCGCCTTTTCAGTAG 59.339 52.381 2.29 0.00 0.00 2.57
2313 2596 1.722011 GCTGTAGCGCCTTTTCAGTA 58.278 50.000 2.29 0.00 0.00 2.74
2314 2597 2.544726 GCTGTAGCGCCTTTTCAGT 58.455 52.632 2.29 0.00 0.00 3.41
2332 2615 3.001330 GGCACGCTACTGCTATTTGTTAG 59.999 47.826 0.00 0.00 37.33 2.34
2333 2616 2.933906 GGCACGCTACTGCTATTTGTTA 59.066 45.455 0.00 0.00 37.33 2.41
2334 2617 1.737793 GGCACGCTACTGCTATTTGTT 59.262 47.619 0.00 0.00 37.33 2.83
2335 2618 1.066143 AGGCACGCTACTGCTATTTGT 60.066 47.619 0.00 0.00 37.33 2.83
2336 2619 1.594862 GAGGCACGCTACTGCTATTTG 59.405 52.381 0.00 0.00 37.33 2.32
2337 2620 1.473434 GGAGGCACGCTACTGCTATTT 60.473 52.381 0.00 0.00 37.33 1.40
2338 2621 0.105039 GGAGGCACGCTACTGCTATT 59.895 55.000 0.00 0.00 37.33 1.73
2339 2622 1.043116 TGGAGGCACGCTACTGCTAT 61.043 55.000 0.00 0.00 37.33 2.97
2340 2623 1.680989 TGGAGGCACGCTACTGCTA 60.681 57.895 0.00 0.00 37.33 3.49
2341 2624 2.997315 TGGAGGCACGCTACTGCT 60.997 61.111 0.00 0.00 37.33 4.24
2342 2625 2.815647 GTGGAGGCACGCTACTGC 60.816 66.667 0.00 0.00 36.60 4.40
2343 2626 2.125512 GGTGGAGGCACGCTACTG 60.126 66.667 0.00 0.00 39.84 2.74
2344 2627 3.391382 GGGTGGAGGCACGCTACT 61.391 66.667 0.00 0.00 39.84 2.57
2345 2628 3.702048 TGGGTGGAGGCACGCTAC 61.702 66.667 0.00 0.00 39.12 3.58
2346 2629 3.702048 GTGGGTGGAGGCACGCTA 61.702 66.667 0.00 0.00 38.60 4.26
2350 2633 3.702048 TAGCGTGGGTGGAGGCAC 61.702 66.667 0.00 0.00 0.00 5.01
2351 2634 3.702048 GTAGCGTGGGTGGAGGCA 61.702 66.667 0.00 0.00 0.00 4.75
2352 2635 4.814294 CGTAGCGTGGGTGGAGGC 62.814 72.222 0.00 0.00 0.00 4.70
2353 2636 4.143333 CCGTAGCGTGGGTGGAGG 62.143 72.222 0.00 0.00 0.00 4.30
2354 2637 4.814294 GCCGTAGCGTGGGTGGAG 62.814 72.222 0.00 0.00 0.00 3.86
2355 2638 3.942377 TAGCCGTAGCGTGGGTGGA 62.942 63.158 6.84 0.00 46.67 4.02
2356 2639 2.510064 TTTAGCCGTAGCGTGGGTGG 62.510 60.000 6.84 0.00 46.67 4.61
2357 2640 0.461339 ATTTAGCCGTAGCGTGGGTG 60.461 55.000 6.84 0.00 46.67 4.61
2358 2641 0.179092 GATTTAGCCGTAGCGTGGGT 60.179 55.000 2.36 2.36 46.67 4.51
2359 2642 1.213094 CGATTTAGCCGTAGCGTGGG 61.213 60.000 0.00 0.00 46.67 4.61
2360 2643 0.248743 TCGATTTAGCCGTAGCGTGG 60.249 55.000 0.00 0.00 46.67 4.94
2361 2644 1.767289 ATCGATTTAGCCGTAGCGTG 58.233 50.000 0.00 0.00 46.67 5.34
2362 2645 2.503920 AATCGATTTAGCCGTAGCGT 57.496 45.000 4.39 0.00 46.67 5.07
2363 2646 4.547956 CTAAATCGATTTAGCCGTAGCG 57.452 45.455 33.52 16.49 46.67 4.26
2372 2655 5.828747 ACTCGCTGCTACTAAATCGATTTA 58.171 37.500 25.03 25.03 0.00 1.40
2373 2656 4.683832 ACTCGCTGCTACTAAATCGATTT 58.316 39.130 25.48 25.48 0.00 2.17
2374 2657 4.308899 ACTCGCTGCTACTAAATCGATT 57.691 40.909 4.39 4.39 0.00 3.34
2375 2658 3.992260 ACTCGCTGCTACTAAATCGAT 57.008 42.857 0.00 0.00 0.00 3.59
2376 2659 3.777465 AACTCGCTGCTACTAAATCGA 57.223 42.857 0.00 0.00 0.00 3.59
2377 2660 3.857665 TGAAACTCGCTGCTACTAAATCG 59.142 43.478 0.00 0.00 0.00 3.34
2378 2661 4.268884 CCTGAAACTCGCTGCTACTAAATC 59.731 45.833 0.00 0.00 0.00 2.17
2379 2662 4.081642 TCCTGAAACTCGCTGCTACTAAAT 60.082 41.667 0.00 0.00 0.00 1.40
2380 2663 3.257375 TCCTGAAACTCGCTGCTACTAAA 59.743 43.478 0.00 0.00 0.00 1.85
2381 2664 2.823747 TCCTGAAACTCGCTGCTACTAA 59.176 45.455 0.00 0.00 0.00 2.24
2382 2665 2.423892 CTCCTGAAACTCGCTGCTACTA 59.576 50.000 0.00 0.00 0.00 1.82
2383 2666 1.203523 CTCCTGAAACTCGCTGCTACT 59.796 52.381 0.00 0.00 0.00 2.57
2384 2667 1.634702 CTCCTGAAACTCGCTGCTAC 58.365 55.000 0.00 0.00 0.00 3.58
2385 2668 0.532573 CCTCCTGAAACTCGCTGCTA 59.467 55.000 0.00 0.00 0.00 3.49
2386 2669 1.188219 TCCTCCTGAAACTCGCTGCT 61.188 55.000 0.00 0.00 0.00 4.24
2387 2670 0.739112 CTCCTCCTGAAACTCGCTGC 60.739 60.000 0.00 0.00 0.00 5.25
2388 2671 0.739112 GCTCCTCCTGAAACTCGCTG 60.739 60.000 0.00 0.00 0.00 5.18
2389 2672 1.188219 TGCTCCTCCTGAAACTCGCT 61.188 55.000 0.00 0.00 0.00 4.93
2390 2673 1.016653 GTGCTCCTCCTGAAACTCGC 61.017 60.000 0.00 0.00 0.00 5.03
2391 2674 0.605589 AGTGCTCCTCCTGAAACTCG 59.394 55.000 0.00 0.00 0.00 4.18
2392 2675 1.943507 GCAGTGCTCCTCCTGAAACTC 60.944 57.143 8.18 0.00 0.00 3.01
2393 2676 0.036022 GCAGTGCTCCTCCTGAAACT 59.964 55.000 8.18 0.00 0.00 2.66
2394 2677 0.036022 AGCAGTGCTCCTCCTGAAAC 59.964 55.000 13.14 0.00 30.62 2.78
2395 2678 0.035881 CAGCAGTGCTCCTCCTGAAA 59.964 55.000 16.58 0.00 36.40 2.69
2396 2679 1.675801 CAGCAGTGCTCCTCCTGAA 59.324 57.895 16.58 0.00 36.40 3.02
2397 2680 2.288778 CCAGCAGTGCTCCTCCTGA 61.289 63.158 16.58 0.00 36.40 3.86
2398 2681 1.260538 TACCAGCAGTGCTCCTCCTG 61.261 60.000 16.58 3.46 36.40 3.86
2399 2682 0.545309 TTACCAGCAGTGCTCCTCCT 60.545 55.000 16.58 0.00 36.40 3.69
2400 2683 0.543749 ATTACCAGCAGTGCTCCTCC 59.456 55.000 16.58 0.00 36.40 4.30
2401 2684 2.409948 AATTACCAGCAGTGCTCCTC 57.590 50.000 16.58 0.00 36.40 3.71
2402 2685 2.840651 ACTAATTACCAGCAGTGCTCCT 59.159 45.455 16.58 5.41 36.40 3.69
2403 2686 3.268023 ACTAATTACCAGCAGTGCTCC 57.732 47.619 16.58 0.00 36.40 4.70
2404 2687 5.012328 ACTACTAATTACCAGCAGTGCTC 57.988 43.478 16.58 0.00 36.40 4.26
2405 2688 5.452077 GCTACTACTAATTACCAGCAGTGCT 60.452 44.000 13.14 13.14 40.77 4.40
2406 2689 4.745620 GCTACTACTAATTACCAGCAGTGC 59.254 45.833 7.13 7.13 0.00 4.40
2407 2690 4.976731 CGCTACTACTAATTACCAGCAGTG 59.023 45.833 0.00 0.00 0.00 3.66
2408 2691 4.499357 GCGCTACTACTAATTACCAGCAGT 60.499 45.833 0.00 0.00 0.00 4.40
2409 2692 3.982058 GCGCTACTACTAATTACCAGCAG 59.018 47.826 0.00 0.00 0.00 4.24
2410 2693 3.635373 AGCGCTACTACTAATTACCAGCA 59.365 43.478 8.99 0.00 0.00 4.41
2411 2694 4.240175 AGCGCTACTACTAATTACCAGC 57.760 45.455 8.99 0.00 0.00 4.85
2412 2695 6.016943 AGAGAAGCGCTACTACTAATTACCAG 60.017 42.308 12.05 0.00 0.00 4.00
2413 2696 5.826737 AGAGAAGCGCTACTACTAATTACCA 59.173 40.000 12.05 0.00 0.00 3.25
2414 2697 6.205270 AGAGAGAAGCGCTACTACTAATTACC 59.795 42.308 12.05 0.00 0.00 2.85
2415 2698 7.073265 CAGAGAGAAGCGCTACTACTAATTAC 58.927 42.308 12.05 0.00 0.00 1.89
2416 2699 6.293516 GCAGAGAGAAGCGCTACTACTAATTA 60.294 42.308 12.05 0.00 0.00 1.40
2417 2700 5.506649 GCAGAGAGAAGCGCTACTACTAATT 60.507 44.000 12.05 0.00 0.00 1.40
2418 2701 4.023536 GCAGAGAGAAGCGCTACTACTAAT 60.024 45.833 12.05 0.00 0.00 1.73
2419 2702 3.312973 GCAGAGAGAAGCGCTACTACTAA 59.687 47.826 12.05 0.00 0.00 2.24
2420 2703 2.873472 GCAGAGAGAAGCGCTACTACTA 59.127 50.000 12.05 0.00 0.00 1.82
2421 2704 1.673920 GCAGAGAGAAGCGCTACTACT 59.326 52.381 12.05 8.28 0.00 2.57
2422 2705 1.268845 GGCAGAGAGAAGCGCTACTAC 60.269 57.143 12.05 2.73 0.00 2.73
2423 2706 1.025812 GGCAGAGAGAAGCGCTACTA 58.974 55.000 12.05 0.00 0.00 1.82
2424 2707 1.671901 GGGCAGAGAGAAGCGCTACT 61.672 60.000 12.05 11.14 40.16 2.57
2425 2708 1.227118 GGGCAGAGAGAAGCGCTAC 60.227 63.158 12.05 5.62 40.16 3.58
2426 2709 2.775856 CGGGCAGAGAGAAGCGCTA 61.776 63.158 12.05 0.00 41.01 4.26
2427 2710 4.140599 CGGGCAGAGAGAAGCGCT 62.141 66.667 2.64 2.64 41.01 5.92
2431 2714 4.140599 AGCGCGGGCAGAGAGAAG 62.141 66.667 27.20 0.00 43.41 2.85
2432 2715 4.441695 CAGCGCGGGCAGAGAGAA 62.442 66.667 27.20 0.00 43.41 2.87
2438 2721 2.978452 AATAGTAGCAGCGCGGGCAG 62.978 60.000 27.20 20.04 43.41 4.85
2439 2722 1.740332 TAATAGTAGCAGCGCGGGCA 61.740 55.000 27.20 3.81 43.41 5.36
2440 2723 0.389948 ATAATAGTAGCAGCGCGGGC 60.390 55.000 17.92 17.92 40.37 6.13
2441 2724 2.080286 AATAATAGTAGCAGCGCGGG 57.920 50.000 8.83 3.39 0.00 6.13
2442 2725 2.090658 CGAAATAATAGTAGCAGCGCGG 59.909 50.000 8.83 2.11 0.00 6.46
2443 2726 2.724690 ACGAAATAATAGTAGCAGCGCG 59.275 45.455 0.00 0.00 0.00 6.86
2444 2727 6.390987 AATACGAAATAATAGTAGCAGCGC 57.609 37.500 0.00 0.00 0.00 5.92
2477 2760 9.828852 GGTGTACGAATACAACATGAAATAAAA 57.171 29.630 0.00 0.00 46.67 1.52
2489 2772 7.783090 TTTGTGTAAAGGTGTACGAATACAA 57.217 32.000 0.00 0.00 42.99 2.41
2490 2773 7.966246 ATTTGTGTAAAGGTGTACGAATACA 57.034 32.000 0.00 0.00 39.06 2.29
2491 2774 9.667989 AAAATTTGTGTAAAGGTGTACGAATAC 57.332 29.630 0.00 0.00 0.00 1.89
2492 2775 9.881529 GAAAATTTGTGTAAAGGTGTACGAATA 57.118 29.630 0.00 0.00 0.00 1.75
2493 2776 8.407064 TGAAAATTTGTGTAAAGGTGTACGAAT 58.593 29.630 0.00 0.00 0.00 3.34
2494 2777 7.759465 TGAAAATTTGTGTAAAGGTGTACGAA 58.241 30.769 0.00 0.00 0.00 3.85
2495 2778 7.317842 TGAAAATTTGTGTAAAGGTGTACGA 57.682 32.000 0.00 0.00 0.00 3.43
2496 2779 9.109533 GTATGAAAATTTGTGTAAAGGTGTACG 57.890 33.333 0.00 0.00 0.00 3.67
2497 2780 9.953697 TGTATGAAAATTTGTGTAAAGGTGTAC 57.046 29.630 0.00 0.00 0.00 2.90
2499 2782 9.308318 GTTGTATGAAAATTTGTGTAAAGGTGT 57.692 29.630 0.00 0.00 0.00 4.16
2500 2783 9.307121 TGTTGTATGAAAATTTGTGTAAAGGTG 57.693 29.630 0.00 0.00 0.00 4.00
2501 2784 9.528018 CTGTTGTATGAAAATTTGTGTAAAGGT 57.472 29.630 0.00 0.00 0.00 3.50
2502 2785 8.977505 CCTGTTGTATGAAAATTTGTGTAAAGG 58.022 33.333 0.00 0.00 0.00 3.11
2503 2786 9.743057 TCCTGTTGTATGAAAATTTGTGTAAAG 57.257 29.630 0.00 0.00 0.00 1.85
2507 2790 9.612066 AAATTCCTGTTGTATGAAAATTTGTGT 57.388 25.926 0.00 0.00 0.00 3.72
2547 2830 9.208022 CCGTGATGTAATAACTCATTATGATGT 57.792 33.333 0.00 0.00 34.77 3.06
2548 2831 8.659491 CCCGTGATGTAATAACTCATTATGATG 58.341 37.037 0.00 0.00 31.78 3.07
2549 2832 7.824289 CCCCGTGATGTAATAACTCATTATGAT 59.176 37.037 0.00 0.00 31.78 2.45
2550 2833 7.158697 CCCCGTGATGTAATAACTCATTATGA 58.841 38.462 0.00 0.00 31.78 2.15
2551 2834 6.934645 ACCCCGTGATGTAATAACTCATTATG 59.065 38.462 0.00 0.00 31.78 1.90
2552 2835 6.934645 CACCCCGTGATGTAATAACTCATTAT 59.065 38.462 0.00 0.00 35.23 1.28
2553 2836 6.098552 TCACCCCGTGATGTAATAACTCATTA 59.901 38.462 0.00 0.00 37.67 1.90
2554 2837 5.104693 TCACCCCGTGATGTAATAACTCATT 60.105 40.000 0.00 0.00 37.67 2.57
2555 2838 4.407621 TCACCCCGTGATGTAATAACTCAT 59.592 41.667 0.00 0.00 37.67 2.90
2556 2839 3.770388 TCACCCCGTGATGTAATAACTCA 59.230 43.478 0.00 0.00 37.67 3.41
2557 2840 4.395959 TCACCCCGTGATGTAATAACTC 57.604 45.455 0.00 0.00 37.67 3.01
2558 2841 4.829872 TTCACCCCGTGATGTAATAACT 57.170 40.909 0.00 0.00 42.40 2.24
2559 2842 5.883503 TTTTCACCCCGTGATGTAATAAC 57.116 39.130 0.00 0.00 42.40 1.89
2579 2862 4.263435 TGAAACTAGTCCACACGGTTTTT 58.737 39.130 0.00 0.00 35.21 1.94
2580 2863 3.876341 TGAAACTAGTCCACACGGTTTT 58.124 40.909 0.00 0.00 35.21 2.43
2581 2864 3.547054 TGAAACTAGTCCACACGGTTT 57.453 42.857 0.00 0.00 36.63 3.27
2582 2865 3.118519 ACTTGAAACTAGTCCACACGGTT 60.119 43.478 0.00 0.00 0.00 4.44
2583 2866 2.433239 ACTTGAAACTAGTCCACACGGT 59.567 45.455 0.00 0.00 0.00 4.83
2584 2867 2.800544 CACTTGAAACTAGTCCACACGG 59.199 50.000 0.00 0.00 0.00 4.94
2585 2868 2.800544 CCACTTGAAACTAGTCCACACG 59.199 50.000 0.00 0.00 0.00 4.49
2586 2869 3.808174 GTCCACTTGAAACTAGTCCACAC 59.192 47.826 0.00 0.00 0.00 3.82
2587 2870 3.491964 CGTCCACTTGAAACTAGTCCACA 60.492 47.826 0.00 0.00 0.00 4.17
2588 2871 3.057734 CGTCCACTTGAAACTAGTCCAC 58.942 50.000 0.00 0.00 0.00 4.02
2589 2872 2.036733 CCGTCCACTTGAAACTAGTCCA 59.963 50.000 0.00 0.00 0.00 4.02
2590 2873 2.298163 TCCGTCCACTTGAAACTAGTCC 59.702 50.000 0.00 0.00 0.00 3.85
2591 2874 3.243636 TGTCCGTCCACTTGAAACTAGTC 60.244 47.826 0.00 0.00 0.00 2.59
2592 2875 2.696707 TGTCCGTCCACTTGAAACTAGT 59.303 45.455 0.00 0.00 0.00 2.57
2593 2876 3.380479 TGTCCGTCCACTTGAAACTAG 57.620 47.619 0.00 0.00 0.00 2.57
2594 2877 3.306502 GGATGTCCGTCCACTTGAAACTA 60.307 47.826 0.54 0.00 38.20 2.24
2595 2878 2.550208 GGATGTCCGTCCACTTGAAACT 60.550 50.000 0.54 0.00 38.20 2.66
2596 2879 1.804748 GGATGTCCGTCCACTTGAAAC 59.195 52.381 0.54 0.00 38.20 2.78
2597 2880 1.418264 TGGATGTCCGTCCACTTGAAA 59.582 47.619 4.08 0.00 43.20 2.69
2598 2881 1.052617 TGGATGTCCGTCCACTTGAA 58.947 50.000 4.08 0.00 43.20 2.69
2599 2882 2.753319 TGGATGTCCGTCCACTTGA 58.247 52.632 4.08 0.00 43.20 3.02


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

AutoCloner maintained by Alex Coulton.