Multiple sequence alignment - TraesCS2D01G393400

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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 TraesCS2D01G393400 chr2D 100.000 2615 0 0 1 2615 502928848 502931462 0.000000e+00 4830.0
1 TraesCS2D01G393400 chr2D 95.620 137 6 0 2442 2578 83539588 83539724 1.220000e-53 220.0
2 TraesCS2D01G393400 chr2D 90.196 102 10 0 2272 2373 25037884 25037985 1.630000e-27 134.0
3 TraesCS2D01G393400 chr2D 86.567 67 9 0 2387 2453 222895238 222895304 1.000000e-09 75.0
4 TraesCS2D01G393400 chr2B 90.115 2256 87 45 7 2204 590917888 590920065 0.000000e+00 2806.0
5 TraesCS2D01G393400 chr2B 90.110 91 9 0 2359 2449 484931153 484931063 4.570000e-23 119.0
6 TraesCS2D01G393400 chr2A 91.251 983 41 19 403 1365 648341002 648341959 0.000000e+00 1297.0
7 TraesCS2D01G393400 chr2A 88.851 592 20 12 1708 2259 648341951 648342536 0.000000e+00 686.0
8 TraesCS2D01G393400 chr2A 91.304 92 8 0 2359 2450 240465889 240465980 2.730000e-25 126.0
9 TraesCS2D01G393400 chr2A 91.209 91 8 0 2359 2449 578387690 578387600 9.830000e-25 124.0
10 TraesCS2D01G393400 chr6D 78.714 653 83 37 993 1616 341117433 341116808 4.080000e-103 385.0
11 TraesCS2D01G393400 chr6D 95.489 133 6 0 2439 2571 49271981 49272113 2.040000e-51 213.0
12 TraesCS2D01G393400 chr6D 93.878 49 2 1 2567 2615 454249112 454249159 3.610000e-09 73.1
13 TraesCS2D01G393400 chr6D 97.368 38 1 0 17 54 27481078 27481041 6.040000e-07 65.8
14 TraesCS2D01G393400 chr6B 78.582 649 91 30 990 1616 479299711 479300333 4.080000e-103 385.0
15 TraesCS2D01G393400 chr6B 97.037 135 3 1 2434 2568 30348239 30348372 2.620000e-55 226.0
16 TraesCS2D01G393400 chr6B 93.878 49 3 0 2566 2614 192060056 192060104 1.000000e-09 75.0
17 TraesCS2D01G393400 chr6B 100.000 31 0 0 21 51 519408055 519408085 1.010000e-04 58.4
18 TraesCS2D01G393400 chr6A 77.896 656 91 31 993 1617 481083075 481082443 2.470000e-95 359.0
19 TraesCS2D01G393400 chr6A 92.000 50 4 0 2566 2615 613890072 613890121 1.300000e-08 71.3
20 TraesCS2D01G393400 chr5D 98.425 127 2 0 2442 2568 393056275 393056401 9.420000e-55 224.0
21 TraesCS2D01G393400 chr5D 95.588 136 5 1 2433 2568 538584809 538584675 1.580000e-52 217.0
22 TraesCS2D01G393400 chr5D 98.864 88 1 0 2272 2359 342696382 342696469 9.690000e-35 158.0
23 TraesCS2D01G393400 chr5D 91.011 89 8 0 2359 2447 204324581 204324493 1.270000e-23 121.0
24 TraesCS2D01G393400 chr5D 89.062 64 7 0 2390 2453 294005682 294005619 2.160000e-11 80.5
25 TraesCS2D01G393400 chr5D 92.157 51 3 1 2566 2615 354813164 354813214 1.300000e-08 71.3
26 TraesCS2D01G393400 chr5A 95.620 137 4 2 2442 2577 687681053 687680918 4.380000e-53 219.0
27 TraesCS2D01G393400 chr5A 91.398 93 7 1 2357 2449 643329395 643329486 2.730000e-25 126.0
28 TraesCS2D01G393400 chr5A 95.455 44 2 0 2572 2615 323754528 323754485 1.300000e-08 71.3
29 TraesCS2D01G393400 chr7A 94.326 141 6 1 2430 2570 610452972 610452834 5.670000e-52 215.0
30 TraesCS2D01G393400 chr7A 88.288 111 9 4 2250 2356 554916821 554916931 2.110000e-26 130.0
31 TraesCS2D01G393400 chr7A 92.000 50 3 1 2566 2615 606634257 606634305 4.670000e-08 69.4
32 TraesCS2D01G393400 chr3D 94.891 137 6 1 2440 2575 600658139 600658275 2.040000e-51 213.0
33 TraesCS2D01G393400 chr3D 94.203 138 8 0 2441 2578 496172755 496172892 7.330000e-51 211.0
34 TraesCS2D01G393400 chr3D 84.762 105 14 2 2359 2461 359728187 359728083 1.280000e-18 104.0
35 TraesCS2D01G393400 chr7D 95.652 92 4 0 2272 2363 626199969 626199878 5.830000e-32 148.0
36 TraesCS2D01G393400 chr7D 93.407 91 6 0 2359 2449 485104905 485104995 4.540000e-28 135.0
37 TraesCS2D01G393400 chr7D 94.000 50 3 0 2566 2615 82296597 82296548 2.790000e-10 76.8
38 TraesCS2D01G393400 chr5B 93.750 96 4 2 2272 2365 496801842 496801937 2.710000e-30 143.0
39 TraesCS2D01G393400 chr5B 91.176 102 6 3 2272 2370 711237966 711237865 4.540000e-28 135.0
40 TraesCS2D01G393400 chr5B 88.889 108 10 2 2260 2366 375770601 375770495 5.870000e-27 132.0
41 TraesCS2D01G393400 chr5B 84.314 102 14 2 2353 2454 7934668 7934767 5.960000e-17 99.0
42 TraesCS2D01G393400 chr5B 97.959 49 1 0 2566 2614 22764167 22764215 4.640000e-13 86.1
43 TraesCS2D01G393400 chr7B 91.346 104 8 1 2271 2374 208276707 208276809 9.760000e-30 141.0
44 TraesCS2D01G393400 chr7B 87.179 78 10 0 2384 2461 234058974 234058897 3.580000e-14 89.8
45 TraesCS2D01G393400 chr7B 92.000 50 4 0 2566 2615 592716450 592716401 1.300000e-08 71.3
46 TraesCS2D01G393400 chr7B 100.000 36 0 0 18 53 116121492 116121527 1.680000e-07 67.6
47 TraesCS2D01G393400 chr3B 85.950 121 13 3 2271 2389 700318917 700319035 2.730000e-25 126.0
48 TraesCS2D01G393400 chr3B 87.234 94 12 0 2360 2453 793346655 793346562 9.900000e-20 108.0
49 TraesCS2D01G393400 chr4B 91.209 91 8 0 2359 2449 178081237 178081147 9.830000e-25 124.0
50 TraesCS2D01G393400 chr1A 90.110 91 9 0 2359 2449 564757311 564757221 4.570000e-23 119.0
51 TraesCS2D01G393400 chr3A 83.929 112 18 0 2359 2470 10301891 10301780 9.900000e-20 108.0
52 TraesCS2D01G393400 chr4A 88.095 84 8 1 2368 2451 332131722 332131641 5.960000e-17 99.0


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 TraesCS2D01G393400 chr2D 502928848 502931462 2614 False 4830.0 4830 100.000 1 2615 1 chr2D.!!$F4 2614
1 TraesCS2D01G393400 chr2B 590917888 590920065 2177 False 2806.0 2806 90.115 7 2204 1 chr2B.!!$F1 2197
2 TraesCS2D01G393400 chr2A 648341002 648342536 1534 False 991.5 1297 90.051 403 2259 2 chr2A.!!$F2 1856
3 TraesCS2D01G393400 chr6D 341116808 341117433 625 True 385.0 385 78.714 993 1616 1 chr6D.!!$R2 623
4 TraesCS2D01G393400 chr6B 479299711 479300333 622 False 385.0 385 78.582 990 1616 1 chr6B.!!$F3 626
5 TraesCS2D01G393400 chr6A 481082443 481083075 632 True 359.0 359 77.896 993 1617 1 chr6A.!!$R1 624

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
726 747 1.001269 AGTCGGTCATCGGGTCAGA 60.001 57.895 0.0 0.0 39.77 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2381 0.459759 CGGAGGGAGTAAACGGAAGC 60.46 60.0 0.0 0.0 0.0 3.86 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
22 23 2.687370 TCATGTTGTCCACACGATGAG 58.313 47.619 0.00 0.00 38.61 2.90
33 34 2.097056 CACACGATGAGCGCTCAATATG 60.097 50.000 40.83 34.84 46.04 1.78
37 38 4.209080 CACGATGAGCGCTCAATATGTTTA 59.791 41.667 40.83 17.22 46.04 2.01
47 49 5.585390 GCTCAATATGTTTAGCATGCAGTT 58.415 37.500 21.98 1.04 38.47 3.16
57 59 8.972458 TGTTTAGCATGCAGTTAATATCCTTA 57.028 30.769 21.98 0.00 0.00 2.69
61 63 7.516198 AGCATGCAGTTAATATCCTTAAAGG 57.484 36.000 21.98 0.00 36.46 3.11
82 85 4.709397 AGGATCCAATGCCAACGATTTTTA 59.291 37.500 15.82 0.00 0.00 1.52
139 142 8.823220 ATTAGCACATAAATAATATCCCACCC 57.177 34.615 0.00 0.00 0.00 4.61
156 159 2.164219 CACCCAATATCTGTGTGCAACC 59.836 50.000 0.00 0.00 34.36 3.77
160 163 4.644234 CCCAATATCTGTGTGCAACCAATA 59.356 41.667 0.00 0.00 34.36 1.90
165 168 7.734924 ATATCTGTGTGCAACCAATATACTG 57.265 36.000 0.00 0.00 34.36 2.74
173 176 7.012894 GTGTGCAACCAATATACTGCCTAATAA 59.987 37.037 0.00 0.00 34.36 1.40
189 194 5.816777 GCCTAATAATTTTTGAATGCCAGCA 59.183 36.000 0.00 0.00 0.00 4.41
324 329 9.840427 AAAGATTTGTGTGCAACTAATATACAC 57.160 29.630 0.00 0.00 41.36 2.90
325 330 8.792830 AGATTTGTGTGCAACTAATATACACT 57.207 30.769 0.00 0.00 41.50 3.55
326 331 8.668353 AGATTTGTGTGCAACTAATATACACTG 58.332 33.333 0.00 0.00 41.50 3.66
327 332 5.794687 TGTGTGCAACTAATATACACTGC 57.205 39.130 0.00 0.00 41.50 4.40
328 333 4.634004 TGTGTGCAACTAATATACACTGCC 59.366 41.667 0.00 0.00 41.50 4.85
329 334 4.876107 GTGTGCAACTAATATACACTGCCT 59.124 41.667 0.00 0.00 38.76 4.75
330 335 6.046593 GTGTGCAACTAATATACACTGCCTA 58.953 40.000 0.00 0.00 38.76 3.93
331 336 6.537301 GTGTGCAACTAATATACACTGCCTAA 59.463 38.462 0.00 0.00 38.76 2.69
332 337 7.226720 GTGTGCAACTAATATACACTGCCTAAT 59.773 37.037 0.00 0.00 38.76 1.73
333 338 8.425703 TGTGCAACTAATATACACTGCCTAATA 58.574 33.333 0.00 0.00 38.04 0.98
334 339 9.436957 GTGCAACTAATATACACTGCCTAATAT 57.563 33.333 0.00 0.00 0.00 1.28
435 443 3.904339 ACCCTATGCATCTAGTCGGAAAT 59.096 43.478 0.19 0.00 0.00 2.17
442 451 3.738282 GCATCTAGTCGGAAATAGCACTG 59.262 47.826 0.00 0.00 0.00 3.66
492 501 3.585428 ATGCACCGGGGTTGGGAA 61.585 61.111 5.12 0.00 0.00 3.97
493 502 2.929964 ATGCACCGGGGTTGGGAAT 61.930 57.895 5.12 0.00 0.00 3.01
494 503 2.754254 GCACCGGGGTTGGGAATC 60.754 66.667 5.12 0.00 0.00 2.52
495 504 2.437716 CACCGGGGTTGGGAATCG 60.438 66.667 6.32 0.00 0.00 3.34
496 505 3.723922 ACCGGGGTTGGGAATCGG 61.724 66.667 6.32 0.00 45.42 4.18
497 506 3.404438 CCGGGGTTGGGAATCGGA 61.404 66.667 0.00 0.00 42.94 4.55
593 602 3.634157 TTGGGGGATCAGGAGGCGA 62.634 63.158 0.00 0.00 0.00 5.54
726 747 1.001269 AGTCGGTCATCGGGTCAGA 60.001 57.895 0.00 0.00 39.77 3.27
775 796 4.631740 CCACCCAACCCCAACCCC 62.632 72.222 0.00 0.00 0.00 4.95
777 798 3.036959 ACCCAACCCCAACCCCAA 61.037 61.111 0.00 0.00 0.00 4.12
778 799 2.525629 CCCAACCCCAACCCCAAC 60.526 66.667 0.00 0.00 0.00 3.77
780 801 2.915137 CAACCCCAACCCCAACCG 60.915 66.667 0.00 0.00 0.00 4.44
781 802 4.227583 AACCCCAACCCCAACCGG 62.228 66.667 0.00 0.00 0.00 5.28
894 929 2.203337 CACCACCACCACCACCAG 60.203 66.667 0.00 0.00 0.00 4.00
895 930 4.204028 ACCACCACCACCACCAGC 62.204 66.667 0.00 0.00 0.00 4.85
985 1030 1.302511 GGACGCTTCTCCTTGGCAA 60.303 57.895 0.00 0.00 0.00 4.52
986 1031 1.301677 GGACGCTTCTCCTTGGCAAG 61.302 60.000 20.31 20.31 0.00 4.01
1621 1699 2.202810 GCTACCAGTGAGCCGAGC 60.203 66.667 0.00 0.00 33.60 5.03
1622 1700 2.496817 CTACCAGTGAGCCGAGCC 59.503 66.667 0.00 0.00 0.00 4.70
1642 1720 1.376683 CCGATTCGGTCCAGGCAAA 60.377 57.895 17.08 0.00 42.73 3.68
1643 1721 0.958382 CCGATTCGGTCCAGGCAAAA 60.958 55.000 17.08 0.00 42.73 2.44
1644 1722 1.094785 CGATTCGGTCCAGGCAAAAT 58.905 50.000 0.00 0.00 0.00 1.82
1645 1723 1.472480 CGATTCGGTCCAGGCAAAATT 59.528 47.619 0.00 0.00 0.00 1.82
1646 1724 2.731968 CGATTCGGTCCAGGCAAAATTG 60.732 50.000 0.00 0.00 0.00 2.32
1647 1725 1.698506 TTCGGTCCAGGCAAAATTGT 58.301 45.000 0.00 0.00 0.00 2.71
1899 1981 0.388006 CCGGGTGCAAAATTTCGGTC 60.388 55.000 0.00 0.00 33.63 4.79
1929 2011 0.875059 CTTCTCTTTCCCCGTGTTGC 59.125 55.000 0.00 0.00 0.00 4.17
1971 2077 9.569122 AGTAGTACAAATTTAGAAAGGCTTCAA 57.431 29.630 0.00 0.00 33.64 2.69
1986 2092 0.111446 TTCAATCAACTTCCCCCGCA 59.889 50.000 0.00 0.00 0.00 5.69
2116 2229 6.463614 CCTTCCCTTGATTGGATCTACTAGTG 60.464 46.154 5.39 0.00 0.00 2.74
2117 2230 5.529289 TCCCTTGATTGGATCTACTAGTGT 58.471 41.667 5.39 0.00 0.00 3.55
2192 2311 3.760684 AGTGGAAGAATGTTCTGGAATGC 59.239 43.478 0.00 0.00 37.65 3.56
2206 2325 7.552687 TGTTCTGGAATGCTAGTAAATTAGGTG 59.447 37.037 0.00 0.00 0.00 4.00
2217 2336 9.774742 GCTAGTAAATTAGGTGAAAATGAACAG 57.225 33.333 0.00 0.00 0.00 3.16
2230 2349 7.922811 GTGAAAATGAACAGATTTGAACCTTCT 59.077 33.333 0.00 0.00 0.00 2.85
2231 2350 8.477256 TGAAAATGAACAGATTTGAACCTTCTT 58.523 29.630 0.00 0.00 0.00 2.52
2244 2363 9.946165 ATTTGAACCTTCTTTTAGAAACTTACG 57.054 29.630 0.00 0.00 33.19 3.18
2263 2382 8.403606 ACTTACGATACAAAATACTACAGTGC 57.596 34.615 0.00 0.00 0.00 4.40
2264 2383 8.248945 ACTTACGATACAAAATACTACAGTGCT 58.751 33.333 0.00 0.00 0.00 4.40
2265 2384 8.991243 TTACGATACAAAATACTACAGTGCTT 57.009 30.769 0.00 0.00 0.00 3.91
2266 2385 7.521509 ACGATACAAAATACTACAGTGCTTC 57.478 36.000 0.00 0.00 0.00 3.86
2267 2386 6.534079 ACGATACAAAATACTACAGTGCTTCC 59.466 38.462 0.00 0.00 0.00 3.46
2268 2387 6.291637 CGATACAAAATACTACAGTGCTTCCG 60.292 42.308 0.00 0.00 0.00 4.30
2269 2388 4.638304 ACAAAATACTACAGTGCTTCCGT 58.362 39.130 0.00 0.00 0.00 4.69
2270 2389 5.061179 ACAAAATACTACAGTGCTTCCGTT 58.939 37.500 0.00 0.00 0.00 4.44
2271 2390 5.529800 ACAAAATACTACAGTGCTTCCGTTT 59.470 36.000 0.00 0.00 0.00 3.60
2272 2391 6.707161 ACAAAATACTACAGTGCTTCCGTTTA 59.293 34.615 0.00 0.00 0.00 2.01
2273 2392 6.716898 AAATACTACAGTGCTTCCGTTTAC 57.283 37.500 0.00 0.00 0.00 2.01
2274 2393 5.656213 ATACTACAGTGCTTCCGTTTACT 57.344 39.130 0.00 0.00 0.00 2.24
2275 2394 3.910648 ACTACAGTGCTTCCGTTTACTC 58.089 45.455 0.00 0.00 0.00 2.59
2276 2395 2.165319 ACAGTGCTTCCGTTTACTCC 57.835 50.000 0.00 0.00 0.00 3.85
2277 2396 1.270678 ACAGTGCTTCCGTTTACTCCC 60.271 52.381 0.00 0.00 0.00 4.30
2278 2397 1.002087 CAGTGCTTCCGTTTACTCCCT 59.998 52.381 0.00 0.00 0.00 4.20
2279 2398 1.275573 AGTGCTTCCGTTTACTCCCTC 59.724 52.381 0.00 0.00 0.00 4.30
2280 2399 0.611714 TGCTTCCGTTTACTCCCTCC 59.388 55.000 0.00 0.00 0.00 4.30
2281 2400 0.459759 GCTTCCGTTTACTCCCTCCG 60.460 60.000 0.00 0.00 0.00 4.63
2282 2401 0.893447 CTTCCGTTTACTCCCTCCGT 59.107 55.000 0.00 0.00 0.00 4.69
2283 2402 0.890683 TTCCGTTTACTCCCTCCGTC 59.109 55.000 0.00 0.00 0.00 4.79
2284 2403 0.967380 TCCGTTTACTCCCTCCGTCC 60.967 60.000 0.00 0.00 0.00 4.79
2285 2404 1.514553 CGTTTACTCCCTCCGTCCC 59.485 63.158 0.00 0.00 0.00 4.46
2286 2405 1.252904 CGTTTACTCCCTCCGTCCCA 61.253 60.000 0.00 0.00 0.00 4.37
2287 2406 1.201424 GTTTACTCCCTCCGTCCCAT 58.799 55.000 0.00 0.00 0.00 4.00
2288 2407 2.391678 GTTTACTCCCTCCGTCCCATA 58.608 52.381 0.00 0.00 0.00 2.74
2289 2408 2.767960 GTTTACTCCCTCCGTCCCATAA 59.232 50.000 0.00 0.00 0.00 1.90
2290 2409 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
2291 2410 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
2292 2411 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
2293 2412 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
2294 2413 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
2295 2414 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
2296 2415 2.969950 CCCTCCGTCCCATAATGTAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2297 2416 3.244112 CCCTCCGTCCCATAATGTAAGAC 60.244 52.174 0.00 0.00 0.00 3.01
2299 2418 3.025978 TCCGTCCCATAATGTAAGACGT 58.974 45.455 9.63 0.00 46.62 4.34
2300 2419 3.067180 TCCGTCCCATAATGTAAGACGTC 59.933 47.826 7.70 7.70 46.62 4.34
2301 2420 3.067742 CCGTCCCATAATGTAAGACGTCT 59.932 47.826 13.58 13.58 46.62 4.18
2302 2421 4.441079 CCGTCCCATAATGTAAGACGTCTT 60.441 45.833 31.70 31.70 46.62 3.01
2303 2422 5.107133 CGTCCCATAATGTAAGACGTCTTT 58.893 41.667 33.82 19.31 43.89 2.52
2304 2423 5.579511 CGTCCCATAATGTAAGACGTCTTTT 59.420 40.000 33.82 23.87 43.89 2.27
2305 2424 6.455113 CGTCCCATAATGTAAGACGTCTTTTG 60.455 42.308 33.82 20.03 43.89 2.44
2306 2425 6.592607 GTCCCATAATGTAAGACGTCTTTTGA 59.407 38.462 33.82 18.81 37.40 2.69
2307 2426 6.592607 TCCCATAATGTAAGACGTCTTTTGAC 59.407 38.462 33.82 25.38 45.55 3.18
2328 2447 5.796350 ACACAACACTAGTGTCAGAAAAC 57.204 39.130 28.04 0.00 46.57 2.43
2329 2448 4.328983 ACACAACACTAGTGTCAGAAAACG 59.671 41.667 28.04 13.08 46.57 3.60
2330 2449 4.328983 CACAACACTAGTGTCAGAAAACGT 59.671 41.667 28.04 7.10 44.13 3.99
2331 2450 4.565564 ACAACACTAGTGTCAGAAAACGTC 59.434 41.667 28.04 0.00 44.13 4.34
2332 2451 4.650754 ACACTAGTGTCAGAAAACGTCT 57.349 40.909 22.95 0.00 40.24 4.18
2333 2452 5.007385 ACACTAGTGTCAGAAAACGTCTT 57.993 39.130 22.95 0.00 40.24 3.01
2334 2453 6.140303 ACACTAGTGTCAGAAAACGTCTTA 57.860 37.500 22.95 0.00 40.24 2.10
2335 2454 5.975939 ACACTAGTGTCAGAAAACGTCTTAC 59.024 40.000 22.95 0.00 40.24 2.34
2336 2455 5.975344 CACTAGTGTCAGAAAACGTCTTACA 59.025 40.000 15.06 0.00 38.00 2.41
2337 2456 6.641314 CACTAGTGTCAGAAAACGTCTTACAT 59.359 38.462 15.06 0.00 41.41 2.29
2338 2457 7.169308 CACTAGTGTCAGAAAACGTCTTACATT 59.831 37.037 15.06 0.00 41.41 2.71
2339 2458 8.355169 ACTAGTGTCAGAAAACGTCTTACATTA 58.645 33.333 0.00 0.00 41.41 1.90
2340 2459 9.355215 CTAGTGTCAGAAAACGTCTTACATTAT 57.645 33.333 0.00 0.00 41.41 1.28
2341 2460 8.018677 AGTGTCAGAAAACGTCTTACATTATG 57.981 34.615 0.00 0.00 41.41 1.90
2342 2461 7.117812 AGTGTCAGAAAACGTCTTACATTATGG 59.882 37.037 0.00 0.00 41.41 2.74
2343 2462 6.370442 TGTCAGAAAACGTCTTACATTATGGG 59.630 38.462 0.00 0.00 35.89 4.00
2344 2463 6.592607 GTCAGAAAACGTCTTACATTATGGGA 59.407 38.462 0.00 0.00 32.70 4.37
2345 2464 6.592607 TCAGAAAACGTCTTACATTATGGGAC 59.407 38.462 0.00 1.75 32.70 4.46
2346 2465 6.370442 CAGAAAACGTCTTACATTATGGGACA 59.630 38.462 12.60 0.00 37.30 4.02
2347 2466 6.594159 AGAAAACGTCTTACATTATGGGACAG 59.406 38.462 12.60 9.07 35.01 3.51
2348 2467 7.526526 AGAAAACGTCTTACATTATGGGACAGA 60.527 37.037 12.60 0.57 35.01 3.41
2364 2483 7.374975 TGGGACAGAGGGAGTATATTTTTAG 57.625 40.000 0.00 0.00 0.00 1.85
2365 2484 7.136885 TGGGACAGAGGGAGTATATTTTTAGA 58.863 38.462 0.00 0.00 0.00 2.10
2366 2485 7.626084 TGGGACAGAGGGAGTATATTTTTAGAA 59.374 37.037 0.00 0.00 0.00 2.10
2367 2486 8.491958 GGGACAGAGGGAGTATATTTTTAGAAA 58.508 37.037 0.00 0.00 0.00 2.52
2394 2513 9.872721 TTTCAATACAAACTACATACGGATGTA 57.127 29.630 19.32 19.32 44.77 2.29
2435 2554 9.240734 AGAGGATATATTCATTCATTTTGCTCC 57.759 33.333 0.00 0.00 0.00 4.70
2436 2555 8.048534 AGGATATATTCATTCATTTTGCTCCG 57.951 34.615 0.00 0.00 0.00 4.63
2437 2556 7.667219 AGGATATATTCATTCATTTTGCTCCGT 59.333 33.333 0.00 0.00 0.00 4.69
2438 2557 8.946085 GGATATATTCATTCATTTTGCTCCGTA 58.054 33.333 0.00 0.00 0.00 4.02
2441 2560 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
2442 2561 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
2443 2562 6.358118 TCATTCATTTTGCTCCGTATGTAC 57.642 37.500 0.00 0.00 0.00 2.90
2444 2563 6.112734 TCATTCATTTTGCTCCGTATGTACT 58.887 36.000 0.00 0.00 0.00 2.73
2445 2564 6.257849 TCATTCATTTTGCTCCGTATGTACTC 59.742 38.462 0.00 0.00 0.00 2.59
2446 2565 4.439057 TCATTTTGCTCCGTATGTACTCC 58.561 43.478 0.00 0.00 0.00 3.85
2447 2566 2.973694 TTTGCTCCGTATGTACTCCC 57.026 50.000 0.00 0.00 0.00 4.30
2448 2567 2.154567 TTGCTCCGTATGTACTCCCT 57.845 50.000 0.00 0.00 0.00 4.20
2449 2568 1.688772 TGCTCCGTATGTACTCCCTC 58.311 55.000 0.00 0.00 0.00 4.30
2450 2569 0.960286 GCTCCGTATGTACTCCCTCC 59.040 60.000 0.00 0.00 0.00 4.30
2451 2570 1.236628 CTCCGTATGTACTCCCTCCG 58.763 60.000 0.00 0.00 0.00 4.63
2452 2571 0.548031 TCCGTATGTACTCCCTCCGT 59.452 55.000 0.00 0.00 0.00 4.69
2453 2572 1.064463 TCCGTATGTACTCCCTCCGTT 60.064 52.381 0.00 0.00 0.00 4.44
2454 2573 1.753073 CCGTATGTACTCCCTCCGTTT 59.247 52.381 0.00 0.00 0.00 3.60
2455 2574 2.223665 CCGTATGTACTCCCTCCGTTTC 60.224 54.545 0.00 0.00 0.00 2.78
2456 2575 2.424601 CGTATGTACTCCCTCCGTTTCA 59.575 50.000 0.00 0.00 0.00 2.69
2457 2576 3.119388 CGTATGTACTCCCTCCGTTTCAA 60.119 47.826 0.00 0.00 0.00 2.69
2458 2577 4.618927 CGTATGTACTCCCTCCGTTTCAAA 60.619 45.833 0.00 0.00 0.00 2.69
2459 2578 3.842007 TGTACTCCCTCCGTTTCAAAA 57.158 42.857 0.00 0.00 0.00 2.44
2460 2579 4.360951 TGTACTCCCTCCGTTTCAAAAT 57.639 40.909 0.00 0.00 0.00 1.82
2461 2580 4.721132 TGTACTCCCTCCGTTTCAAAATT 58.279 39.130 0.00 0.00 0.00 1.82
2462 2581 4.758165 TGTACTCCCTCCGTTTCAAAATTC 59.242 41.667 0.00 0.00 0.00 2.17
2463 2582 4.100279 ACTCCCTCCGTTTCAAAATTCT 57.900 40.909 0.00 0.00 0.00 2.40
2464 2583 4.470602 ACTCCCTCCGTTTCAAAATTCTT 58.529 39.130 0.00 0.00 0.00 2.52
2465 2584 4.278419 ACTCCCTCCGTTTCAAAATTCTTG 59.722 41.667 0.00 0.00 0.00 3.02
2466 2585 4.211920 TCCCTCCGTTTCAAAATTCTTGT 58.788 39.130 0.00 0.00 0.00 3.16
2467 2586 4.277423 TCCCTCCGTTTCAAAATTCTTGTC 59.723 41.667 0.00 0.00 0.00 3.18
2468 2587 4.278419 CCCTCCGTTTCAAAATTCTTGTCT 59.722 41.667 0.00 0.00 0.00 3.41
2469 2588 5.221244 CCCTCCGTTTCAAAATTCTTGTCTT 60.221 40.000 0.00 0.00 0.00 3.01
2470 2589 6.016610 CCCTCCGTTTCAAAATTCTTGTCTTA 60.017 38.462 0.00 0.00 0.00 2.10
2471 2590 7.078228 CCTCCGTTTCAAAATTCTTGTCTTAG 58.922 38.462 0.00 0.00 0.00 2.18
2472 2591 7.041372 CCTCCGTTTCAAAATTCTTGTCTTAGA 60.041 37.037 0.00 0.00 0.00 2.10
2473 2592 8.391075 TCCGTTTCAAAATTCTTGTCTTAGAT 57.609 30.769 0.00 0.00 0.00 1.98
2474 2593 8.846211 TCCGTTTCAAAATTCTTGTCTTAGATT 58.154 29.630 0.00 0.00 0.00 2.40
2475 2594 9.463443 CCGTTTCAAAATTCTTGTCTTAGATTT 57.537 29.630 0.00 0.00 0.00 2.17
2522 2641 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
2523 2642 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
2524 2643 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
2525 2644 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
2526 2645 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
2527 2646 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
2528 2647 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
2529 2648 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
2530 2649 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
2531 2650 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
2532 2651 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
2533 2652 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
2534 2653 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
2535 2654 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
2536 2655 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
2555 2674 9.546428 AGACAAATTTAAGACAAGAATTTTGGG 57.454 29.630 0.00 0.00 33.39 4.12
2556 2675 9.541143 GACAAATTTAAGACAAGAATTTTGGGA 57.459 29.630 0.00 0.00 33.39 4.37
2557 2676 9.325198 ACAAATTTAAGACAAGAATTTTGGGAC 57.675 29.630 0.00 0.00 33.39 4.46
2558 2677 9.323985 CAAATTTAAGACAAGAATTTTGGGACA 57.676 29.630 0.00 0.00 32.35 4.02
2559 2678 9.546428 AAATTTAAGACAAGAATTTTGGGACAG 57.454 29.630 0.00 0.00 42.39 3.51
2560 2679 7.889873 TTTAAGACAAGAATTTTGGGACAGA 57.110 32.000 5.68 0.00 42.39 3.41
2561 2680 7.510549 TTAAGACAAGAATTTTGGGACAGAG 57.489 36.000 5.68 0.00 42.39 3.35
2562 2681 4.401925 AGACAAGAATTTTGGGACAGAGG 58.598 43.478 5.68 0.00 42.39 3.69
2563 2682 3.500343 ACAAGAATTTTGGGACAGAGGG 58.500 45.455 5.68 0.00 42.39 4.30
2564 2683 3.140144 ACAAGAATTTTGGGACAGAGGGA 59.860 43.478 5.68 0.00 42.39 4.20
2565 2684 3.728385 AGAATTTTGGGACAGAGGGAG 57.272 47.619 0.00 0.00 42.39 4.30
2566 2685 2.989571 AGAATTTTGGGACAGAGGGAGT 59.010 45.455 0.00 0.00 42.39 3.85
2567 2686 4.175962 AGAATTTTGGGACAGAGGGAGTA 58.824 43.478 0.00 0.00 42.39 2.59
2568 2687 4.226168 AGAATTTTGGGACAGAGGGAGTAG 59.774 45.833 0.00 0.00 42.39 2.57
2569 2688 2.715763 TTTGGGACAGAGGGAGTAGT 57.284 50.000 0.00 0.00 42.39 2.73
2570 2689 2.715763 TTGGGACAGAGGGAGTAGTT 57.284 50.000 0.00 0.00 42.39 2.24
2571 2690 2.715763 TGGGACAGAGGGAGTAGTTT 57.284 50.000 0.00 0.00 0.00 2.66
2572 2691 2.537143 TGGGACAGAGGGAGTAGTTTC 58.463 52.381 0.00 0.00 0.00 2.78
2573 2692 2.111972 TGGGACAGAGGGAGTAGTTTCT 59.888 50.000 0.00 0.00 0.00 2.52
2574 2693 3.174779 GGGACAGAGGGAGTAGTTTCTT 58.825 50.000 0.00 0.00 0.00 2.52
2575 2694 4.202749 TGGGACAGAGGGAGTAGTTTCTTA 60.203 45.833 0.00 0.00 0.00 2.10
2576 2695 4.963628 GGGACAGAGGGAGTAGTTTCTTAT 59.036 45.833 0.00 0.00 0.00 1.73
2577 2696 5.425862 GGGACAGAGGGAGTAGTTTCTTATT 59.574 44.000 0.00 0.00 0.00 1.40
2578 2697 6.342111 GGACAGAGGGAGTAGTTTCTTATTG 58.658 44.000 0.00 0.00 0.00 1.90
2579 2698 6.301169 ACAGAGGGAGTAGTTTCTTATTGG 57.699 41.667 0.00 0.00 0.00 3.16
2580 2699 6.023603 ACAGAGGGAGTAGTTTCTTATTGGA 58.976 40.000 0.00 0.00 0.00 3.53
2581 2700 6.500751 ACAGAGGGAGTAGTTTCTTATTGGAA 59.499 38.462 0.00 0.00 0.00 3.53
2582 2701 7.182930 ACAGAGGGAGTAGTTTCTTATTGGAAT 59.817 37.037 0.00 0.00 0.00 3.01
2583 2702 7.713073 CAGAGGGAGTAGTTTCTTATTGGAATC 59.287 40.741 0.00 0.00 0.00 2.52
2584 2703 7.403231 AGAGGGAGTAGTTTCTTATTGGAATCA 59.597 37.037 0.00 0.00 0.00 2.57
2585 2704 7.339482 AGGGAGTAGTTTCTTATTGGAATCAC 58.661 38.462 0.00 0.00 0.00 3.06
2586 2705 7.182930 AGGGAGTAGTTTCTTATTGGAATCACT 59.817 37.037 0.00 0.00 0.00 3.41
2587 2706 8.483758 GGGAGTAGTTTCTTATTGGAATCACTA 58.516 37.037 0.00 0.00 0.00 2.74
2588 2707 9.886132 GGAGTAGTTTCTTATTGGAATCACTAA 57.114 33.333 0.00 0.00 0.00 2.24
2614 2733 8.959705 AAAGACTTATATTTAGGAACGAAGGG 57.040 34.615 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.442769 GCTCATCGTGTGGACAACAT 58.557 50.000 0.00 0.00 41.97 2.71
5 6 0.943835 CGCTCATCGTGTGGACAACA 60.944 55.000 0.00 0.00 36.04 3.33
10 11 2.153547 TTGAGCGCTCATCGTGTGGA 62.154 55.000 38.40 19.84 39.64 4.02
16 17 3.867055 AAACATATTGAGCGCTCATCG 57.133 42.857 38.40 26.98 39.64 3.84
22 23 2.975851 GCATGCTAAACATATTGAGCGC 59.024 45.455 11.37 0.00 44.56 5.92
37 38 7.290061 TCCTTTAAGGATATTAACTGCATGCT 58.710 34.615 20.33 0.40 40.06 3.79
54 56 3.694072 TCGTTGGCATTGGATCCTTTAAG 59.306 43.478 14.23 0.00 0.00 1.85
57 59 2.214376 TCGTTGGCATTGGATCCTTT 57.786 45.000 14.23 0.00 0.00 3.11
60 62 3.525268 AAAATCGTTGGCATTGGATCC 57.475 42.857 4.20 4.20 0.00 3.36
61 63 6.329496 TCTTAAAAATCGTTGGCATTGGATC 58.671 36.000 0.00 0.00 0.00 3.36
62 64 6.279513 TCTTAAAAATCGTTGGCATTGGAT 57.720 33.333 0.00 0.00 0.00 3.41
63 65 5.713792 TCTTAAAAATCGTTGGCATTGGA 57.286 34.783 0.00 0.00 0.00 3.53
64 66 6.813152 AGATTCTTAAAAATCGTTGGCATTGG 59.187 34.615 0.00 0.00 40.00 3.16
139 142 8.071967 CAGTATATTGGTTGCACACAGATATTG 58.928 37.037 0.00 0.00 0.00 1.90
146 149 2.752354 GGCAGTATATTGGTTGCACACA 59.248 45.455 0.00 0.00 38.27 3.72
160 163 8.703743 TGGCATTCAAAAATTATTAGGCAGTAT 58.296 29.630 0.00 0.00 0.00 2.12
165 168 5.816777 TGCTGGCATTCAAAAATTATTAGGC 59.183 36.000 0.00 0.00 0.00 3.93
222 227 7.701924 CGCCGGCATTAATATTTTGAATGATAT 59.298 33.333 28.98 0.00 33.28 1.63
223 228 7.026562 CGCCGGCATTAATATTTTGAATGATA 58.973 34.615 28.98 0.00 33.28 2.15
224 229 5.863397 CGCCGGCATTAATATTTTGAATGAT 59.137 36.000 28.98 0.00 33.28 2.45
225 230 5.009110 TCGCCGGCATTAATATTTTGAATGA 59.991 36.000 28.98 5.89 33.28 2.57
226 231 5.218885 TCGCCGGCATTAATATTTTGAATG 58.781 37.500 28.98 3.18 34.37 2.67
301 306 7.429340 GCAGTGTATATTAGTTGCACACAAATC 59.571 37.037 6.01 0.00 41.49 2.17
304 309 5.123186 GGCAGTGTATATTAGTTGCACACAA 59.877 40.000 6.01 0.00 41.49 3.33
305 310 4.634004 GGCAGTGTATATTAGTTGCACACA 59.366 41.667 6.01 0.00 41.49 3.72
342 347 8.792633 GCATGGTATTAATATTAGGCAGTTCAA 58.207 33.333 11.34 0.00 0.00 2.69
343 348 7.941790 TGCATGGTATTAATATTAGGCAGTTCA 59.058 33.333 13.66 0.00 0.00 3.18
344 349 8.335532 TGCATGGTATTAATATTAGGCAGTTC 57.664 34.615 13.66 0.00 0.00 3.01
345 350 8.884124 ATGCATGGTATTAATATTAGGCAGTT 57.116 30.769 19.04 7.58 0.00 3.16
393 401 4.035208 GGGTGCATAGTAGAAAACGGATTG 59.965 45.833 0.00 0.00 0.00 2.67
394 402 4.080526 AGGGTGCATAGTAGAAAACGGATT 60.081 41.667 0.00 0.00 0.00 3.01
398 406 5.907197 CATAGGGTGCATAGTAGAAAACG 57.093 43.478 0.00 0.00 0.00 3.60
435 443 1.893137 ACACGTTGATCCTCAGTGCTA 59.107 47.619 7.37 0.00 36.38 3.49
442 451 2.015736 AGATGCACACGTTGATCCTC 57.984 50.000 0.00 0.00 0.00 3.71
492 501 1.809619 CGTGCACCGTTCATCCGAT 60.810 57.895 12.15 0.00 0.00 4.18
493 502 2.431771 CGTGCACCGTTCATCCGA 60.432 61.111 12.15 0.00 0.00 4.55
494 503 4.147322 GCGTGCACCGTTCATCCG 62.147 66.667 12.15 0.00 39.32 4.18
495 504 3.047280 TGCGTGCACCGTTCATCC 61.047 61.111 12.15 0.00 39.32 3.51
496 505 2.173382 GTGCGTGCACCGTTCATC 59.827 61.111 13.90 0.00 40.79 2.92
703 724 2.355986 CCCGATGACCGACTCCCAA 61.356 63.158 0.00 0.00 41.76 4.12
755 776 4.906537 GTTGGGGTTGGGTGGCGT 62.907 66.667 0.00 0.00 0.00 5.68
818 853 1.578583 TATAAAAGCGAAGGAGCGGC 58.421 50.000 0.00 0.00 43.00 6.53
894 929 3.188786 GTGAGGACGATGGTGCGC 61.189 66.667 0.00 0.00 39.82 6.09
895 930 2.094659 GTGTGAGGACGATGGTGCG 61.095 63.158 0.00 0.00 39.82 5.34
896 931 0.320771 AAGTGTGAGGACGATGGTGC 60.321 55.000 0.00 0.00 34.21 5.01
985 1030 4.827087 CATGCCTGTCGCTCGCCT 62.827 66.667 0.00 0.00 38.78 5.52
989 1034 3.984193 AAGCCCATGCCTGTCGCTC 62.984 63.158 2.11 0.00 38.69 5.03
1451 1526 1.455773 ATCTCGTCGGGGATGAGCA 60.456 57.895 9.46 1.21 43.22 4.26
1843 1925 8.366401 TCATCAACAAATTTAATTGGCAGAAGA 58.634 29.630 12.19 0.00 34.56 2.87
1899 1981 2.441410 GAAAGAGAAGGAGCAAAGGGG 58.559 52.381 0.00 0.00 0.00 4.79
1929 2011 7.981102 TGTACTACTAGTATATGTGCCTGAG 57.019 40.000 2.33 0.00 32.65 3.35
1971 2077 1.604378 CTCTGCGGGGGAAGTTGAT 59.396 57.895 0.00 0.00 0.00 2.57
1986 2092 5.416271 TCCTTCCTAAATTTGTACGCTCT 57.584 39.130 0.00 0.00 0.00 4.09
2018 2124 1.095600 GGTTTCAGAAATCCTCGGCC 58.904 55.000 0.00 0.00 0.00 6.13
2116 2229 6.755190 GTTGTAGCAATAACAACGGTACTAC 58.245 40.000 3.61 0.00 45.02 2.73
2117 2230 6.949578 GTTGTAGCAATAACAACGGTACTA 57.050 37.500 3.61 0.00 45.02 1.82
2206 2325 8.877808 AAGAAGGTTCAAATCTGTTCATTTTC 57.122 30.769 0.00 0.00 0.00 2.29
2223 2342 9.768662 TGTATCGTAAGTTTCTAAAAGAAGGTT 57.231 29.630 0.00 0.00 35.37 3.50
2224 2343 9.768662 TTGTATCGTAAGTTTCTAAAAGAAGGT 57.231 29.630 0.00 0.00 35.37 3.50
2244 2363 6.534079 ACGGAAGCACTGTAGTATTTTGTATC 59.466 38.462 0.00 0.00 36.20 2.24
2259 2378 1.275573 GAGGGAGTAAACGGAAGCACT 59.724 52.381 0.00 0.00 0.00 4.40
2260 2379 1.675116 GGAGGGAGTAAACGGAAGCAC 60.675 57.143 0.00 0.00 0.00 4.40
2261 2380 0.611714 GGAGGGAGTAAACGGAAGCA 59.388 55.000 0.00 0.00 0.00 3.91
2262 2381 0.459759 CGGAGGGAGTAAACGGAAGC 60.460 60.000 0.00 0.00 0.00 3.86
2263 2382 0.893447 ACGGAGGGAGTAAACGGAAG 59.107 55.000 0.00 0.00 0.00 3.46
2264 2383 0.890683 GACGGAGGGAGTAAACGGAA 59.109 55.000 0.00 0.00 0.00 4.30
2265 2384 0.967380 GGACGGAGGGAGTAAACGGA 60.967 60.000 0.00 0.00 0.00 4.69
2266 2385 1.514553 GGACGGAGGGAGTAAACGG 59.485 63.158 0.00 0.00 0.00 4.44
2267 2386 1.252904 TGGGACGGAGGGAGTAAACG 61.253 60.000 0.00 0.00 0.00 3.60
2268 2387 1.201424 ATGGGACGGAGGGAGTAAAC 58.799 55.000 0.00 0.00 0.00 2.01
2269 2388 2.852714 TATGGGACGGAGGGAGTAAA 57.147 50.000 0.00 0.00 0.00 2.01
2270 2389 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
2271 2390 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
2272 2391 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
2273 2392 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2274 2393 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2275 2394 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2276 2395 3.552273 CGTCTTACATTATGGGACGGAGG 60.552 52.174 20.50 5.87 43.69 4.30
2277 2396 3.639538 CGTCTTACATTATGGGACGGAG 58.360 50.000 20.50 2.74 43.69 4.63
2278 2397 3.720949 CGTCTTACATTATGGGACGGA 57.279 47.619 20.50 2.30 43.69 4.69
2281 2400 6.592607 TCAAAAGACGTCTTACATTATGGGAC 59.407 38.462 29.91 1.75 34.61 4.46
2282 2401 6.592607 GTCAAAAGACGTCTTACATTATGGGA 59.407 38.462 29.91 11.86 34.61 4.37
2283 2402 6.370442 TGTCAAAAGACGTCTTACATTATGGG 59.630 38.462 29.91 9.91 34.61 4.00
2284 2403 7.095397 TGTGTCAAAAGACGTCTTACATTATGG 60.095 37.037 29.91 11.93 34.61 2.74
2285 2404 7.792925 TGTGTCAAAAGACGTCTTACATTATG 58.207 34.615 29.91 19.87 34.61 1.90
2286 2405 7.956420 TGTGTCAAAAGACGTCTTACATTAT 57.044 32.000 29.91 11.56 34.61 1.28
2287 2406 7.278203 TGTTGTGTCAAAAGACGTCTTACATTA 59.722 33.333 29.91 19.04 34.61 1.90
2288 2407 6.092944 TGTTGTGTCAAAAGACGTCTTACATT 59.907 34.615 29.91 18.24 34.61 2.71
2289 2408 5.583061 TGTTGTGTCAAAAGACGTCTTACAT 59.417 36.000 29.91 16.77 34.61 2.29
2290 2409 4.930405 TGTTGTGTCAAAAGACGTCTTACA 59.070 37.500 29.91 25.69 34.61 2.41
2291 2410 5.063060 AGTGTTGTGTCAAAAGACGTCTTAC 59.937 40.000 29.91 23.56 34.61 2.34
2292 2411 5.172934 AGTGTTGTGTCAAAAGACGTCTTA 58.827 37.500 29.91 13.09 34.61 2.10
2293 2412 4.000988 AGTGTTGTGTCAAAAGACGTCTT 58.999 39.130 24.93 24.93 37.91 3.01
2294 2413 3.596214 AGTGTTGTGTCAAAAGACGTCT 58.404 40.909 13.58 13.58 0.00 4.18
2295 2414 4.565564 ACTAGTGTTGTGTCAAAAGACGTC 59.434 41.667 7.70 7.70 0.00 4.34
2296 2415 4.328983 CACTAGTGTTGTGTCAAAAGACGT 59.671 41.667 15.06 0.00 0.00 4.34
2297 2416 4.328983 ACACTAGTGTTGTGTCAAAAGACG 59.671 41.667 22.95 0.00 44.24 4.18
2298 2417 5.796350 ACACTAGTGTTGTGTCAAAAGAC 57.204 39.130 22.95 0.00 44.24 3.01
2307 2426 4.328983 ACGTTTTCTGACACTAGTGTTGTG 59.671 41.667 28.49 20.03 45.05 3.33
2308 2427 4.501071 ACGTTTTCTGACACTAGTGTTGT 58.499 39.130 28.49 13.92 45.05 3.32
2309 2428 4.804139 AGACGTTTTCTGACACTAGTGTTG 59.196 41.667 28.49 22.57 45.05 3.33
2310 2429 5.007385 AGACGTTTTCTGACACTAGTGTT 57.993 39.130 28.49 13.24 45.05 3.32
2311 2430 5.007385 AAGACGTTTTCTGACACTAGTGT 57.993 39.130 28.27 28.27 39.29 3.55
2312 2431 5.975344 TGTAAGACGTTTTCTGACACTAGTG 59.025 40.000 21.44 21.44 40.44 2.74
2313 2432 6.140303 TGTAAGACGTTTTCTGACACTAGT 57.860 37.500 0.00 0.00 40.44 2.57
2319 2438 6.592607 TCCCATAATGTAAGACGTTTTCTGAC 59.407 38.462 0.00 0.00 36.30 3.51
2320 2439 6.592607 GTCCCATAATGTAAGACGTTTTCTGA 59.407 38.462 0.00 0.00 33.46 3.27
2321 2440 6.370442 TGTCCCATAATGTAAGACGTTTTCTG 59.630 38.462 0.00 0.00 33.46 3.02
2322 2441 6.469410 TGTCCCATAATGTAAGACGTTTTCT 58.531 36.000 0.00 0.00 35.32 2.52
2323 2442 6.592607 TCTGTCCCATAATGTAAGACGTTTTC 59.407 38.462 0.00 0.00 0.00 2.29
2324 2443 6.469410 TCTGTCCCATAATGTAAGACGTTTT 58.531 36.000 0.00 0.00 0.00 2.43
2325 2444 6.045072 TCTGTCCCATAATGTAAGACGTTT 57.955 37.500 0.00 0.00 0.00 3.60
2326 2445 5.395324 CCTCTGTCCCATAATGTAAGACGTT 60.395 44.000 0.00 0.00 0.00 3.99
2327 2446 4.099573 CCTCTGTCCCATAATGTAAGACGT 59.900 45.833 0.00 0.00 0.00 4.34
2328 2447 4.501571 CCCTCTGTCCCATAATGTAAGACG 60.502 50.000 0.00 0.00 0.00 4.18
2329 2448 4.654262 TCCCTCTGTCCCATAATGTAAGAC 59.346 45.833 0.00 0.00 0.00 3.01
2330 2449 4.890988 TCCCTCTGTCCCATAATGTAAGA 58.109 43.478 0.00 0.00 0.00 2.10
2331 2450 4.656112 ACTCCCTCTGTCCCATAATGTAAG 59.344 45.833 0.00 0.00 0.00 2.34
2332 2451 4.631234 ACTCCCTCTGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2333 2452 4.280789 ACTCCCTCTGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2334 2453 3.136641 ACTCCCTCTGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2335 2454 7.502060 AATATACTCCCTCTGTCCCATAATG 57.498 40.000 0.00 0.00 0.00 1.90
2336 2455 8.525729 AAAATATACTCCCTCTGTCCCATAAT 57.474 34.615 0.00 0.00 0.00 1.28
2337 2456 7.947782 AAAATATACTCCCTCTGTCCCATAA 57.052 36.000 0.00 0.00 0.00 1.90
2338 2457 7.947782 AAAAATATACTCCCTCTGTCCCATA 57.052 36.000 0.00 0.00 0.00 2.74
2339 2458 6.848562 AAAAATATACTCCCTCTGTCCCAT 57.151 37.500 0.00 0.00 0.00 4.00
2340 2459 7.136885 TCTAAAAATATACTCCCTCTGTCCCA 58.863 38.462 0.00 0.00 0.00 4.37
2341 2460 7.613551 TCTAAAAATATACTCCCTCTGTCCC 57.386 40.000 0.00 0.00 0.00 4.46
2367 2486 9.391006 ACATCCGTATGTAGTTTGTATTGAAAT 57.609 29.630 0.00 0.00 44.66 2.17
2368 2487 8.780846 ACATCCGTATGTAGTTTGTATTGAAA 57.219 30.769 0.00 0.00 44.66 2.69
2409 2528 9.240734 GGAGCAAAATGAATGAATATATCCTCT 57.759 33.333 0.00 0.00 0.00 3.69
2410 2529 8.180267 CGGAGCAAAATGAATGAATATATCCTC 58.820 37.037 0.00 0.00 0.00 3.71
2411 2530 7.667219 ACGGAGCAAAATGAATGAATATATCCT 59.333 33.333 0.00 0.00 0.00 3.24
2412 2531 7.820648 ACGGAGCAAAATGAATGAATATATCC 58.179 34.615 0.00 0.00 0.00 2.59
2415 2534 9.283768 ACATACGGAGCAAAATGAATGAATATA 57.716 29.630 0.00 0.00 0.00 0.86
2416 2535 8.169977 ACATACGGAGCAAAATGAATGAATAT 57.830 30.769 0.00 0.00 0.00 1.28
2417 2536 7.566760 ACATACGGAGCAAAATGAATGAATA 57.433 32.000 0.00 0.00 0.00 1.75
2418 2537 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
2419 2538 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
2420 2539 6.112734 AGTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
2421 2540 6.363577 AGTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
2422 2541 5.527582 GGAGTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
2423 2542 4.873827 GGAGTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
2424 2543 4.439057 GGAGTACATACGGAGCAAAATGA 58.561 43.478 0.00 0.00 0.00 2.57
2425 2544 3.560068 GGGAGTACATACGGAGCAAAATG 59.440 47.826 0.00 0.00 0.00 2.32
2426 2545 3.454812 AGGGAGTACATACGGAGCAAAAT 59.545 43.478 0.00 0.00 0.00 1.82
2427 2546 2.835764 AGGGAGTACATACGGAGCAAAA 59.164 45.455 0.00 0.00 0.00 2.44
2428 2547 2.429610 GAGGGAGTACATACGGAGCAAA 59.570 50.000 0.00 0.00 0.00 3.68
2429 2548 2.029623 GAGGGAGTACATACGGAGCAA 58.970 52.381 0.00 0.00 0.00 3.91
2430 2549 1.688772 GAGGGAGTACATACGGAGCA 58.311 55.000 0.00 0.00 0.00 4.26
2431 2550 0.960286 GGAGGGAGTACATACGGAGC 59.040 60.000 0.00 0.00 0.00 4.70
2432 2551 1.236628 CGGAGGGAGTACATACGGAG 58.763 60.000 0.00 0.00 0.00 4.63
2433 2552 0.548031 ACGGAGGGAGTACATACGGA 59.452 55.000 0.00 0.00 0.00 4.69
2434 2553 1.396653 AACGGAGGGAGTACATACGG 58.603 55.000 0.00 0.00 0.00 4.02
2435 2554 2.424601 TGAAACGGAGGGAGTACATACG 59.575 50.000 0.00 0.00 0.00 3.06
2436 2555 4.460948 TTGAAACGGAGGGAGTACATAC 57.539 45.455 0.00 0.00 0.00 2.39
2437 2556 5.486735 TTTTGAAACGGAGGGAGTACATA 57.513 39.130 0.00 0.00 0.00 2.29
2438 2557 4.360951 TTTTGAAACGGAGGGAGTACAT 57.639 40.909 0.00 0.00 0.00 2.29
2439 2558 3.842007 TTTTGAAACGGAGGGAGTACA 57.158 42.857 0.00 0.00 0.00 2.90
2440 2559 5.001874 AGAATTTTGAAACGGAGGGAGTAC 58.998 41.667 0.00 0.00 0.00 2.73
2441 2560 5.237236 AGAATTTTGAAACGGAGGGAGTA 57.763 39.130 0.00 0.00 0.00 2.59
2442 2561 4.100279 AGAATTTTGAAACGGAGGGAGT 57.900 40.909 0.00 0.00 0.00 3.85
2443 2562 4.278419 ACAAGAATTTTGAAACGGAGGGAG 59.722 41.667 7.18 0.00 0.00 4.30
2444 2563 4.211920 ACAAGAATTTTGAAACGGAGGGA 58.788 39.130 7.18 0.00 0.00 4.20
2445 2564 4.278419 AGACAAGAATTTTGAAACGGAGGG 59.722 41.667 7.18 0.00 0.00 4.30
2446 2565 5.438761 AGACAAGAATTTTGAAACGGAGG 57.561 39.130 7.18 0.00 0.00 4.30
2447 2566 7.861630 TCTAAGACAAGAATTTTGAAACGGAG 58.138 34.615 7.18 0.00 0.00 4.63
2448 2567 7.795482 TCTAAGACAAGAATTTTGAAACGGA 57.205 32.000 7.18 0.00 0.00 4.69
2449 2568 9.463443 AAATCTAAGACAAGAATTTTGAAACGG 57.537 29.630 7.18 0.00 0.00 4.44
2496 2615 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
2497 2616 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
2498 2617 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
2499 2618 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
2500 2619 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
2501 2620 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
2502 2621 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
2503 2622 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
2504 2623 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
2505 2624 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
2506 2625 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
2507 2626 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
2508 2627 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
2509 2628 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
2510 2629 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
2529 2648 9.546428 CCCAAAATTCTTGTCTTAAATTTGTCT 57.454 29.630 0.00 0.00 33.95 3.41
2530 2649 9.541143 TCCCAAAATTCTTGTCTTAAATTTGTC 57.459 29.630 0.00 0.00 33.95 3.18
2531 2650 9.325198 GTCCCAAAATTCTTGTCTTAAATTTGT 57.675 29.630 0.00 0.00 33.95 2.83
2532 2651 9.323985 TGTCCCAAAATTCTTGTCTTAAATTTG 57.676 29.630 0.00 0.00 33.95 2.32
2533 2652 9.546428 CTGTCCCAAAATTCTTGTCTTAAATTT 57.454 29.630 0.00 0.00 34.86 1.82
2534 2653 8.923270 TCTGTCCCAAAATTCTTGTCTTAAATT 58.077 29.630 0.00 0.00 0.00 1.82
2535 2654 8.477419 TCTGTCCCAAAATTCTTGTCTTAAAT 57.523 30.769 0.00 0.00 0.00 1.40
2536 2655 7.014230 CCTCTGTCCCAAAATTCTTGTCTTAAA 59.986 37.037 0.00 0.00 0.00 1.52
2537 2656 6.490040 CCTCTGTCCCAAAATTCTTGTCTTAA 59.510 38.462 0.00 0.00 0.00 1.85
2538 2657 6.003950 CCTCTGTCCCAAAATTCTTGTCTTA 58.996 40.000 0.00 0.00 0.00 2.10
2539 2658 4.829492 CCTCTGTCCCAAAATTCTTGTCTT 59.171 41.667 0.00 0.00 0.00 3.01
2540 2659 4.401925 CCTCTGTCCCAAAATTCTTGTCT 58.598 43.478 0.00 0.00 0.00 3.41
2541 2660 3.507622 CCCTCTGTCCCAAAATTCTTGTC 59.492 47.826 0.00 0.00 0.00 3.18
2542 2661 3.140144 TCCCTCTGTCCCAAAATTCTTGT 59.860 43.478 0.00 0.00 0.00 3.16
2543 2662 3.760684 CTCCCTCTGTCCCAAAATTCTTG 59.239 47.826 0.00 0.00 0.00 3.02
2544 2663 3.399305 ACTCCCTCTGTCCCAAAATTCTT 59.601 43.478 0.00 0.00 0.00 2.52
2545 2664 2.989571 ACTCCCTCTGTCCCAAAATTCT 59.010 45.455 0.00 0.00 0.00 2.40
2546 2665 3.441500 ACTCCCTCTGTCCCAAAATTC 57.558 47.619 0.00 0.00 0.00 2.17
2547 2666 3.916989 ACTACTCCCTCTGTCCCAAAATT 59.083 43.478 0.00 0.00 0.00 1.82
2548 2667 3.532102 ACTACTCCCTCTGTCCCAAAAT 58.468 45.455 0.00 0.00 0.00 1.82
2549 2668 2.986050 ACTACTCCCTCTGTCCCAAAA 58.014 47.619 0.00 0.00 0.00 2.44
2550 2669 2.715763 ACTACTCCCTCTGTCCCAAA 57.284 50.000 0.00 0.00 0.00 3.28
2551 2670 2.715763 AACTACTCCCTCTGTCCCAA 57.284 50.000 0.00 0.00 0.00 4.12
2552 2671 2.111972 AGAAACTACTCCCTCTGTCCCA 59.888 50.000 0.00 0.00 0.00 4.37
2553 2672 2.822697 AGAAACTACTCCCTCTGTCCC 58.177 52.381 0.00 0.00 0.00 4.46
2554 2673 6.342111 CAATAAGAAACTACTCCCTCTGTCC 58.658 44.000 0.00 0.00 0.00 4.02
2555 2674 6.154706 TCCAATAAGAAACTACTCCCTCTGTC 59.845 42.308 0.00 0.00 0.00 3.51
2556 2675 6.023603 TCCAATAAGAAACTACTCCCTCTGT 58.976 40.000 0.00 0.00 0.00 3.41
2557 2676 6.546428 TCCAATAAGAAACTACTCCCTCTG 57.454 41.667 0.00 0.00 0.00 3.35
2558 2677 7.403231 TGATTCCAATAAGAAACTACTCCCTCT 59.597 37.037 0.00 0.00 0.00 3.69
2559 2678 7.496263 GTGATTCCAATAAGAAACTACTCCCTC 59.504 40.741 0.00 0.00 0.00 4.30
2560 2679 7.182930 AGTGATTCCAATAAGAAACTACTCCCT 59.817 37.037 0.00 0.00 0.00 4.20
2561 2680 7.339482 AGTGATTCCAATAAGAAACTACTCCC 58.661 38.462 0.00 0.00 0.00 4.30
2562 2681 9.886132 TTAGTGATTCCAATAAGAAACTACTCC 57.114 33.333 0.00 0.00 30.45 3.85
2588 2707 9.392259 CCCTTCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
2589 2708 8.959705 CCCTTCGTTCCTAAATATAAGTCTTT 57.040 34.615 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.