Multiple sequence alignment - TraesCS7B01G150000

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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 TraesCS7B01G150000 chr7B 100.000 3213 0 0 1 3213 199261012 199264224 0.000000e+00 5934.0
1 TraesCS7B01G150000 chr7B 96.267 750 25 3 2466 3213 27309172 27309920 0.000000e+00 1227.0
2 TraesCS7B01G150000 chr7B 95.238 231 10 1 2237 2466 199272946 199273176 6.550000e-97 364.0
3 TraesCS7B01G150000 chr7B 86.207 174 23 1 1 174 465598710 465598538 1.520000e-43 187.0
4 TraesCS7B01G150000 chr7A 91.593 2046 106 27 229 2234 239543932 239545951 0.000000e+00 2765.0
5 TraesCS7B01G150000 chr7A 86.581 544 58 8 2467 3006 679112395 679111863 1.280000e-163 586.0
6 TraesCS7B01G150000 chr7A 88.636 132 13 2 4 134 485493790 485493920 3.320000e-35 159.0
7 TraesCS7B01G150000 chr7D 93.375 1585 70 22 478 2049 227543394 227544956 0.000000e+00 2313.0
8 TraesCS7B01G150000 chr7D 90.987 466 31 3 1 465 227542691 227543146 4.550000e-173 617.0
9 TraesCS7B01G150000 chr7D 80.488 123 20 4 3020 3139 54719863 54719742 1.230000e-14 91.6
10 TraesCS7B01G150000 chr3B 88.697 752 69 9 2465 3211 22600153 22599413 0.000000e+00 904.0
11 TraesCS7B01G150000 chr5A 86.296 540 59 8 2471 3006 611818216 611818744 1.000000e-159 573.0
12 TraesCS7B01G150000 chr5A 97.778 45 1 0 2297 2341 692393023 692393067 9.560000e-11 78.7
13 TraesCS7B01G150000 chr1D 94.850 233 8 2 2236 2465 366182957 366183188 8.470000e-96 361.0
14 TraesCS7B01G150000 chr1D 95.745 141 3 1 2326 2463 366194160 366194300 1.160000e-54 224.0
15 TraesCS7B01G150000 chr1D 88.406 138 14 2 1 138 457086447 457086312 7.130000e-37 165.0
16 TraesCS7B01G150000 chr1D 96.000 100 3 1 2237 2335 366192351 366192450 9.220000e-36 161.0
17 TraesCS7B01G150000 chr1D 100.000 41 0 0 2295 2335 232380190 232380230 3.440000e-10 76.8
18 TraesCS7B01G150000 chr2B 92.511 227 17 0 2240 2466 186664450 186664224 3.090000e-85 326.0
19 TraesCS7B01G150000 chr2B 88.235 153 18 0 3 155 431775717 431775565 1.970000e-42 183.0
20 TraesCS7B01G150000 chr4A 92.511 227 16 1 2240 2466 127812782 127813007 1.110000e-84 324.0
21 TraesCS7B01G150000 chr4A 90.476 147 13 1 2320 2466 127831895 127832040 3.270000e-45 193.0
22 TraesCS7B01G150000 chr5D 85.714 168 22 2 6 172 390412671 390412505 3.290000e-40 176.0
23 TraesCS7B01G150000 chrUn 85.802 162 21 2 1 161 105338242 105338082 1.530000e-38 171.0
24 TraesCS7B01G150000 chr1A 84.483 174 23 4 1 172 455825717 455825546 5.510000e-38 169.0
25 TraesCS7B01G150000 chr2A 77.061 279 62 2 2935 3211 667942806 667943084 3.320000e-35 159.0
26 TraesCS7B01G150000 chr6D 83.735 166 23 2 1 163 29138675 29138839 1.540000e-33 154.0
27 TraesCS7B01G150000 chr6D 80.153 131 24 2 1410 1539 405650833 405650704 2.640000e-16 97.1
28 TraesCS7B01G150000 chr6B 78.626 131 26 2 1410 1539 609854828 609854699 5.710000e-13 86.1


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 TraesCS7B01G150000 chr7B 199261012 199264224 3212 False 5934 5934 100.000 1 3213 1 chr7B.!!$F2 3212
1 TraesCS7B01G150000 chr7B 27309172 27309920 748 False 1227 1227 96.267 2466 3213 1 chr7B.!!$F1 747
2 TraesCS7B01G150000 chr7A 239543932 239545951 2019 False 2765 2765 91.593 229 2234 1 chr7A.!!$F1 2005
3 TraesCS7B01G150000 chr7A 679111863 679112395 532 True 586 586 86.581 2467 3006 1 chr7A.!!$R1 539
4 TraesCS7B01G150000 chr7D 227542691 227544956 2265 False 1465 2313 92.181 1 2049 2 chr7D.!!$F1 2048
5 TraesCS7B01G150000 chr3B 22599413 22600153 740 True 904 904 88.697 2465 3211 1 chr3B.!!$R1 746
6 TraesCS7B01G150000 chr5A 611818216 611818744 528 False 573 573 86.296 2471 3006 1 chr5A.!!$F1 535

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
402 408 0.175302 GCTTGCTAGCTGCTCTCTGA 59.825 55.0 17.23 0.0 44.27 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 2693 0.101759 GCGGTTCCACGATACTAGCA 59.898 55.0 0.0 0.0 35.47 3.49 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 62 9.847706 CTAGACTTACTTGCATACTATGTATGG 57.152 37.037 16.38 5.71 0.00 2.74
62 63 8.478775 AGACTTACTTGCATACTATGTATGGA 57.521 34.615 16.38 12.28 0.00 3.41
69 70 9.006839 ACTTGCATACTATGTATGGATGATTTG 57.993 33.333 21.98 9.59 0.00 2.32
85 86 8.030692 TGGATGATTTGTGCTATTTTCTTTCTG 58.969 33.333 0.00 0.00 0.00 3.02
103 104 5.828299 TTCTGAACTTTGTTGAAATCCGT 57.172 34.783 0.00 0.00 0.00 4.69
131 132 4.850859 TGCATGAATTTCGTACGGTTAG 57.149 40.909 16.52 3.95 0.00 2.34
135 136 5.478001 CATGAATTTCGTACGGTTAGTTCG 58.522 41.667 16.52 0.00 43.59 3.95
181 182 7.093640 ACAGACAATATTGAATGGCTTCATGTT 60.094 33.333 22.16 0.00 40.95 2.71
186 187 5.925506 ATTGAATGGCTTCATGTTCATGA 57.074 34.783 10.88 10.88 40.95 3.07
209 210 3.199677 CGGATACCGGAGCAAATTTACA 58.800 45.455 9.46 0.00 44.15 2.41
215 216 2.420022 CCGGAGCAAATTTACAGGTCAG 59.580 50.000 0.00 4.62 0.00 3.51
254 255 3.730215 TTTTTCTGGTAGGCATGGCTA 57.270 42.857 24.04 24.04 0.00 3.93
265 266 1.650912 CATGGCTACATTCAGCGCC 59.349 57.895 2.29 0.00 42.76 6.53
294 295 1.293924 GAGAGTGCATGTCGAATGGG 58.706 55.000 0.00 0.00 0.00 4.00
402 408 0.175302 GCTTGCTAGCTGCTCTCTGA 59.825 55.000 17.23 0.00 44.27 3.27
404 410 2.475818 CTTGCTAGCTGCTCTCTGATG 58.524 52.381 17.23 0.00 43.37 3.07
409 415 1.570803 AGCTGCTCTCTGATGGACTT 58.429 50.000 0.00 0.00 0.00 3.01
468 712 5.318630 GGTGGGTTGGAATACTCTTAAACA 58.681 41.667 0.00 0.00 0.00 2.83
474 718 7.177744 GGGTTGGAATACTCTTAAACAAATGGA 59.822 37.037 0.00 0.00 0.00 3.41
475 719 8.244113 GGTTGGAATACTCTTAAACAAATGGAG 58.756 37.037 0.00 0.00 0.00 3.86
476 720 8.793592 GTTGGAATACTCTTAAACAAATGGAGT 58.206 33.333 0.00 0.00 39.95 3.85
493 737 1.893801 GAGTAGTACTGTGGTGTGGCT 59.106 52.381 7.76 0.00 0.00 4.75
623 871 1.065764 CATGCGGCGCTCTGTAGTA 59.934 57.895 33.26 10.41 0.00 1.82
629 877 1.321074 GGCGCTCTGTAGTAGGTGGT 61.321 60.000 7.64 0.00 0.00 4.16
677 925 0.246086 CAGGCACGCTCTTTCTCTCT 59.754 55.000 0.00 0.00 0.00 3.10
683 931 3.248602 GCACGCTCTTTCTCTCTTTCAAA 59.751 43.478 0.00 0.00 0.00 2.69
689 937 6.292168 CGCTCTTTCTCTCTTTCAAACGTTTA 60.292 38.462 14.20 0.00 0.00 2.01
730 978 4.250305 AGCGGGTGTGGTGTGGTC 62.250 66.667 0.00 0.00 0.00 4.02
903 1166 2.349969 TGTCGCTGACTGACGCAGTT 62.350 55.000 12.63 0.00 45.44 3.16
924 1187 1.004560 AGTGACAGTGGCACCATCG 60.005 57.895 25.75 3.12 36.95 3.84
965 1228 3.569701 AGCACTCGTCAATGGAATGTTTT 59.430 39.130 0.00 0.00 0.00 2.43
966 1229 4.759693 AGCACTCGTCAATGGAATGTTTTA 59.240 37.500 0.00 0.00 0.00 1.52
1023 1286 1.734047 GCTTCAACAAACAACACCGCA 60.734 47.619 0.00 0.00 0.00 5.69
1438 1708 2.811317 GTGCCTCAGCGAGTTCCG 60.811 66.667 0.00 0.00 44.31 4.30
1600 1870 6.016610 CCCCACATTATACTTAACCAAATCGG 60.017 42.308 0.00 0.00 42.50 4.18
1619 1889 1.078759 GCATCGTCAACGTCCTCCAG 61.079 60.000 2.09 0.00 40.80 3.86
1722 2010 1.227380 ATGGGAGACGAGCGCATTC 60.227 57.895 11.47 1.90 35.70 2.67
1743 2031 2.711922 CCGAGGAGGGACGAGTTGG 61.712 68.421 0.00 0.00 35.97 3.77
2009 2297 8.258007 CCAATCTGAAACTATGGTTCAGTAGTA 58.742 37.037 20.37 6.20 34.89 1.82
2010 2298 9.088512 CAATCTGAAACTATGGTTCAGTAGTAC 57.911 37.037 20.37 0.00 34.89 2.73
2039 2333 5.971763 ACATTTCTTGTGGCTAGACTAGAG 58.028 41.667 13.91 1.49 37.11 2.43
2092 2386 5.752472 ACTAGATGATTGATTGCTCAACTCG 59.248 40.000 0.00 0.00 43.92 4.18
2093 2387 4.763073 AGATGATTGATTGCTCAACTCGA 58.237 39.130 0.00 0.00 43.92 4.04
2094 2388 4.569966 AGATGATTGATTGCTCAACTCGAC 59.430 41.667 0.00 0.00 43.92 4.20
2095 2389 3.930336 TGATTGATTGCTCAACTCGACT 58.070 40.909 0.00 0.00 43.92 4.18
2096 2390 4.318332 TGATTGATTGCTCAACTCGACTT 58.682 39.130 0.00 0.00 43.92 3.01
2097 2391 5.478407 TGATTGATTGCTCAACTCGACTTA 58.522 37.500 0.00 0.00 43.92 2.24
2098 2392 6.108687 TGATTGATTGCTCAACTCGACTTAT 58.891 36.000 0.00 0.00 43.92 1.73
2099 2393 7.264947 TGATTGATTGCTCAACTCGACTTATA 58.735 34.615 0.00 0.00 43.92 0.98
2100 2394 6.887376 TTGATTGCTCAACTCGACTTATAC 57.113 37.500 0.00 0.00 36.46 1.47
2103 2397 4.012319 TGCTCAACTCGACTTATACGAC 57.988 45.455 0.00 0.00 35.88 4.34
2105 2399 4.872124 TGCTCAACTCGACTTATACGACTA 59.128 41.667 0.00 0.00 35.88 2.59
2121 2415 2.033065 CGACTAATACGACCCTCTCACG 60.033 54.545 0.00 0.00 0.00 4.35
2129 2423 1.872237 CGACCCTCTCACGCTTTTCAA 60.872 52.381 0.00 0.00 0.00 2.69
2134 2428 4.825085 ACCCTCTCACGCTTTTCAATTTTA 59.175 37.500 0.00 0.00 0.00 1.52
2136 2430 6.015434 ACCCTCTCACGCTTTTCAATTTTATT 60.015 34.615 0.00 0.00 0.00 1.40
2137 2431 6.868339 CCCTCTCACGCTTTTCAATTTTATTT 59.132 34.615 0.00 0.00 0.00 1.40
2138 2432 7.148755 CCCTCTCACGCTTTTCAATTTTATTTG 60.149 37.037 0.00 0.00 0.00 2.32
2145 2439 8.454894 ACGCTTTTCAATTTTATTTGTTTTGGT 58.545 25.926 0.00 0.00 0.00 3.67
2165 2459 3.664025 GGTTTTCTGTTTTCAAGATCGCG 59.336 43.478 0.00 0.00 0.00 5.87
2179 2473 1.577328 ATCGCGTGTTCAGCTTTGGG 61.577 55.000 5.77 0.00 0.00 4.12
2197 2491 1.278238 GGTTGCACTCTAATCGACGG 58.722 55.000 0.00 0.00 0.00 4.79
2202 2496 1.654105 GCACTCTAATCGACGGTGTTG 59.346 52.381 0.00 0.00 0.00 3.33
2205 2499 2.163815 ACTCTAATCGACGGTGTTGAGG 59.836 50.000 0.00 0.00 28.70 3.86
2206 2500 2.422479 CTCTAATCGACGGTGTTGAGGA 59.578 50.000 0.00 0.00 28.70 3.71
2218 2512 4.630069 CGGTGTTGAGGAAGTAAATCGAAT 59.370 41.667 0.00 0.00 0.00 3.34
2221 2515 6.183360 GGTGTTGAGGAAGTAAATCGAATGAG 60.183 42.308 0.00 0.00 0.00 2.90
2238 2532 8.912787 TCGAATGAGTCTTGACTAGATAAAAC 57.087 34.615 3.00 0.00 34.79 2.43
2239 2533 8.740906 TCGAATGAGTCTTGACTAGATAAAACT 58.259 33.333 3.00 0.00 34.79 2.66
2240 2534 8.802856 CGAATGAGTCTTGACTAGATAAAACTG 58.197 37.037 3.00 0.00 34.79 3.16
2241 2535 9.646427 GAATGAGTCTTGACTAGATAAAACTGT 57.354 33.333 3.00 0.00 34.79 3.55
2242 2536 8.994429 ATGAGTCTTGACTAGATAAAACTGTG 57.006 34.615 3.00 0.00 34.79 3.66
2243 2537 8.178313 TGAGTCTTGACTAGATAAAACTGTGA 57.822 34.615 3.00 0.00 34.79 3.58
2244 2538 8.638873 TGAGTCTTGACTAGATAAAACTGTGAA 58.361 33.333 3.00 0.00 34.79 3.18
2245 2539 9.134734 GAGTCTTGACTAGATAAAACTGTGAAG 57.865 37.037 3.00 0.00 34.79 3.02
2246 2540 8.861086 AGTCTTGACTAGATAAAACTGTGAAGA 58.139 33.333 0.89 0.00 34.79 2.87
2247 2541 9.477484 GTCTTGACTAGATAAAACTGTGAAGAA 57.523 33.333 0.00 0.00 34.79 2.52
2250 2544 8.689251 TGACTAGATAAAACTGTGAAGAATCG 57.311 34.615 0.00 0.00 0.00 3.34
2251 2545 8.520351 TGACTAGATAAAACTGTGAAGAATCGA 58.480 33.333 0.00 0.00 0.00 3.59
2252 2546 9.522804 GACTAGATAAAACTGTGAAGAATCGAT 57.477 33.333 0.00 0.00 0.00 3.59
2253 2547 9.877178 ACTAGATAAAACTGTGAAGAATCGATT 57.123 29.630 11.20 11.20 0.00 3.34
2255 2549 8.553459 AGATAAAACTGTGAAGAATCGATTGT 57.447 30.769 16.96 9.03 0.00 2.71
2256 2550 9.653287 AGATAAAACTGTGAAGAATCGATTGTA 57.347 29.630 16.96 0.00 0.00 2.41
2260 2554 6.727824 ACTGTGAAGAATCGATTGTAAAGG 57.272 37.500 16.96 4.76 0.00 3.11
2261 2555 6.464222 ACTGTGAAGAATCGATTGTAAAGGA 58.536 36.000 16.96 0.00 0.00 3.36
2262 2556 6.934645 ACTGTGAAGAATCGATTGTAAAGGAA 59.065 34.615 16.96 0.00 0.00 3.36
2263 2557 7.095187 ACTGTGAAGAATCGATTGTAAAGGAAC 60.095 37.037 16.96 5.39 0.00 3.62
2264 2558 6.708502 TGTGAAGAATCGATTGTAAAGGAACA 59.291 34.615 16.96 7.74 0.00 3.18
2265 2559 7.227711 TGTGAAGAATCGATTGTAAAGGAACAA 59.772 33.333 16.96 0.00 43.16 2.83
2266 2560 7.746475 GTGAAGAATCGATTGTAAAGGAACAAG 59.254 37.037 16.96 0.00 42.33 3.16
2267 2561 7.659799 TGAAGAATCGATTGTAAAGGAACAAGA 59.340 33.333 16.96 0.00 42.33 3.02
2268 2562 8.567285 AAGAATCGATTGTAAAGGAACAAGAT 57.433 30.769 16.96 0.00 42.33 2.40
2269 2563 9.667107 AAGAATCGATTGTAAAGGAACAAGATA 57.333 29.630 16.96 0.00 42.33 1.98
2270 2564 9.667107 AGAATCGATTGTAAAGGAACAAGATAA 57.333 29.630 16.96 0.00 42.33 1.75
2273 2567 8.126871 TCGATTGTAAAGGAACAAGATAATCG 57.873 34.615 0.00 0.00 42.33 3.34
2274 2568 7.977293 TCGATTGTAAAGGAACAAGATAATCGA 59.023 33.333 12.41 12.41 42.33 3.59
2275 2569 8.600625 CGATTGTAAAGGAACAAGATAATCGAA 58.399 33.333 0.00 0.00 42.33 3.71
2276 2570 9.704098 GATTGTAAAGGAACAAGATAATCGAAC 57.296 33.333 0.00 0.00 42.33 3.95
2277 2571 8.610248 TTGTAAAGGAACAAGATAATCGAACA 57.390 30.769 0.00 0.00 34.50 3.18
2278 2572 8.610248 TGTAAAGGAACAAGATAATCGAACAA 57.390 30.769 0.00 0.00 0.00 2.83
2279 2573 9.058174 TGTAAAGGAACAAGATAATCGAACAAA 57.942 29.630 0.00 0.00 0.00 2.83
2281 2575 8.970691 AAAGGAACAAGATAATCGAACAAATG 57.029 30.769 0.00 0.00 0.00 2.32
2282 2576 7.921786 AGGAACAAGATAATCGAACAAATGA 57.078 32.000 0.00 0.00 0.00 2.57
2283 2577 8.511604 AGGAACAAGATAATCGAACAAATGAT 57.488 30.769 0.00 0.00 0.00 2.45
2284 2578 8.960591 AGGAACAAGATAATCGAACAAATGATT 58.039 29.630 0.00 0.00 38.34 2.57
2285 2579 9.013490 GGAACAAGATAATCGAACAAATGATTG 57.987 33.333 0.00 0.00 42.46 2.67
2286 2580 9.773328 GAACAAGATAATCGAACAAATGATTGA 57.227 29.630 0.00 0.00 38.94 2.57
2290 2584 9.655769 AAGATAATCGAACAAATGATTGAATCG 57.344 29.630 0.18 12.02 43.73 3.34
2291 2585 8.285394 AGATAATCGAACAAATGATTGAATCGG 58.715 33.333 15.59 0.00 43.18 4.18
2292 2586 5.818136 ATCGAACAAATGATTGAATCGGT 57.182 34.783 15.59 9.81 43.18 4.69
2293 2587 4.968626 TCGAACAAATGATTGAATCGGTG 58.031 39.130 15.59 1.41 43.18 4.94
2294 2588 4.454161 TCGAACAAATGATTGAATCGGTGT 59.546 37.500 15.59 2.01 43.18 4.16
2295 2589 4.788100 CGAACAAATGATTGAATCGGTGTC 59.212 41.667 8.13 3.54 41.33 3.67
2296 2590 4.701956 ACAAATGATTGAATCGGTGTCC 57.298 40.909 0.18 0.00 38.94 4.02
2297 2591 4.335416 ACAAATGATTGAATCGGTGTCCT 58.665 39.130 0.18 0.00 38.94 3.85
2298 2592 4.766891 ACAAATGATTGAATCGGTGTCCTT 59.233 37.500 0.18 0.00 38.94 3.36
2299 2593 5.243730 ACAAATGATTGAATCGGTGTCCTTT 59.756 36.000 0.18 0.00 38.94 3.11
2300 2594 6.432783 ACAAATGATTGAATCGGTGTCCTTTA 59.567 34.615 0.18 0.00 38.94 1.85
2301 2595 7.122650 ACAAATGATTGAATCGGTGTCCTTTAT 59.877 33.333 0.18 0.00 38.94 1.40
2302 2596 7.645058 AATGATTGAATCGGTGTCCTTTATT 57.355 32.000 0.18 0.00 0.00 1.40
2303 2597 6.435430 TGATTGAATCGGTGTCCTTTATTG 57.565 37.500 0.18 0.00 0.00 1.90
2304 2598 6.176896 TGATTGAATCGGTGTCCTTTATTGA 58.823 36.000 0.18 0.00 0.00 2.57
2305 2599 6.828273 TGATTGAATCGGTGTCCTTTATTGAT 59.172 34.615 0.18 0.00 0.00 2.57
2306 2600 6.435430 TTGAATCGGTGTCCTTTATTGATG 57.565 37.500 0.00 0.00 0.00 3.07
2307 2601 5.739959 TGAATCGGTGTCCTTTATTGATGA 58.260 37.500 0.00 0.00 0.00 2.92
2308 2602 6.356556 TGAATCGGTGTCCTTTATTGATGAT 58.643 36.000 0.00 0.00 0.00 2.45
2309 2603 6.828273 TGAATCGGTGTCCTTTATTGATGATT 59.172 34.615 0.00 0.00 0.00 2.57
2310 2604 6.624352 ATCGGTGTCCTTTATTGATGATTG 57.376 37.500 0.00 0.00 0.00 2.67
2311 2605 5.739959 TCGGTGTCCTTTATTGATGATTGA 58.260 37.500 0.00 0.00 0.00 2.57
2312 2606 5.584649 TCGGTGTCCTTTATTGATGATTGAC 59.415 40.000 0.00 0.00 0.00 3.18
2313 2607 5.353956 CGGTGTCCTTTATTGATGATTGACA 59.646 40.000 0.00 0.00 0.00 3.58
2314 2608 6.038603 CGGTGTCCTTTATTGATGATTGACAT 59.961 38.462 0.00 0.00 42.47 3.06
2315 2609 7.198390 GGTGTCCTTTATTGATGATTGACATG 58.802 38.462 0.00 0.00 39.56 3.21
2316 2610 6.694411 GTGTCCTTTATTGATGATTGACATGC 59.306 38.462 0.00 0.00 39.56 4.06
2317 2611 6.604396 TGTCCTTTATTGATGATTGACATGCT 59.396 34.615 0.00 0.00 39.56 3.79
2318 2612 7.774625 TGTCCTTTATTGATGATTGACATGCTA 59.225 33.333 0.00 0.00 39.56 3.49
2319 2613 8.790718 GTCCTTTATTGATGATTGACATGCTAT 58.209 33.333 0.00 0.00 39.56 2.97
2320 2614 9.358406 TCCTTTATTGATGATTGACATGCTATT 57.642 29.630 0.00 0.00 39.56 1.73
2321 2615 9.976511 CCTTTATTGATGATTGACATGCTATTT 57.023 29.630 0.00 0.00 39.56 1.40
2331 2625 8.795513 TGATTGACATGCTATTTATACAATGGG 58.204 33.333 0.00 0.00 0.00 4.00
2332 2626 8.938801 ATTGACATGCTATTTATACAATGGGA 57.061 30.769 0.00 0.00 0.00 4.37
2333 2627 8.759481 TTGACATGCTATTTATACAATGGGAA 57.241 30.769 0.00 0.00 0.00 3.97
2334 2628 8.165239 TGACATGCTATTTATACAATGGGAAC 57.835 34.615 0.00 0.00 0.00 3.62
2346 2640 3.213264 GGGAACCGTCGCCTCATA 58.787 61.111 0.00 0.00 40.86 2.15
2347 2641 1.067582 GGGAACCGTCGCCTCATAG 59.932 63.158 0.00 0.00 40.86 2.23
2348 2642 1.067582 GGAACCGTCGCCTCATAGG 59.932 63.158 0.00 0.00 38.80 2.57
2349 2643 1.067582 GAACCGTCGCCTCATAGGG 59.932 63.158 0.00 0.00 35.37 3.53
2350 2644 1.380785 AACCGTCGCCTCATAGGGA 60.381 57.895 0.00 0.00 35.37 4.20
2351 2645 1.673808 AACCGTCGCCTCATAGGGAC 61.674 60.000 0.00 0.00 35.37 4.46
2352 2646 2.331805 CGTCGCCTCATAGGGACG 59.668 66.667 15.08 15.08 45.39 4.79
2353 2647 2.027751 GTCGCCTCATAGGGACGC 59.972 66.667 0.00 0.00 35.37 5.19
2356 2650 3.052081 GCCTCATAGGGACGCGAT 58.948 61.111 15.93 0.00 35.37 4.58
2357 2651 1.373497 GCCTCATAGGGACGCGATG 60.373 63.158 15.93 5.62 35.37 3.84
2358 2652 1.290324 CCTCATAGGGACGCGATGG 59.710 63.158 15.93 0.00 0.00 3.51
2359 2653 1.464376 CCTCATAGGGACGCGATGGT 61.464 60.000 15.93 0.00 0.00 3.55
2360 2654 0.389391 CTCATAGGGACGCGATGGTT 59.611 55.000 15.93 0.00 0.00 3.67
2361 2655 0.387929 TCATAGGGACGCGATGGTTC 59.612 55.000 15.93 0.00 0.00 3.62
2362 2656 0.104120 CATAGGGACGCGATGGTTCA 59.896 55.000 15.93 0.00 0.00 3.18
2363 2657 0.828022 ATAGGGACGCGATGGTTCAA 59.172 50.000 15.93 0.00 0.00 2.69
2364 2658 0.174845 TAGGGACGCGATGGTTCAAG 59.825 55.000 15.93 0.00 0.00 3.02
2365 2659 1.079405 GGGACGCGATGGTTCAAGA 60.079 57.895 15.93 0.00 0.00 3.02
2366 2660 1.084370 GGGACGCGATGGTTCAAGAG 61.084 60.000 15.93 0.00 0.00 2.85
2367 2661 1.084370 GGACGCGATGGTTCAAGAGG 61.084 60.000 15.93 0.00 0.00 3.69
2368 2662 1.696832 GACGCGATGGTTCAAGAGGC 61.697 60.000 15.93 0.00 0.00 4.70
2369 2663 1.741401 CGCGATGGTTCAAGAGGCA 60.741 57.895 0.00 0.00 0.00 4.75
2370 2664 1.091771 CGCGATGGTTCAAGAGGCAT 61.092 55.000 0.00 0.00 0.00 4.40
2371 2665 0.659957 GCGATGGTTCAAGAGGCATC 59.340 55.000 0.00 0.00 0.00 3.91
2372 2666 0.933097 CGATGGTTCAAGAGGCATCG 59.067 55.000 0.00 0.00 36.47 3.84
2373 2667 1.740380 CGATGGTTCAAGAGGCATCGT 60.740 52.381 0.00 0.00 37.65 3.73
2374 2668 2.359900 GATGGTTCAAGAGGCATCGTT 58.640 47.619 0.00 0.00 0.00 3.85
2375 2669 1.808411 TGGTTCAAGAGGCATCGTTC 58.192 50.000 0.00 0.00 0.00 3.95
2376 2670 1.087501 GGTTCAAGAGGCATCGTTCC 58.912 55.000 0.00 0.00 0.00 3.62
2377 2671 1.610624 GGTTCAAGAGGCATCGTTCCA 60.611 52.381 0.00 0.00 0.00 3.53
2378 2672 1.734465 GTTCAAGAGGCATCGTTCCAG 59.266 52.381 0.00 0.00 0.00 3.86
2379 2673 0.250234 TCAAGAGGCATCGTTCCAGG 59.750 55.000 0.00 0.00 0.00 4.45
2380 2674 1.078143 AAGAGGCATCGTTCCAGGC 60.078 57.895 0.00 0.00 0.00 4.85
2381 2675 1.557269 AAGAGGCATCGTTCCAGGCT 61.557 55.000 0.00 0.00 41.21 4.58
2382 2676 1.817099 GAGGCATCGTTCCAGGCTG 60.817 63.158 7.75 7.75 38.37 4.85
2383 2677 3.512516 GGCATCGTTCCAGGCTGC 61.513 66.667 9.56 0.00 0.00 5.25
2384 2678 2.747460 GCATCGTTCCAGGCTGCA 60.747 61.111 9.56 0.00 33.13 4.41
2385 2679 2.334946 GCATCGTTCCAGGCTGCAA 61.335 57.895 9.56 0.00 33.13 4.08
2386 2680 1.503542 CATCGTTCCAGGCTGCAAC 59.496 57.895 11.34 11.34 0.00 4.17
2387 2681 1.675641 ATCGTTCCAGGCTGCAACC 60.676 57.895 15.38 0.00 0.00 3.77
2388 2682 3.726517 CGTTCCAGGCTGCAACCG 61.727 66.667 15.38 7.17 33.69 4.44
2389 2683 2.281484 GTTCCAGGCTGCAACCGA 60.281 61.111 10.26 0.00 33.69 4.69
2390 2684 2.281484 TTCCAGGCTGCAACCGAC 60.281 61.111 9.56 0.00 33.69 4.79
2391 2685 3.113514 TTCCAGGCTGCAACCGACA 62.114 57.895 9.56 0.00 33.69 4.35
2392 2686 2.360350 CCAGGCTGCAACCGACAT 60.360 61.111 9.56 0.00 33.69 3.06
2393 2687 2.693762 CCAGGCTGCAACCGACATG 61.694 63.158 9.56 0.00 33.69 3.21
2394 2688 3.058160 AGGCTGCAACCGACATGC 61.058 61.111 0.50 0.00 44.08 4.06
2395 2689 4.120331 GGCTGCAACCGACATGCC 62.120 66.667 0.50 0.00 43.16 4.40
2396 2690 4.465512 GCTGCAACCGACATGCCG 62.466 66.667 0.00 0.00 43.16 5.69
2403 2697 2.125310 CCGACATGCCGGTTGCTA 60.125 61.111 12.90 0.00 44.23 3.49
2404 2698 2.173669 CCGACATGCCGGTTGCTAG 61.174 63.158 12.90 0.00 44.23 3.42
2405 2699 1.447838 CGACATGCCGGTTGCTAGT 60.448 57.895 1.90 0.00 42.00 2.57
2406 2700 0.179121 CGACATGCCGGTTGCTAGTA 60.179 55.000 1.90 0.00 42.00 1.82
2407 2701 1.538204 CGACATGCCGGTTGCTAGTAT 60.538 52.381 1.90 0.00 42.00 2.12
2408 2702 2.135933 GACATGCCGGTTGCTAGTATC 58.864 52.381 1.90 0.00 42.00 2.24
2409 2703 1.139989 CATGCCGGTTGCTAGTATCG 58.860 55.000 1.90 0.00 42.00 2.92
2410 2704 0.750850 ATGCCGGTTGCTAGTATCGT 59.249 50.000 1.90 0.00 42.00 3.73
2411 2705 0.179121 TGCCGGTTGCTAGTATCGTG 60.179 55.000 1.90 0.00 42.00 4.35
2412 2706 0.874607 GCCGGTTGCTAGTATCGTGG 60.875 60.000 1.90 0.00 36.87 4.94
2413 2707 0.742505 CCGGTTGCTAGTATCGTGGA 59.257 55.000 0.00 0.00 0.00 4.02
2414 2708 1.135527 CCGGTTGCTAGTATCGTGGAA 59.864 52.381 0.00 0.00 0.00 3.53
2415 2709 2.190981 CGGTTGCTAGTATCGTGGAAC 58.809 52.381 0.00 0.00 0.00 3.62
2416 2710 2.547826 GGTTGCTAGTATCGTGGAACC 58.452 52.381 0.00 0.00 42.93 3.62
2417 2711 2.190981 GTTGCTAGTATCGTGGAACCG 58.809 52.381 0.00 0.00 0.00 4.44
2418 2712 0.101759 TGCTAGTATCGTGGAACCGC 59.898 55.000 0.00 0.00 0.00 5.68
2419 2713 0.101759 GCTAGTATCGTGGAACCGCA 59.898 55.000 5.27 0.00 0.00 5.69
2420 2714 1.836383 CTAGTATCGTGGAACCGCAC 58.164 55.000 5.27 0.00 0.00 5.34
2421 2715 0.099259 TAGTATCGTGGAACCGCACG 59.901 55.000 6.92 6.92 45.09 5.34
2422 2716 2.162754 GTATCGTGGAACCGCACGG 61.163 63.158 7.71 7.71 44.03 4.94
2423 2717 3.359515 TATCGTGGAACCGCACGGG 62.360 63.158 14.51 0.00 44.03 5.28
2435 2729 4.547367 CACGGGAGCGGGGATTCC 62.547 72.222 0.00 0.00 0.00 3.01
2449 2743 3.581265 GGATTCCCCCAATAACCGTAA 57.419 47.619 0.00 0.00 0.00 3.18
2450 2744 3.483421 GGATTCCCCCAATAACCGTAAG 58.517 50.000 0.00 0.00 0.00 2.34
2496 2790 4.397417 GCTCCTCTGCAGTCATGTAAAAAT 59.603 41.667 14.67 0.00 0.00 1.82
2522 2817 1.618343 GGTGTTGTAGCTGCCCAAATT 59.382 47.619 0.00 0.00 0.00 1.82
2525 2820 3.056607 GTGTTGTAGCTGCCCAAATTCAT 60.057 43.478 0.00 0.00 0.00 2.57
2551 2846 4.657504 TCCATTACAATCTGATGGCTCTCT 59.342 41.667 0.00 0.00 40.09 3.10
2655 2950 1.651987 CACACTGACGGTCTTGTGTT 58.348 50.000 25.75 15.16 41.04 3.32
2721 3016 0.108662 ACGACGTTTACGAATCCCCC 60.109 55.000 9.53 0.00 43.02 5.40
2783 3078 4.142049 CCTTTTCTCTATGAGACCTTCGCT 60.142 45.833 0.00 0.00 38.51 4.93
2894 3195 3.325716 AGGTAAGCCCTTCGTAGTTTTCA 59.674 43.478 0.00 0.00 42.73 2.69
2907 3208 1.150536 TTTTCAAGGGAGCGTGGCT 59.849 52.632 0.00 0.00 43.88 4.75
2908 3209 0.398696 TTTTCAAGGGAGCGTGGCTA 59.601 50.000 0.00 0.00 39.88 3.93
2909 3210 0.036388 TTTCAAGGGAGCGTGGCTAG 60.036 55.000 0.00 0.00 39.88 3.42
2910 3211 1.899437 TTCAAGGGAGCGTGGCTAGG 61.899 60.000 0.00 0.00 39.88 3.02
2911 3212 2.038975 AAGGGAGCGTGGCTAGGA 59.961 61.111 0.00 0.00 39.88 2.94
2912 3213 1.612442 AAGGGAGCGTGGCTAGGAA 60.612 57.895 0.00 0.00 39.88 3.36
2913 3214 1.617947 AAGGGAGCGTGGCTAGGAAG 61.618 60.000 0.00 0.00 39.88 3.46
2926 3234 2.306219 GCTAGGAAGTGGGAAGGAGTTT 59.694 50.000 0.00 0.00 0.00 2.66
3173 3482 2.631062 ACTGTCCTACGGAACAATGTCA 59.369 45.455 0.00 0.00 31.38 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 9.630098 TTCAGAAAGAAAATAGCACAAATCATC 57.370 29.630 0.00 0.00 32.05 2.92
62 63 9.415544 GTTCAGAAAGAAAATAGCACAAATCAT 57.584 29.630 0.00 0.00 38.13 2.45
69 70 8.534778 CAACAAAGTTCAGAAAGAAAATAGCAC 58.465 33.333 0.00 0.00 38.13 4.40
85 86 8.638565 CAAATATGACGGATTTCAACAAAGTTC 58.361 33.333 0.00 0.00 0.00 3.01
103 104 6.037720 ACCGTACGAAATTCATGCAAATATGA 59.962 34.615 18.76 0.00 35.38 2.15
175 176 3.453424 CGGTATCCGTTCATGAACATGA 58.547 45.455 32.06 27.10 42.56 3.07
181 182 0.387929 GCTCCGGTATCCGTTCATGA 59.612 55.000 0.00 0.00 46.80 3.07
186 187 2.413310 AATTTGCTCCGGTATCCGTT 57.587 45.000 0.00 0.00 46.80 4.44
234 235 2.603075 AGCCATGCCTACCAGAAAAA 57.397 45.000 0.00 0.00 0.00 1.94
294 295 4.564769 GCAGCAAGTACAGTCAATCTAGAC 59.435 45.833 0.00 0.00 38.81 2.59
402 408 0.179073 CGGATTGCTCGGAAGTCCAT 60.179 55.000 0.00 0.00 35.14 3.41
404 410 1.084370 CACGGATTGCTCGGAAGTCC 61.084 60.000 0.00 0.00 0.00 3.85
409 415 1.252215 TGTACCACGGATTGCTCGGA 61.252 55.000 0.00 0.00 0.00 4.55
468 712 4.262894 CCACACCACAGTACTACTCCATTT 60.263 45.833 0.00 0.00 0.00 2.32
474 718 1.618837 CAGCCACACCACAGTACTACT 59.381 52.381 0.00 0.00 0.00 2.57
475 719 1.939838 GCAGCCACACCACAGTACTAC 60.940 57.143 0.00 0.00 0.00 2.73
476 720 0.320374 GCAGCCACACCACAGTACTA 59.680 55.000 0.00 0.00 0.00 1.82
493 737 4.680237 CCTCCGCTGGTCAACGCA 62.680 66.667 0.00 0.00 0.00 5.24
536 784 2.270986 GGCCCATCGGATCATTGCC 61.271 63.158 0.00 0.00 0.00 4.52
623 871 1.850345 TGAAGGGAAAGAACACCACCT 59.150 47.619 0.00 0.00 0.00 4.00
629 877 1.210967 ACCACGTGAAGGGAAAGAACA 59.789 47.619 19.30 0.00 0.00 3.18
677 925 5.504994 GGTGTCAGCTGATAAACGTTTGAAA 60.505 40.000 21.47 3.95 0.00 2.69
683 931 1.671850 CCGGTGTCAGCTGATAAACGT 60.672 52.381 27.67 0.00 0.00 3.99
689 937 3.402681 CCCCCGGTGTCAGCTGAT 61.403 66.667 21.47 0.00 0.00 2.90
730 978 4.228912 ACAAACAGAAAAAGCGATCCAG 57.771 40.909 0.00 0.00 0.00 3.86
903 1166 2.203195 GGTGCCACTGTCACTGCA 60.203 61.111 0.00 0.00 34.97 4.41
910 1173 1.079127 GTAGCGATGGTGCCACTGT 60.079 57.895 0.00 0.00 34.65 3.55
924 1187 3.202097 GCTTGAGAAGGAATCTGGTAGC 58.798 50.000 0.00 0.00 38.96 3.58
1023 1286 1.898094 TGAATGCTGCGCTGTGGTT 60.898 52.632 16.05 8.18 0.00 3.67
1072 1335 2.500795 CGAGATCGATCGCTCGCC 60.501 66.667 24.95 15.09 45.97 5.54
1093 1360 3.061848 CGCCCATGGTGGTTGGTC 61.062 66.667 11.73 0.00 35.17 4.02
1128 1395 2.032634 CGAAGCTGTTGCCCGCTAA 61.033 57.895 0.00 0.00 40.80 3.09
1133 1400 1.648467 GGATGACGAAGCTGTTGCCC 61.648 60.000 0.00 0.00 40.80 5.36
1185 1452 0.254154 TAGGTGAGGAGGAGGAGGGA 60.254 60.000 0.00 0.00 0.00 4.20
1186 1453 0.105913 GTAGGTGAGGAGGAGGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
1265 1532 4.639906 TGGTGATGCTGCGTGGCA 62.640 61.111 0.00 6.87 46.63 4.92
1438 1708 4.890306 GGAGCCTCTCCCCCTCCC 62.890 77.778 1.44 0.00 44.36 4.30
1600 1870 1.078759 CTGGAGGACGTTGACGATGC 61.079 60.000 10.87 2.19 43.02 3.91
1619 1889 1.741770 GATGACTGTGTGGTCGGCC 60.742 63.158 0.00 0.00 38.91 6.13
1684 1972 1.154016 CTCACTACCGTCGCAGGTG 60.154 63.158 11.18 4.97 45.54 4.00
1695 1983 1.066303 CTCGTCTCCCATGCTCACTAC 59.934 57.143 0.00 0.00 0.00 2.73
1808 2096 1.599606 GGACCTTCTGCAGAGCGAGA 61.600 60.000 17.43 0.05 0.00 4.04
1926 2214 2.279784 GAGGAAGGATCGCCGCAG 60.280 66.667 0.00 0.00 39.96 5.18
2009 2297 4.357918 AGCCACAAGAAATGTACAGAGT 57.642 40.909 0.33 0.00 41.46 3.24
2010 2298 5.578727 GTCTAGCCACAAGAAATGTACAGAG 59.421 44.000 0.33 0.00 41.46 3.35
2039 2333 6.381801 CCACAAGTAATGTTTGAGTTCATCC 58.618 40.000 0.00 0.00 41.46 3.51
2092 2386 6.648725 AGAGGGTCGTATTAGTCGTATAAGTC 59.351 42.308 0.00 0.00 0.00 3.01
2093 2387 6.529220 AGAGGGTCGTATTAGTCGTATAAGT 58.471 40.000 0.00 0.00 0.00 2.24
2094 2388 6.648310 TGAGAGGGTCGTATTAGTCGTATAAG 59.352 42.308 0.00 0.00 0.00 1.73
2095 2389 6.425114 GTGAGAGGGTCGTATTAGTCGTATAA 59.575 42.308 0.00 0.00 0.00 0.98
2096 2390 5.928839 GTGAGAGGGTCGTATTAGTCGTATA 59.071 44.000 0.00 0.00 0.00 1.47
2097 2391 4.754114 GTGAGAGGGTCGTATTAGTCGTAT 59.246 45.833 0.00 0.00 0.00 3.06
2098 2392 4.122776 GTGAGAGGGTCGTATTAGTCGTA 58.877 47.826 0.00 0.00 0.00 3.43
2099 2393 2.941720 GTGAGAGGGTCGTATTAGTCGT 59.058 50.000 0.00 0.00 0.00 4.34
2100 2394 2.033065 CGTGAGAGGGTCGTATTAGTCG 60.033 54.545 0.00 0.00 0.00 4.18
2103 2397 1.948145 AGCGTGAGAGGGTCGTATTAG 59.052 52.381 0.00 0.00 0.00 1.73
2105 2399 1.183549 AAGCGTGAGAGGGTCGTATT 58.816 50.000 0.00 0.00 0.00 1.89
2134 2428 9.061435 TCTTGAAAACAGAAAACCAAAACAAAT 57.939 25.926 0.00 0.00 0.00 2.32
2136 2430 8.614469 ATCTTGAAAACAGAAAACCAAAACAA 57.386 26.923 0.00 0.00 0.00 2.83
2137 2431 7.062839 CGATCTTGAAAACAGAAAACCAAAACA 59.937 33.333 0.00 0.00 0.00 2.83
2138 2432 7.391016 CGATCTTGAAAACAGAAAACCAAAAC 58.609 34.615 0.00 0.00 0.00 2.43
2145 2439 4.201871 ACACGCGATCTTGAAAACAGAAAA 60.202 37.500 15.93 0.00 0.00 2.29
2165 2459 0.459489 TGCAACCCAAAGCTGAACAC 59.541 50.000 0.00 0.00 0.00 3.32
2179 2473 1.654105 CACCGTCGATTAGAGTGCAAC 59.346 52.381 0.00 0.00 0.00 4.17
2197 2491 6.369065 ACTCATTCGATTTACTTCCTCAACAC 59.631 38.462 0.00 0.00 0.00 3.32
2202 2496 7.009723 GTCAAGACTCATTCGATTTACTTCCTC 59.990 40.741 0.00 0.00 0.00 3.71
2205 2499 7.820044 AGTCAAGACTCATTCGATTTACTTC 57.180 36.000 0.00 0.00 36.92 3.01
2206 2500 8.740906 TCTAGTCAAGACTCATTCGATTTACTT 58.259 33.333 5.91 0.00 42.54 2.24
2218 2512 8.178313 TCACAGTTTTATCTAGTCAAGACTCA 57.822 34.615 5.91 0.00 42.54 3.41
2221 2515 9.477484 TTCTTCACAGTTTTATCTAGTCAAGAC 57.523 33.333 0.00 0.00 36.93 3.01
2234 2528 8.076178 CCTTTACAATCGATTCTTCACAGTTTT 58.924 33.333 7.92 0.00 0.00 2.43
2235 2529 7.444183 TCCTTTACAATCGATTCTTCACAGTTT 59.556 33.333 7.92 0.00 0.00 2.66
2236 2530 6.934645 TCCTTTACAATCGATTCTTCACAGTT 59.065 34.615 7.92 0.00 0.00 3.16
2237 2531 6.464222 TCCTTTACAATCGATTCTTCACAGT 58.536 36.000 7.92 4.01 0.00 3.55
2238 2532 6.968131 TCCTTTACAATCGATTCTTCACAG 57.032 37.500 7.92 0.00 0.00 3.66
2239 2533 6.708502 TGTTCCTTTACAATCGATTCTTCACA 59.291 34.615 7.92 1.13 0.00 3.58
2240 2534 7.129109 TGTTCCTTTACAATCGATTCTTCAC 57.871 36.000 7.92 0.00 0.00 3.18
2241 2535 7.659799 TCTTGTTCCTTTACAATCGATTCTTCA 59.340 33.333 7.92 0.00 37.39 3.02
2242 2536 8.029642 TCTTGTTCCTTTACAATCGATTCTTC 57.970 34.615 7.92 0.00 37.39 2.87
2243 2537 7.979444 TCTTGTTCCTTTACAATCGATTCTT 57.021 32.000 7.92 0.59 37.39 2.52
2244 2538 9.667107 TTATCTTGTTCCTTTACAATCGATTCT 57.333 29.630 7.92 0.00 37.39 2.40
2247 2541 8.765219 CGATTATCTTGTTCCTTTACAATCGAT 58.235 33.333 6.98 0.00 37.55 3.59
2248 2542 7.977293 TCGATTATCTTGTTCCTTTACAATCGA 59.023 33.333 10.48 10.48 39.87 3.59
2249 2543 8.126871 TCGATTATCTTGTTCCTTTACAATCG 57.873 34.615 0.00 0.00 37.39 3.34
2250 2544 9.704098 GTTCGATTATCTTGTTCCTTTACAATC 57.296 33.333 0.00 0.00 37.39 2.67
2251 2545 9.226606 TGTTCGATTATCTTGTTCCTTTACAAT 57.773 29.630 0.00 0.00 37.39 2.71
2252 2546 8.610248 TGTTCGATTATCTTGTTCCTTTACAA 57.390 30.769 0.00 0.00 36.63 2.41
2253 2547 8.610248 TTGTTCGATTATCTTGTTCCTTTACA 57.390 30.769 0.00 0.00 0.00 2.41
2256 2550 8.792633 TCATTTGTTCGATTATCTTGTTCCTTT 58.207 29.630 0.00 0.00 0.00 3.11
2257 2551 8.335532 TCATTTGTTCGATTATCTTGTTCCTT 57.664 30.769 0.00 0.00 0.00 3.36
2258 2552 7.921786 TCATTTGTTCGATTATCTTGTTCCT 57.078 32.000 0.00 0.00 0.00 3.36
2259 2553 9.013490 CAATCATTTGTTCGATTATCTTGTTCC 57.987 33.333 0.00 0.00 30.74 3.62
2260 2554 9.773328 TCAATCATTTGTTCGATTATCTTGTTC 57.227 29.630 0.00 0.00 34.32 3.18
2264 2558 9.655769 CGATTCAATCATTTGTTCGATTATCTT 57.344 29.630 0.00 0.00 39.58 2.40
2265 2559 8.285394 CCGATTCAATCATTTGTTCGATTATCT 58.715 33.333 0.00 0.00 39.58 1.98
2266 2560 8.070171 ACCGATTCAATCATTTGTTCGATTATC 58.930 33.333 0.00 0.00 39.58 1.75
2267 2561 7.857389 CACCGATTCAATCATTTGTTCGATTAT 59.143 33.333 0.00 0.00 39.58 1.28
2268 2562 7.148323 ACACCGATTCAATCATTTGTTCGATTA 60.148 33.333 0.00 0.00 39.58 1.75
2269 2563 6.029607 CACCGATTCAATCATTTGTTCGATT 58.970 36.000 0.00 0.00 39.58 3.34
2270 2564 5.123820 ACACCGATTCAATCATTTGTTCGAT 59.876 36.000 0.00 0.00 39.58 3.59
2271 2565 4.454161 ACACCGATTCAATCATTTGTTCGA 59.546 37.500 0.00 0.00 39.58 3.71
2272 2566 4.722194 ACACCGATTCAATCATTTGTTCG 58.278 39.130 0.00 0.00 38.30 3.95
2273 2567 5.095490 GGACACCGATTCAATCATTTGTTC 58.905 41.667 0.00 0.00 34.32 3.18
2274 2568 4.766891 AGGACACCGATTCAATCATTTGTT 59.233 37.500 0.00 0.00 34.32 2.83
2275 2569 4.335416 AGGACACCGATTCAATCATTTGT 58.665 39.130 0.00 0.00 34.32 2.83
2276 2570 4.970662 AGGACACCGATTCAATCATTTG 57.029 40.909 0.00 0.00 0.00 2.32
2277 2571 5.982890 AAAGGACACCGATTCAATCATTT 57.017 34.783 0.00 0.00 0.00 2.32
2278 2572 7.339212 TCAATAAAGGACACCGATTCAATCATT 59.661 33.333 0.00 0.00 0.00 2.57
2279 2573 6.828273 TCAATAAAGGACACCGATTCAATCAT 59.172 34.615 0.00 0.00 0.00 2.45
2280 2574 6.176896 TCAATAAAGGACACCGATTCAATCA 58.823 36.000 0.00 0.00 0.00 2.57
2281 2575 6.677781 TCAATAAAGGACACCGATTCAATC 57.322 37.500 0.00 0.00 0.00 2.67
2282 2576 6.828273 TCATCAATAAAGGACACCGATTCAAT 59.172 34.615 0.00 0.00 0.00 2.57
2283 2577 6.176896 TCATCAATAAAGGACACCGATTCAA 58.823 36.000 0.00 0.00 0.00 2.69
2284 2578 5.739959 TCATCAATAAAGGACACCGATTCA 58.260 37.500 0.00 0.00 0.00 2.57
2285 2579 6.867662 ATCATCAATAAAGGACACCGATTC 57.132 37.500 0.00 0.00 0.00 2.52
2286 2580 6.828273 TCAATCATCAATAAAGGACACCGATT 59.172 34.615 0.00 0.00 0.00 3.34
2287 2581 6.260936 GTCAATCATCAATAAAGGACACCGAT 59.739 38.462 0.00 0.00 0.00 4.18
2288 2582 5.584649 GTCAATCATCAATAAAGGACACCGA 59.415 40.000 0.00 0.00 0.00 4.69
2289 2583 5.353956 TGTCAATCATCAATAAAGGACACCG 59.646 40.000 0.00 0.00 0.00 4.94
2290 2584 6.757897 TGTCAATCATCAATAAAGGACACC 57.242 37.500 0.00 0.00 0.00 4.16
2291 2585 6.694411 GCATGTCAATCATCAATAAAGGACAC 59.306 38.462 0.00 0.00 36.92 3.67
2292 2586 6.604396 AGCATGTCAATCATCAATAAAGGACA 59.396 34.615 0.00 0.00 38.26 4.02
2293 2587 7.035840 AGCATGTCAATCATCAATAAAGGAC 57.964 36.000 0.00 0.00 34.09 3.85
2294 2588 8.929260 ATAGCATGTCAATCATCAATAAAGGA 57.071 30.769 0.00 0.00 34.09 3.36
2295 2589 9.976511 AAATAGCATGTCAATCATCAATAAAGG 57.023 29.630 0.00 0.00 34.09 3.11
2305 2599 8.795513 CCCATTGTATAAATAGCATGTCAATCA 58.204 33.333 0.00 0.00 0.00 2.57
2306 2600 9.013229 TCCCATTGTATAAATAGCATGTCAATC 57.987 33.333 0.00 0.00 0.00 2.67
2307 2601 8.938801 TCCCATTGTATAAATAGCATGTCAAT 57.061 30.769 0.00 0.00 0.00 2.57
2308 2602 8.629158 GTTCCCATTGTATAAATAGCATGTCAA 58.371 33.333 0.00 0.00 0.00 3.18
2309 2603 7.230510 GGTTCCCATTGTATAAATAGCATGTCA 59.769 37.037 0.00 0.00 0.00 3.58
2310 2604 7.573096 CGGTTCCCATTGTATAAATAGCATGTC 60.573 40.741 0.00 0.00 0.00 3.06
2311 2605 6.206634 CGGTTCCCATTGTATAAATAGCATGT 59.793 38.462 0.00 0.00 0.00 3.21
2312 2606 6.206634 ACGGTTCCCATTGTATAAATAGCATG 59.793 38.462 0.00 0.00 0.00 4.06
2313 2607 6.303839 ACGGTTCCCATTGTATAAATAGCAT 58.696 36.000 0.00 0.00 0.00 3.79
2314 2608 5.686753 ACGGTTCCCATTGTATAAATAGCA 58.313 37.500 0.00 0.00 0.00 3.49
2315 2609 5.107220 CGACGGTTCCCATTGTATAAATAGC 60.107 44.000 0.00 0.00 0.00 2.97
2316 2610 5.107220 GCGACGGTTCCCATTGTATAAATAG 60.107 44.000 0.00 0.00 0.00 1.73
2317 2611 4.751098 GCGACGGTTCCCATTGTATAAATA 59.249 41.667 0.00 0.00 0.00 1.40
2318 2612 3.562557 GCGACGGTTCCCATTGTATAAAT 59.437 43.478 0.00 0.00 0.00 1.40
2319 2613 2.937799 GCGACGGTTCCCATTGTATAAA 59.062 45.455 0.00 0.00 0.00 1.40
2320 2614 2.553086 GCGACGGTTCCCATTGTATAA 58.447 47.619 0.00 0.00 0.00 0.98
2321 2615 1.202557 GGCGACGGTTCCCATTGTATA 60.203 52.381 0.00 0.00 0.00 1.47
2322 2616 0.463116 GGCGACGGTTCCCATTGTAT 60.463 55.000 0.00 0.00 0.00 2.29
2323 2617 1.078988 GGCGACGGTTCCCATTGTA 60.079 57.895 0.00 0.00 0.00 2.41
2324 2618 2.359478 GGCGACGGTTCCCATTGT 60.359 61.111 0.00 0.00 0.00 2.71
2325 2619 2.046314 AGGCGACGGTTCCCATTG 60.046 61.111 0.00 0.00 0.00 2.82
2326 2620 1.910580 ATGAGGCGACGGTTCCCATT 61.911 55.000 0.00 0.00 0.00 3.16
2327 2621 1.046472 TATGAGGCGACGGTTCCCAT 61.046 55.000 0.00 0.00 0.00 4.00
2328 2622 1.672854 CTATGAGGCGACGGTTCCCA 61.673 60.000 0.00 0.00 0.00 4.37
2329 2623 1.067582 CTATGAGGCGACGGTTCCC 59.932 63.158 0.00 0.00 0.00 3.97
2330 2624 1.067582 CCTATGAGGCGACGGTTCC 59.932 63.158 0.00 0.00 0.00 3.62
2331 2625 1.067582 CCCTATGAGGCGACGGTTC 59.932 63.158 0.00 0.00 32.73 3.62
2332 2626 1.380785 TCCCTATGAGGCGACGGTT 60.381 57.895 0.00 0.00 32.73 4.44
2333 2627 2.125961 GTCCCTATGAGGCGACGGT 61.126 63.158 0.00 0.00 32.73 4.83
2334 2628 2.728817 GTCCCTATGAGGCGACGG 59.271 66.667 0.00 0.00 32.73 4.79
2335 2629 2.331805 CGTCCCTATGAGGCGACG 59.668 66.667 16.65 16.65 45.39 5.12
2336 2630 2.027751 GCGTCCCTATGAGGCGAC 59.972 66.667 0.00 0.00 44.11 5.19
2340 2634 1.290324 CCATCGCGTCCCTATGAGG 59.710 63.158 5.77 0.00 34.30 3.86
2341 2635 0.389391 AACCATCGCGTCCCTATGAG 59.611 55.000 5.77 0.00 0.00 2.90
2342 2636 0.387929 GAACCATCGCGTCCCTATGA 59.612 55.000 5.77 0.00 0.00 2.15
2343 2637 0.104120 TGAACCATCGCGTCCCTATG 59.896 55.000 5.77 1.24 0.00 2.23
2344 2638 0.828022 TTGAACCATCGCGTCCCTAT 59.172 50.000 5.77 0.00 0.00 2.57
2345 2639 0.174845 CTTGAACCATCGCGTCCCTA 59.825 55.000 5.77 0.00 0.00 3.53
2346 2640 1.079127 CTTGAACCATCGCGTCCCT 60.079 57.895 5.77 0.00 0.00 4.20
2347 2641 1.079405 TCTTGAACCATCGCGTCCC 60.079 57.895 5.77 0.00 0.00 4.46
2348 2642 1.084370 CCTCTTGAACCATCGCGTCC 61.084 60.000 5.77 0.00 0.00 4.79
2349 2643 1.696832 GCCTCTTGAACCATCGCGTC 61.697 60.000 5.77 0.00 0.00 5.19
2350 2644 1.741770 GCCTCTTGAACCATCGCGT 60.742 57.895 5.77 0.00 0.00 6.01
2351 2645 1.091771 ATGCCTCTTGAACCATCGCG 61.092 55.000 0.00 0.00 0.00 5.87
2352 2646 0.659957 GATGCCTCTTGAACCATCGC 59.340 55.000 0.00 0.00 0.00 4.58
2354 2648 2.029838 ACGATGCCTCTTGAACCATC 57.970 50.000 0.00 0.00 0.00 3.51
2355 2649 2.359900 GAACGATGCCTCTTGAACCAT 58.640 47.619 0.00 0.00 0.00 3.55
2356 2650 1.610624 GGAACGATGCCTCTTGAACCA 60.611 52.381 0.00 0.00 0.00 3.67
2357 2651 1.087501 GGAACGATGCCTCTTGAACC 58.912 55.000 0.00 0.00 0.00 3.62
2358 2652 1.734465 CTGGAACGATGCCTCTTGAAC 59.266 52.381 0.00 0.00 0.00 3.18
2359 2653 1.339055 CCTGGAACGATGCCTCTTGAA 60.339 52.381 0.00 0.00 0.00 2.69
2360 2654 0.250234 CCTGGAACGATGCCTCTTGA 59.750 55.000 0.00 0.00 0.00 3.02
2361 2655 1.372087 GCCTGGAACGATGCCTCTTG 61.372 60.000 0.00 0.00 0.00 3.02
2362 2656 1.078143 GCCTGGAACGATGCCTCTT 60.078 57.895 0.00 0.00 0.00 2.85
2363 2657 1.992277 AGCCTGGAACGATGCCTCT 60.992 57.895 0.00 0.00 0.00 3.69
2364 2658 1.817099 CAGCCTGGAACGATGCCTC 60.817 63.158 0.00 0.00 0.00 4.70
2365 2659 2.270205 CAGCCTGGAACGATGCCT 59.730 61.111 0.00 0.00 0.00 4.75
2366 2660 3.512516 GCAGCCTGGAACGATGCC 61.513 66.667 0.00 0.00 0.00 4.40
2367 2661 2.334946 TTGCAGCCTGGAACGATGC 61.335 57.895 0.00 0.00 37.40 3.91
2368 2662 1.503542 GTTGCAGCCTGGAACGATG 59.496 57.895 13.44 0.00 38.83 3.84
2369 2663 3.987404 GTTGCAGCCTGGAACGAT 58.013 55.556 13.44 0.00 38.83 3.73
2372 2666 2.281484 TCGGTTGCAGCCTGGAAC 60.281 61.111 19.55 19.55 46.14 3.62
2373 2667 2.281484 GTCGGTTGCAGCCTGGAA 60.281 61.111 18.19 0.00 0.00 3.53
2374 2668 2.894257 ATGTCGGTTGCAGCCTGGA 61.894 57.895 18.19 5.53 0.00 3.86
2375 2669 2.360350 ATGTCGGTTGCAGCCTGG 60.360 61.111 18.19 2.94 0.00 4.45
2376 2670 2.872557 CATGTCGGTTGCAGCCTG 59.127 61.111 18.19 11.15 0.00 4.85
2377 2671 3.058160 GCATGTCGGTTGCAGCCT 61.058 61.111 18.19 0.00 39.90 4.58
2378 2672 4.120331 GGCATGTCGGTTGCAGCC 62.120 66.667 10.00 10.00 41.95 4.85
2379 2673 4.465512 CGGCATGTCGGTTGCAGC 62.466 66.667 12.98 0.00 41.95 5.25
2380 2674 3.803082 CCGGCATGTCGGTTGCAG 61.803 66.667 30.40 3.53 44.60 4.41
2393 2687 0.874607 CCACGATACTAGCAACCGGC 60.875 60.000 0.00 0.00 45.30 6.13
2394 2688 0.742505 TCCACGATACTAGCAACCGG 59.257 55.000 0.00 0.00 0.00 5.28
2395 2689 2.190981 GTTCCACGATACTAGCAACCG 58.809 52.381 0.00 0.00 0.00 4.44
2396 2690 2.547826 GGTTCCACGATACTAGCAACC 58.452 52.381 0.00 0.00 0.00 3.77
2397 2691 2.190981 CGGTTCCACGATACTAGCAAC 58.809 52.381 0.00 0.00 35.47 4.17
2398 2692 1.470285 GCGGTTCCACGATACTAGCAA 60.470 52.381 0.00 0.00 35.47 3.91
2399 2693 0.101759 GCGGTTCCACGATACTAGCA 59.898 55.000 0.00 0.00 35.47 3.49
2400 2694 0.101759 TGCGGTTCCACGATACTAGC 59.898 55.000 0.00 0.00 35.47 3.42
2401 2695 1.836383 GTGCGGTTCCACGATACTAG 58.164 55.000 0.00 0.00 35.47 2.57
2403 2697 4.904466 GTGCGGTTCCACGATACT 57.096 55.556 0.00 0.00 35.47 2.12
2418 2712 4.547367 GGAATCCCCGCTCCCGTG 62.547 72.222 0.00 0.00 0.00 4.94
2429 2723 3.483421 CTTACGGTTATTGGGGGAATCC 58.517 50.000 0.00 0.00 0.00 3.01
2430 2724 3.483421 CCTTACGGTTATTGGGGGAATC 58.517 50.000 0.00 0.00 0.00 2.52
2431 2725 2.176148 CCCTTACGGTTATTGGGGGAAT 59.824 50.000 0.00 0.00 34.71 3.01
2432 2726 1.565288 CCCTTACGGTTATTGGGGGAA 59.435 52.381 0.00 0.00 34.71 3.97
2433 2727 1.215140 CCCTTACGGTTATTGGGGGA 58.785 55.000 0.00 0.00 34.71 4.81
2434 2728 0.921166 ACCCTTACGGTTATTGGGGG 59.079 55.000 0.00 0.00 45.36 5.40
2444 2738 5.928264 CCCGTTAAGATAATAACCCTTACGG 59.072 44.000 0.00 0.00 37.13 4.02
2445 2739 6.515832 ACCCGTTAAGATAATAACCCTTACG 58.484 40.000 0.00 0.00 33.19 3.18
2446 2740 7.169813 CGAACCCGTTAAGATAATAACCCTTAC 59.830 40.741 0.00 0.00 33.19 2.34
2447 2741 7.209475 CGAACCCGTTAAGATAATAACCCTTA 58.791 38.462 0.00 0.00 33.19 2.69
2448 2742 6.051074 CGAACCCGTTAAGATAATAACCCTT 58.949 40.000 0.00 0.00 33.19 3.95
2449 2743 5.453762 CCGAACCCGTTAAGATAATAACCCT 60.454 44.000 0.00 0.00 33.19 4.34
2450 2744 4.751600 CCGAACCCGTTAAGATAATAACCC 59.248 45.833 0.00 0.00 33.19 4.11
2451 2745 4.212004 GCCGAACCCGTTAAGATAATAACC 59.788 45.833 0.00 0.00 33.19 2.85
2452 2746 5.052481 AGCCGAACCCGTTAAGATAATAAC 58.948 41.667 0.00 0.00 33.40 1.89
2453 2747 5.280654 AGCCGAACCCGTTAAGATAATAA 57.719 39.130 0.00 0.00 0.00 1.40
2454 2748 4.262164 GGAGCCGAACCCGTTAAGATAATA 60.262 45.833 0.00 0.00 0.00 0.98
2455 2749 3.493873 GGAGCCGAACCCGTTAAGATAAT 60.494 47.826 0.00 0.00 0.00 1.28
2456 2750 2.159057 GGAGCCGAACCCGTTAAGATAA 60.159 50.000 0.00 0.00 0.00 1.75
2457 2751 1.410153 GGAGCCGAACCCGTTAAGATA 59.590 52.381 0.00 0.00 0.00 1.98
2458 2752 0.177373 GGAGCCGAACCCGTTAAGAT 59.823 55.000 0.00 0.00 0.00 2.40
2459 2753 0.901580 AGGAGCCGAACCCGTTAAGA 60.902 55.000 0.00 0.00 0.00 2.10
2460 2754 0.459759 GAGGAGCCGAACCCGTTAAG 60.460 60.000 0.00 0.00 0.00 1.85
2461 2755 0.901580 AGAGGAGCCGAACCCGTTAA 60.902 55.000 0.00 0.00 0.00 2.01
2462 2756 1.304713 AGAGGAGCCGAACCCGTTA 60.305 57.895 0.00 0.00 0.00 3.18
2463 2757 2.603776 AGAGGAGCCGAACCCGTT 60.604 61.111 0.00 0.00 0.00 4.44
2496 2790 1.504359 GCAGCTACAACACCGTACAA 58.496 50.000 0.00 0.00 0.00 2.41
2522 2817 5.708697 GCCATCAGATTGTAATGGATGATGA 59.291 40.000 13.11 0.00 44.22 2.92
2525 2820 5.072736 AGAGCCATCAGATTGTAATGGATGA 59.927 40.000 13.34 3.29 39.19 2.92
2551 2846 2.171840 CGAGGAGAAGGAAGGAGACAA 58.828 52.381 0.00 0.00 0.00 3.18
2655 2950 0.173481 GCTACGGATGACAGCAGTGA 59.827 55.000 6.75 0.00 35.35 3.41
2886 3187 1.880646 GCCACGCTCCCTTGAAAACTA 60.881 52.381 0.00 0.00 0.00 2.24
2890 3191 0.036388 CTAGCCACGCTCCCTTGAAA 60.036 55.000 0.00 0.00 40.44 2.69
2894 3195 1.612442 TTCCTAGCCACGCTCCCTT 60.612 57.895 0.00 0.00 40.44 3.95
2907 3208 3.073946 CCAAAACTCCTTCCCACTTCCTA 59.926 47.826 0.00 0.00 0.00 2.94
2908 3209 2.158460 CCAAAACTCCTTCCCACTTCCT 60.158 50.000 0.00 0.00 0.00 3.36
2909 3210 2.239400 CCAAAACTCCTTCCCACTTCC 58.761 52.381 0.00 0.00 0.00 3.46
2910 3211 1.613925 GCCAAAACTCCTTCCCACTTC 59.386 52.381 0.00 0.00 0.00 3.01
2911 3212 1.063266 TGCCAAAACTCCTTCCCACTT 60.063 47.619 0.00 0.00 0.00 3.16
2912 3213 0.555769 TGCCAAAACTCCTTCCCACT 59.444 50.000 0.00 0.00 0.00 4.00
2913 3214 1.408969 TTGCCAAAACTCCTTCCCAC 58.591 50.000 0.00 0.00 0.00 4.61
3173 3482 4.665483 AGAATTTTCTCTCCCCGGGAATAT 59.335 41.667 26.32 5.46 29.94 1.28


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

AutoCloner maintained by Alex Coulton.