Multiple sequence alignment - TraesCS1B01G248300

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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 TraesCS1B01G248300 chr1B 100.000 4972 0 0 1 4972 439429150 439434121 0.000000e+00 9182
1 TraesCS1B01G248300 chr1D 90.763 2176 110 31 2319 4455 326152499 326154622 0.000000e+00 2820
2 TraesCS1B01G248300 chr1D 98.109 1322 23 2 836 2156 326146562 326147882 0.000000e+00 2302
3 TraesCS1B01G248300 chr1D 96.158 859 28 3 1 854 326145690 326146548 0.000000e+00 1399
4 TraesCS1B01G248300 chr1D 85.170 499 44 13 4502 4972 326154627 326155123 7.480000e-133 484
5 TraesCS1B01G248300 chr1D 81.351 370 53 11 4463 4818 294746418 294746785 2.260000e-73 287
6 TraesCS1B01G248300 chr1A 95.241 1513 55 4 659 2156 415581864 415583374 0.000000e+00 2379
7 TraesCS1B01G248300 chr1A 90.776 1778 75 22 2319 4064 415583507 415585227 0.000000e+00 2292
8 TraesCS1B01G248300 chr1A 92.945 652 27 4 1 647 415581117 415581754 0.000000e+00 931
9 TraesCS1B01G248300 chr1A 87.582 153 8 3 4154 4296 415585242 415585393 3.080000e-37 167
10 TraesCS1B01G248300 chr4A 93.127 291 17 1 1 288 38728528 38728818 1.650000e-114 424
11 TraesCS1B01G248300 chr4A 80.870 345 49 12 4486 4818 666369638 666369977 6.390000e-64 255
12 TraesCS1B01G248300 chr5A 92.281 285 22 0 4 288 478834202 478833918 5.990000e-109 405
13 TraesCS1B01G248300 chr3A 91.667 288 20 3 4 288 692538428 692538142 3.610000e-106 396
14 TraesCS1B01G248300 chr3A 88.845 251 19 9 4579 4823 723562595 723562348 2.910000e-77 300
15 TraesCS1B01G248300 chr3A 81.287 171 21 3 4463 4632 710673867 710673707 1.450000e-25 128
16 TraesCS1B01G248300 chr4B 83.714 350 47 8 4474 4818 460159409 460159065 6.210000e-84 322
17 TraesCS1B01G248300 chr6D 83.333 354 50 9 4464 4814 136464173 136463826 8.030000e-83 318
18 TraesCS1B01G248300 chr7D 83.768 345 38 13 4486 4818 5434349 5434011 1.340000e-80 311
19 TraesCS1B01G248300 chr7D 82.162 370 49 12 4472 4828 401784046 401784411 8.090000e-78 302
20 TraesCS1B01G248300 chr6B 82.571 350 52 8 4464 4810 234675324 234674981 2.910000e-77 300
21 TraesCS1B01G248300 chr3D 88.750 80 9 0 4326 4405 141185110 141185189 1.140000e-16 99


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 TraesCS1B01G248300 chr1B 439429150 439434121 4971 False 9182.00 9182 100.0000 1 4972 1 chr1B.!!$F1 4971
1 TraesCS1B01G248300 chr1D 326145690 326147882 2192 False 1850.50 2302 97.1335 1 2156 2 chr1D.!!$F2 2155
2 TraesCS1B01G248300 chr1D 326152499 326155123 2624 False 1652.00 2820 87.9665 2319 4972 2 chr1D.!!$F3 2653
3 TraesCS1B01G248300 chr1A 415581117 415585393 4276 False 1442.25 2379 91.6360 1 4296 4 chr1A.!!$F1 4295

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
29 30 0.607489 CTGTGCCCAAGACCAAGAGG 60.607 60.000 0.00 0.00 42.21 3.69 F
38 39 2.048127 ACCAAGAGGCGAGCGTTC 60.048 61.111 0.00 0.00 39.06 3.95 F
928 1067 3.492421 TTTCGCTCAAATCAAGGATGC 57.508 42.857 0.00 0.00 0.00 3.91 F
2449 2630 0.321564 TGAGTTCATCACAAGGGCCG 60.322 55.000 0.00 0.00 31.12 6.13 F
3212 3439 0.391263 CGGACCTACCTTGGCAAGTC 60.391 60.000 24.57 15.74 36.31 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1347 1501 1.295357 CGCAGCGGTGAACCATGTTA 61.295 55.000 20.69 0.00 35.14 2.41 R
1365 1519 2.126888 GCGGCACCACAAACATCG 60.127 61.111 0.00 0.00 0.00 3.84 R
2463 2644 0.033781 TGGTACCTTCCGGAACAACG 59.966 55.000 14.35 3.14 0.00 4.10 R
3381 3608 0.250295 TCCTCCTCGTTTTGCCACAG 60.250 55.000 0.00 0.00 0.00 3.66 R
4646 4929 0.038166 GAGGAGTGGTGGGCATGAAA 59.962 55.000 0.00 0.00 0.00 2.69 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
29 30 0.607489 CTGTGCCCAAGACCAAGAGG 60.607 60.000 0.00 0.00 42.21 3.69
38 39 2.048127 ACCAAGAGGCGAGCGTTC 60.048 61.111 0.00 0.00 39.06 3.95
69 70 5.416952 ACCCTGTTCAGAAAAATATGCTGAG 59.583 40.000 1.00 0.00 39.56 3.35
168 170 8.928270 AAAGTATCAGTTAATCAGTAAGTCGG 57.072 34.615 0.00 0.00 0.00 4.79
210 212 5.116882 ACACTAAAGGTCTCAACAAGTGTC 58.883 41.667 0.00 0.00 41.51 3.67
260 262 5.636543 CCAATTTTCTCCTCAATTTCTGCAC 59.363 40.000 0.00 0.00 0.00 4.57
552 560 4.080356 CCTGATCCCTTGACATAGAAACCA 60.080 45.833 0.00 0.00 0.00 3.67
928 1067 3.492421 TTTCGCTCAAATCAAGGATGC 57.508 42.857 0.00 0.00 0.00 3.91
1026 1180 6.381420 TGGACTGGTTGAAGGAACAATTTAAA 59.619 34.615 0.00 0.00 36.12 1.52
1123 1277 6.147821 CACTGTTGGTATACTCAGTCTTTTGG 59.852 42.308 18.42 8.83 38.79 3.28
1126 1280 4.575885 TGGTATACTCAGTCTTTTGGTGC 58.424 43.478 2.25 0.00 0.00 5.01
1347 1501 5.397221 CCTTGGGACAGTGATAACATCAGAT 60.397 44.000 0.00 0.00 42.39 2.90
1365 1519 1.064060 GATAACATGGTTCACCGCTGC 59.936 52.381 0.00 0.00 39.43 5.25
1413 1567 4.240888 CGATCTGCTCTTCAAACTCTCAA 58.759 43.478 0.00 0.00 0.00 3.02
1799 1953 3.081804 ACCGAGGTAAAAGGCAGAAATG 58.918 45.455 0.00 0.00 0.00 2.32
1972 2126 4.618460 GCGAGAGTGATTGTAAAGAGGTCA 60.618 45.833 0.00 0.00 0.00 4.02
2142 2296 3.832490 GGCTACATTTCCTTTTGAACCCT 59.168 43.478 0.00 0.00 31.05 4.34
2161 2315 3.987547 CCTGTGCAGGTCTATGTCATAG 58.012 50.000 12.95 12.95 43.61 2.23
2166 2320 4.098654 GTGCAGGTCTATGTCATAGTCACT 59.901 45.833 17.55 11.90 34.47 3.41
2167 2321 5.299531 GTGCAGGTCTATGTCATAGTCACTA 59.700 44.000 17.55 0.00 34.47 2.74
2168 2322 5.299531 TGCAGGTCTATGTCATAGTCACTAC 59.700 44.000 17.55 9.23 34.47 2.73
2170 2324 6.015856 GCAGGTCTATGTCATAGTCACTACAT 60.016 42.308 17.55 5.16 36.56 2.29
2199 2375 7.624549 ACTAGTGAACATTATCATCAACCTGT 58.375 34.615 0.00 0.00 0.00 4.00
2209 2385 8.739039 CATTATCATCAACCTGTTGTTTTCCTA 58.261 33.333 9.65 0.00 41.16 2.94
2213 2389 8.279970 TCATCAACCTGTTGTTTTCCTATATG 57.720 34.615 9.65 3.77 41.16 1.78
2215 2391 7.447374 TCAACCTGTTGTTTTCCTATATGTG 57.553 36.000 9.65 0.00 41.16 3.21
2216 2392 7.001674 TCAACCTGTTGTTTTCCTATATGTGT 58.998 34.615 9.65 0.00 41.16 3.72
2217 2393 6.817765 ACCTGTTGTTTTCCTATATGTGTG 57.182 37.500 0.00 0.00 0.00 3.82
2219 2395 7.001674 ACCTGTTGTTTTCCTATATGTGTGAA 58.998 34.615 0.00 0.00 0.00 3.18
2220 2396 7.040686 ACCTGTTGTTTTCCTATATGTGTGAAC 60.041 37.037 0.00 0.00 0.00 3.18
2221 2397 7.209471 TGTTGTTTTCCTATATGTGTGAACC 57.791 36.000 0.00 0.00 0.00 3.62
2222 2398 6.773200 TGTTGTTTTCCTATATGTGTGAACCA 59.227 34.615 0.00 0.00 0.00 3.67
2224 2400 8.952278 GTTGTTTTCCTATATGTGTGAACCATA 58.048 33.333 0.00 0.00 0.00 2.74
2225 2401 9.693739 TTGTTTTCCTATATGTGTGAACCATAT 57.306 29.630 0.00 0.00 38.64 1.78
2226 2402 9.119418 TGTTTTCCTATATGTGTGAACCATATG 57.881 33.333 0.00 0.00 36.45 1.78
2227 2403 8.567948 GTTTTCCTATATGTGTGAACCATATGG 58.432 37.037 20.68 20.68 36.45 2.74
2258 2434 5.928601 GTAGAATACAGTAACTGCGTCAC 57.071 43.478 0.00 0.00 42.43 3.67
2259 2435 4.514781 AGAATACAGTAACTGCGTCACA 57.485 40.909 0.00 0.00 34.37 3.58
2261 2437 6.203808 AGAATACAGTAACTGCGTCACATA 57.796 37.500 0.00 0.00 34.37 2.29
2262 2438 6.806751 AGAATACAGTAACTGCGTCACATAT 58.193 36.000 0.00 0.00 34.37 1.78
2263 2439 7.265673 AGAATACAGTAACTGCGTCACATATT 58.734 34.615 0.00 0.00 34.37 1.28
2264 2440 6.828502 ATACAGTAACTGCGTCACATATTG 57.171 37.500 0.00 0.00 34.37 1.90
2265 2441 3.932710 ACAGTAACTGCGTCACATATTGG 59.067 43.478 0.00 0.00 34.37 3.16
2266 2442 3.309682 CAGTAACTGCGTCACATATTGGG 59.690 47.826 0.00 0.00 0.00 4.12
2267 2443 2.489938 AACTGCGTCACATATTGGGT 57.510 45.000 0.00 0.00 0.00 4.51
2268 2444 3.620427 AACTGCGTCACATATTGGGTA 57.380 42.857 0.00 0.00 0.00 3.69
2269 2445 2.901249 ACTGCGTCACATATTGGGTAC 58.099 47.619 0.00 0.00 0.00 3.34
2270 2446 2.500098 ACTGCGTCACATATTGGGTACT 59.500 45.455 0.00 0.00 0.00 2.73
2271 2447 3.055385 ACTGCGTCACATATTGGGTACTT 60.055 43.478 0.00 0.00 0.00 2.24
2272 2448 3.527533 TGCGTCACATATTGGGTACTTC 58.472 45.455 0.00 0.00 0.00 3.01
2273 2449 3.196901 TGCGTCACATATTGGGTACTTCT 59.803 43.478 0.00 0.00 0.00 2.85
2274 2450 4.403113 TGCGTCACATATTGGGTACTTCTA 59.597 41.667 0.00 0.00 0.00 2.10
2275 2451 5.069914 TGCGTCACATATTGGGTACTTCTAT 59.930 40.000 0.00 0.00 0.00 1.98
2276 2452 5.634020 GCGTCACATATTGGGTACTTCTATC 59.366 44.000 0.00 0.00 0.00 2.08
2277 2453 6.157211 CGTCACATATTGGGTACTTCTATCC 58.843 44.000 0.00 0.00 0.00 2.59
2278 2454 6.015350 CGTCACATATTGGGTACTTCTATCCT 60.015 42.308 0.00 0.00 0.00 3.24
2279 2455 7.471539 CGTCACATATTGGGTACTTCTATCCTT 60.472 40.741 0.00 0.00 0.00 3.36
2280 2456 8.211629 GTCACATATTGGGTACTTCTATCCTTT 58.788 37.037 0.00 0.00 0.00 3.11
2281 2457 9.442062 TCACATATTGGGTACTTCTATCCTTTA 57.558 33.333 0.00 0.00 0.00 1.85
2286 2462 6.461110 TGGGTACTTCTATCCTTTAACTCG 57.539 41.667 0.00 0.00 0.00 4.18
2287 2463 5.954150 TGGGTACTTCTATCCTTTAACTCGT 59.046 40.000 0.00 0.00 0.00 4.18
2288 2464 6.096001 TGGGTACTTCTATCCTTTAACTCGTC 59.904 42.308 0.00 0.00 0.00 4.20
2289 2465 6.460814 GGGTACTTCTATCCTTTAACTCGTCC 60.461 46.154 0.00 0.00 0.00 4.79
2290 2466 6.096001 GGTACTTCTATCCTTTAACTCGTCCA 59.904 42.308 0.00 0.00 0.00 4.02
2291 2467 6.793505 ACTTCTATCCTTTAACTCGTCCAT 57.206 37.500 0.00 0.00 0.00 3.41
2292 2468 7.893124 ACTTCTATCCTTTAACTCGTCCATA 57.107 36.000 0.00 0.00 0.00 2.74
2293 2469 8.480133 ACTTCTATCCTTTAACTCGTCCATAT 57.520 34.615 0.00 0.00 0.00 1.78
2294 2470 8.361139 ACTTCTATCCTTTAACTCGTCCATATG 58.639 37.037 0.00 0.00 0.00 1.78
2295 2471 6.688578 TCTATCCTTTAACTCGTCCATATGC 58.311 40.000 0.00 0.00 0.00 3.14
2296 2472 5.552870 ATCCTTTAACTCGTCCATATGCT 57.447 39.130 0.00 0.00 0.00 3.79
2297 2473 4.945246 TCCTTTAACTCGTCCATATGCTC 58.055 43.478 0.00 0.00 0.00 4.26
2298 2474 4.649674 TCCTTTAACTCGTCCATATGCTCT 59.350 41.667 0.00 0.00 0.00 4.09
2299 2475 5.128827 TCCTTTAACTCGTCCATATGCTCTT 59.871 40.000 0.00 0.00 0.00 2.85
2300 2476 5.817816 CCTTTAACTCGTCCATATGCTCTTT 59.182 40.000 0.00 0.00 0.00 2.52
2301 2477 6.018669 CCTTTAACTCGTCCATATGCTCTTTC 60.019 42.308 0.00 0.00 0.00 2.62
2302 2478 4.744795 AACTCGTCCATATGCTCTTTCT 57.255 40.909 0.00 0.00 0.00 2.52
2303 2479 4.744795 ACTCGTCCATATGCTCTTTCTT 57.255 40.909 0.00 0.00 0.00 2.52
2304 2480 4.688021 ACTCGTCCATATGCTCTTTCTTC 58.312 43.478 0.00 0.00 0.00 2.87
2305 2481 4.160439 ACTCGTCCATATGCTCTTTCTTCA 59.840 41.667 0.00 0.00 0.00 3.02
2306 2482 4.433615 TCGTCCATATGCTCTTTCTTCAC 58.566 43.478 0.00 0.00 0.00 3.18
2307 2483 4.081697 TCGTCCATATGCTCTTTCTTCACA 60.082 41.667 0.00 0.00 0.00 3.58
2308 2484 4.269603 CGTCCATATGCTCTTTCTTCACAG 59.730 45.833 0.00 0.00 0.00 3.66
2309 2485 4.574013 GTCCATATGCTCTTTCTTCACAGG 59.426 45.833 0.00 0.00 0.00 4.00
2310 2486 4.471025 TCCATATGCTCTTTCTTCACAGGA 59.529 41.667 0.00 0.00 0.00 3.86
2311 2487 5.045651 TCCATATGCTCTTTCTTCACAGGAA 60.046 40.000 0.00 0.00 0.00 3.36
2312 2488 5.649395 CCATATGCTCTTTCTTCACAGGAAA 59.351 40.000 0.00 0.00 31.35 3.13
2313 2489 6.320672 CCATATGCTCTTTCTTCACAGGAAAT 59.679 38.462 0.00 0.00 33.12 2.17
2314 2490 5.893897 ATGCTCTTTCTTCACAGGAAATC 57.106 39.130 0.00 0.00 33.12 2.17
2315 2491 4.074970 TGCTCTTTCTTCACAGGAAATCC 58.925 43.478 0.00 0.00 33.12 3.01
2316 2492 4.074970 GCTCTTTCTTCACAGGAAATCCA 58.925 43.478 1.67 0.00 38.89 3.41
2317 2493 4.704057 GCTCTTTCTTCACAGGAAATCCAT 59.296 41.667 1.67 0.00 38.89 3.41
2348 2524 6.654582 TGATGCCATATATTAATCGCACAACT 59.345 34.615 0.00 0.00 0.00 3.16
2349 2525 6.239908 TGCCATATATTAATCGCACAACTG 57.760 37.500 0.00 0.00 0.00 3.16
2356 2533 4.921470 TTAATCGCACAACTGACTTAGC 57.079 40.909 0.00 0.00 0.00 3.09
2359 2536 2.556257 TCGCACAACTGACTTAGCAAA 58.444 42.857 0.00 0.00 0.00 3.68
2365 2542 5.519927 GCACAACTGACTTAGCAAATTTTGT 59.480 36.000 10.65 1.20 0.00 2.83
2373 2550 7.939782 TGACTTAGCAAATTTTGTTCAGATCA 58.060 30.769 12.37 9.62 0.00 2.92
2449 2630 0.321564 TGAGTTCATCACAAGGGCCG 60.322 55.000 0.00 0.00 31.12 6.13
2473 2654 0.796312 CAGGATTGTCGTTGTTCCGG 59.204 55.000 0.00 0.00 33.35 5.14
2494 2675 6.359480 CGGAAGGTACCACATTTTAGAATC 57.641 41.667 15.94 0.00 0.00 2.52
2506 2687 4.846779 TTTTAGAATCCTTGTGTGTGGC 57.153 40.909 0.00 0.00 0.00 5.01
2512 2693 3.049674 CTTGTGTGTGGCGGCGAT 61.050 61.111 12.98 0.00 0.00 4.58
2900 3116 3.134623 ACTGGACATTCATAATCTCCGCA 59.865 43.478 0.00 0.00 29.39 5.69
2939 3155 6.334102 AGTTCTACAGTCAGGTAGTTTCTG 57.666 41.667 0.00 0.00 41.20 3.02
2940 3156 5.834204 AGTTCTACAGTCAGGTAGTTTCTGT 59.166 40.000 0.00 0.00 41.20 3.41
2941 3157 6.324254 AGTTCTACAGTCAGGTAGTTTCTGTT 59.676 38.462 0.00 0.00 41.20 3.16
2942 3158 6.726490 TCTACAGTCAGGTAGTTTCTGTTT 57.274 37.500 0.00 0.00 41.20 2.83
2943 3159 6.746120 TCTACAGTCAGGTAGTTTCTGTTTC 58.254 40.000 0.00 0.00 41.20 2.78
2944 3160 5.615925 ACAGTCAGGTAGTTTCTGTTTCT 57.384 39.130 0.00 0.00 36.17 2.52
3057 3284 8.024865 ACTATTATCTTAACAAAACCAAACGGC 58.975 33.333 0.00 0.00 0.00 5.68
3125 3352 7.148573 CGCATGTAGTAACATTTCTCTTCTGTT 60.149 37.037 0.00 0.00 44.07 3.16
3194 3421 2.331809 TCATCGATAGGACATTCGCG 57.668 50.000 0.00 0.00 35.39 5.87
3212 3439 0.391263 CGGACCTACCTTGGCAAGTC 60.391 60.000 24.57 15.74 36.31 3.01
3259 3486 9.213777 TGAGATTGATATACCAGAGGTTTAACT 57.786 33.333 0.00 0.00 37.09 2.24
3273 3500 7.550551 CAGAGGTTTAACTAGATGAATCTTGCA 59.449 37.037 0.00 0.00 38.32 4.08
3381 3608 1.351350 GCTATATGGGAGGGGTTGACC 59.649 57.143 0.00 0.00 39.11 4.02
3532 3761 8.607220 GCATATAACATTTTCGACGAATAAACG 58.393 33.333 11.71 0.00 39.31 3.60
3604 3834 2.501223 TTTCTCGTGCGCGGAGGATT 62.501 55.000 22.93 0.00 38.89 3.01
3640 3870 2.158959 CAAGCTACGGTTCTCGGCG 61.159 63.158 0.00 0.00 44.45 6.46
3706 3936 1.221414 GCACGCTGAAGATATCCCAC 58.779 55.000 0.00 0.00 0.00 4.61
3718 3948 1.979809 TATCCCACCATGGACAGGTT 58.020 50.000 21.47 12.68 40.96 3.50
3719 3949 1.084018 ATCCCACCATGGACAGGTTT 58.916 50.000 21.47 5.45 40.96 3.27
3722 3952 0.178964 CCACCATGGACAGGTTTGGT 60.179 55.000 21.47 0.00 40.96 3.67
3723 3953 1.703411 CACCATGGACAGGTTTGGTT 58.297 50.000 21.47 0.00 40.44 3.67
3724 3954 1.613437 CACCATGGACAGGTTTGGTTC 59.387 52.381 21.47 0.00 40.44 3.62
3725 3955 1.216678 ACCATGGACAGGTTTGGTTCA 59.783 47.619 21.47 0.00 39.41 3.18
3726 3956 2.158325 ACCATGGACAGGTTTGGTTCAT 60.158 45.455 21.47 0.00 39.41 2.57
3727 3957 2.899256 CCATGGACAGGTTTGGTTCATT 59.101 45.455 5.56 0.00 0.00 2.57
3728 3958 3.056607 CCATGGACAGGTTTGGTTCATTC 60.057 47.826 5.56 0.00 0.00 2.67
3729 3959 3.593442 TGGACAGGTTTGGTTCATTCT 57.407 42.857 0.00 0.00 0.00 2.40
3730 3960 3.909732 TGGACAGGTTTGGTTCATTCTT 58.090 40.909 0.00 0.00 0.00 2.52
3731 3961 3.636300 TGGACAGGTTTGGTTCATTCTTG 59.364 43.478 0.00 0.00 0.00 3.02
3732 3962 3.636764 GGACAGGTTTGGTTCATTCTTGT 59.363 43.478 0.00 0.00 0.00 3.16
3733 3963 4.825085 GGACAGGTTTGGTTCATTCTTGTA 59.175 41.667 0.00 0.00 0.00 2.41
3734 3964 5.048713 GGACAGGTTTGGTTCATTCTTGTAG 60.049 44.000 0.00 0.00 0.00 2.74
3735 3965 5.445964 ACAGGTTTGGTTCATTCTTGTAGT 58.554 37.500 0.00 0.00 0.00 2.73
3736 3966 5.891551 ACAGGTTTGGTTCATTCTTGTAGTT 59.108 36.000 0.00 0.00 0.00 2.24
3737 3967 6.379988 ACAGGTTTGGTTCATTCTTGTAGTTT 59.620 34.615 0.00 0.00 0.00 2.66
3738 3968 7.093509 ACAGGTTTGGTTCATTCTTGTAGTTTT 60.094 33.333 0.00 0.00 0.00 2.43
3739 3969 7.763985 CAGGTTTGGTTCATTCTTGTAGTTTTT 59.236 33.333 0.00 0.00 0.00 1.94
3740 3970 7.763985 AGGTTTGGTTCATTCTTGTAGTTTTTG 59.236 33.333 0.00 0.00 0.00 2.44
3741 3971 7.547722 GGTTTGGTTCATTCTTGTAGTTTTTGT 59.452 33.333 0.00 0.00 0.00 2.83
3742 3972 8.931775 GTTTGGTTCATTCTTGTAGTTTTTGTT 58.068 29.630 0.00 0.00 0.00 2.83
3743 3973 9.495572 TTTGGTTCATTCTTGTAGTTTTTGTTT 57.504 25.926 0.00 0.00 0.00 2.83
3744 3974 9.495572 TTGGTTCATTCTTGTAGTTTTTGTTTT 57.504 25.926 0.00 0.00 0.00 2.43
3745 3975 9.495572 TGGTTCATTCTTGTAGTTTTTGTTTTT 57.504 25.926 0.00 0.00 0.00 1.94
3811 4041 1.547820 CTAACTCTGCCTCTGTGCTCA 59.452 52.381 0.00 0.00 0.00 4.26
3884 4114 3.515286 ACCGCGATCGTCACGGAT 61.515 61.111 30.64 16.67 44.24 4.18
3921 4151 1.071605 GACCAGTCAAGTGATCACGC 58.928 55.000 19.85 11.51 36.20 5.34
4109 4340 2.888834 TTTTTGAGGCAGGCAGTTTC 57.111 45.000 0.00 0.00 0.00 2.78
4110 4341 2.071778 TTTTGAGGCAGGCAGTTTCT 57.928 45.000 0.00 0.00 0.00 2.52
4111 4342 2.071778 TTTGAGGCAGGCAGTTTCTT 57.928 45.000 0.00 0.00 0.00 2.52
4112 4343 2.071778 TTGAGGCAGGCAGTTTCTTT 57.928 45.000 0.00 0.00 0.00 2.52
4113 4344 2.071778 TGAGGCAGGCAGTTTCTTTT 57.928 45.000 0.00 0.00 0.00 2.27
4114 4345 2.387757 TGAGGCAGGCAGTTTCTTTTT 58.612 42.857 0.00 0.00 0.00 1.94
4115 4346 2.362077 TGAGGCAGGCAGTTTCTTTTTC 59.638 45.455 0.00 0.00 0.00 2.29
4120 4351 4.271049 GGCAGGCAGTTTCTTTTTCTTTTC 59.729 41.667 0.00 0.00 0.00 2.29
4180 4412 4.487714 AAGGGATATGTACAGTGTGGTG 57.512 45.455 5.88 0.00 0.00 4.17
4221 4453 3.769739 TGTAGGTCTTTGTGCAGTCAT 57.230 42.857 0.00 0.00 0.00 3.06
4298 4541 4.466828 CCACGTTGAAACAATTAGAGCAG 58.533 43.478 0.00 0.00 0.00 4.24
4302 4545 4.670221 CGTTGAAACAATTAGAGCAGCTCC 60.670 45.833 19.40 1.14 0.00 4.70
4305 4548 5.012239 TGAAACAATTAGAGCAGCTCCAAT 58.988 37.500 19.40 14.46 0.00 3.16
4314 4557 2.278857 AGCTCCAATAGACGCGCG 60.279 61.111 30.96 30.96 0.00 6.86
4315 4558 3.989595 GCTCCAATAGACGCGCGC 61.990 66.667 32.58 23.91 0.00 6.86
4316 4559 2.582226 CTCCAATAGACGCGCGCA 60.582 61.111 32.58 16.40 0.00 6.09
4317 4560 2.125872 TCCAATAGACGCGCGCAA 60.126 55.556 32.58 16.35 0.00 4.85
4318 4561 1.692148 CTCCAATAGACGCGCGCAAA 61.692 55.000 32.58 15.93 0.00 3.68
4319 4562 1.133664 CCAATAGACGCGCGCAAAA 59.866 52.632 32.58 13.84 0.00 2.44
4320 4563 0.453615 CCAATAGACGCGCGCAAAAA 60.454 50.000 32.58 13.96 0.00 1.94
4375 4631 2.002586 CGGACCACATAGTTGCTTCAG 58.997 52.381 0.00 0.00 0.00 3.02
4407 4663 1.360551 TTTTTAGCGCGCCAAAGCA 59.639 47.368 30.33 14.40 39.83 3.91
4409 4665 2.064723 TTTTAGCGCGCCAAAGCACA 62.065 50.000 30.33 8.90 39.83 4.57
4433 4689 2.120909 AGCAGGCGCGGCAAAATAT 61.121 52.632 34.94 10.09 45.49 1.28
4436 4692 1.225855 CAGGCGCGGCAAAATATAGA 58.774 50.000 34.94 0.00 0.00 1.98
4438 4694 1.070134 AGGCGCGGCAAAATATAGAGA 59.930 47.619 34.94 0.00 0.00 3.10
4444 4700 2.135933 GGCAAAATATAGAGAGCGCGT 58.864 47.619 8.43 0.00 0.00 6.01
4447 4703 2.333389 AAATATAGAGAGCGCGTCCG 57.667 50.000 8.43 0.00 37.57 4.79
4457 4713 3.943034 CGCGTCCGGCACAAACAA 61.943 61.111 0.00 0.00 43.84 2.83
4458 4714 2.353030 GCGTCCGGCACAAACAAC 60.353 61.111 0.00 0.00 42.87 3.32
4461 4717 0.385473 CGTCCGGCACAAACAACATC 60.385 55.000 0.00 0.00 0.00 3.06
4462 4718 0.665835 GTCCGGCACAAACAACATCA 59.334 50.000 0.00 0.00 0.00 3.07
4463 4719 1.066303 GTCCGGCACAAACAACATCAA 59.934 47.619 0.00 0.00 0.00 2.57
4464 4720 1.751351 TCCGGCACAAACAACATCAAA 59.249 42.857 0.00 0.00 0.00 2.69
4465 4721 2.166459 TCCGGCACAAACAACATCAAAA 59.834 40.909 0.00 0.00 0.00 2.44
4466 4722 3.129871 CCGGCACAAACAACATCAAAAT 58.870 40.909 0.00 0.00 0.00 1.82
4467 4723 4.038042 TCCGGCACAAACAACATCAAAATA 59.962 37.500 0.00 0.00 0.00 1.40
4468 4724 4.928615 CCGGCACAAACAACATCAAAATAT 59.071 37.500 0.00 0.00 0.00 1.28
4469 4725 6.071896 TCCGGCACAAACAACATCAAAATATA 60.072 34.615 0.00 0.00 0.00 0.86
4470 4726 6.253298 CCGGCACAAACAACATCAAAATATAG 59.747 38.462 0.00 0.00 0.00 1.31
4471 4727 7.026562 CGGCACAAACAACATCAAAATATAGA 58.973 34.615 0.00 0.00 0.00 1.98
4472 4728 7.218773 CGGCACAAACAACATCAAAATATAGAG 59.781 37.037 0.00 0.00 0.00 2.43
4473 4729 7.009540 GGCACAAACAACATCAAAATATAGAGC 59.990 37.037 0.00 0.00 0.00 4.09
4474 4730 7.253420 GCACAAACAACATCAAAATATAGAGCG 60.253 37.037 0.00 0.00 0.00 5.03
4475 4731 6.747280 ACAAACAACATCAAAATATAGAGCGC 59.253 34.615 0.00 0.00 0.00 5.92
4476 4732 5.083136 ACAACATCAAAATATAGAGCGCG 57.917 39.130 0.00 0.00 0.00 6.86
4477 4733 3.795561 ACATCAAAATATAGAGCGCGC 57.204 42.857 26.66 26.66 0.00 6.86
4478 4734 2.155732 ACATCAAAATATAGAGCGCGCG 59.844 45.455 28.44 28.44 0.00 6.86
4479 4735 0.506932 TCAAAATATAGAGCGCGCGC 59.493 50.000 45.10 45.10 42.33 6.86
4480 4736 0.451135 CAAAATATAGAGCGCGCGCC 60.451 55.000 46.98 36.71 43.17 6.53
4481 4737 1.566018 AAAATATAGAGCGCGCGCCC 61.566 55.000 46.98 39.11 43.17 6.13
4482 4738 4.778415 ATATAGAGCGCGCGCCCG 62.778 66.667 46.98 14.21 43.17 6.13
4493 4749 4.337060 GCGCCCGGGACAAACAAC 62.337 66.667 29.31 1.69 0.00 3.32
4494 4750 2.902846 CGCCCGGGACAAACAACA 60.903 61.111 29.31 0.00 0.00 3.33
4495 4751 2.265182 CGCCCGGGACAAACAACAT 61.265 57.895 29.31 0.00 0.00 2.71
4496 4752 1.801309 CGCCCGGGACAAACAACATT 61.801 55.000 29.31 0.00 0.00 2.71
4497 4753 0.391228 GCCCGGGACAAACAACATTT 59.609 50.000 29.31 0.00 0.00 2.32
4498 4754 1.202592 GCCCGGGACAAACAACATTTT 60.203 47.619 29.31 0.00 0.00 1.82
4499 4755 2.478831 CCCGGGACAAACAACATTTTG 58.521 47.619 18.48 0.00 41.47 2.44
4500 4756 1.864082 CCGGGACAAACAACATTTTGC 59.136 47.619 0.00 0.00 39.67 3.68
4501 4757 2.544685 CGGGACAAACAACATTTTGCA 58.455 42.857 0.00 0.00 39.67 4.08
4504 4760 4.034975 CGGGACAAACAACATTTTGCATTT 59.965 37.500 0.00 0.00 39.67 2.32
4547 4803 7.672351 TCAAACACACACAAAATAATTCGAC 57.328 32.000 0.00 0.00 0.00 4.20
4552 4808 8.467402 ACACACACAAAATAATTCGACAAAAA 57.533 26.923 0.00 0.00 0.00 1.94
4644 4927 9.959749 AATACAACAAATAACATTTTGTCGTCT 57.040 25.926 3.32 0.00 46.33 4.18
4668 4951 2.660064 ATGCCCACCACTCCTCGAC 61.660 63.158 0.00 0.00 0.00 4.20
4678 4961 2.882137 CCACTCCTCGACTAGATCCTTC 59.118 54.545 0.00 0.00 0.00 3.46
4693 4976 6.310764 AGATCCTTCTGAAGTTCATCATGT 57.689 37.500 15.72 0.00 0.00 3.21
4695 4978 5.233083 TCCTTCTGAAGTTCATCATGTGT 57.767 39.130 15.72 0.00 0.00 3.72
4755 5038 1.229658 CCACCCTCTCAACCCTCCT 60.230 63.158 0.00 0.00 0.00 3.69
4756 5039 1.268283 CCACCCTCTCAACCCTCCTC 61.268 65.000 0.00 0.00 0.00 3.71
4757 5040 1.081277 ACCCTCTCAACCCTCCTCC 59.919 63.158 0.00 0.00 0.00 4.30
4759 5042 1.305381 CCTCTCAACCCTCCTCCGT 60.305 63.158 0.00 0.00 0.00 4.69
4765 5048 0.964358 CAACCCTCCTCCGTACTCGT 60.964 60.000 0.00 0.00 35.01 4.18
4810 5093 8.762645 TCATACTGAGAATAGTCCAAATCTTGT 58.237 33.333 0.00 0.00 32.19 3.16
4814 5097 6.962182 TGAGAATAGTCCAAATCTTGTCCAT 58.038 36.000 0.00 0.00 0.00 3.41
4824 5107 0.874390 TCTTGTCCATGCTTGTTCGC 59.126 50.000 0.00 0.00 0.00 4.70
4896 5179 1.140134 CACCAGGGAAGAGGGGGAAA 61.140 60.000 0.00 0.00 0.00 3.13
4900 5183 2.229203 GGGAAGAGGGGGAAACGGT 61.229 63.158 0.00 0.00 0.00 4.83
4901 5184 0.911045 GGGAAGAGGGGGAAACGGTA 60.911 60.000 0.00 0.00 0.00 4.02
4959 5242 0.683179 TCGCCGAAGAGGATGAGGAA 60.683 55.000 0.00 0.00 45.00 3.36
4963 5246 2.103373 CCGAAGAGGATGAGGAAGTCA 58.897 52.381 0.00 0.00 45.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.747855 CGCCTCTTGGTCTTGGGC 60.748 66.667 0.00 0.00 39.43 5.36
29 30 2.157073 GGTAACTCCGAACGCTCGC 61.157 63.158 1.91 0.00 44.04 5.03
38 39 3.396260 TTTCTGAACAGGGTAACTCCG 57.604 47.619 1.93 0.00 37.00 4.63
69 70 4.538917 CCTGCACAAAAATGGAAAAATGC 58.461 39.130 0.00 0.00 0.00 3.56
210 212 2.074547 CTGATTTTGGGCAGCAAGTG 57.925 50.000 0.00 0.00 0.00 3.16
297 304 8.607459 CCACTCTTTAACTAATTATCAGTGCAG 58.393 37.037 0.00 0.00 0.00 4.41
786 892 1.372872 GGCCGACGCTTGCATTTTT 60.373 52.632 0.00 0.00 34.44 1.94
928 1067 4.142752 ACATCATGACAAGAAACTGCATCG 60.143 41.667 0.00 0.00 0.00 3.84
1026 1180 8.898761 TCACTGTACAAACTGAACATAAACATT 58.101 29.630 0.00 0.00 0.00 2.71
1123 1277 2.157863 GCGAGAAGAGGTACAAAAGCAC 59.842 50.000 0.00 0.00 0.00 4.40
1126 1280 3.430218 CACAGCGAGAAGAGGTACAAAAG 59.570 47.826 0.00 0.00 0.00 2.27
1347 1501 1.295357 CGCAGCGGTGAACCATGTTA 61.295 55.000 20.69 0.00 35.14 2.41
1365 1519 2.126888 GCGGCACCACAAACATCG 60.127 61.111 0.00 0.00 0.00 3.84
1413 1567 2.158623 TGAGACACATTTGCAGTCCCTT 60.159 45.455 0.00 0.00 32.82 3.95
1972 2126 4.537751 TGGAGTCTTCTCGGTTCTGATAT 58.462 43.478 0.00 0.00 41.26 1.63
2142 2296 4.023291 TGACTATGACATAGACCTGCACA 58.977 43.478 25.87 11.97 36.68 4.57
2175 2351 8.393366 CAACAGGTTGATGATAATGTTCACTAG 58.607 37.037 6.29 0.00 42.93 2.57
2187 2363 8.906867 CATATAGGAAAACAACAGGTTGATGAT 58.093 33.333 18.28 0.59 42.93 2.45
2193 2369 7.001674 TCACACATATAGGAAAACAACAGGTT 58.998 34.615 0.00 0.00 42.98 3.50
2195 2371 7.305474 GTTCACACATATAGGAAAACAACAGG 58.695 38.462 0.00 0.00 0.00 4.00
2199 2375 9.693739 ATATGGTTCACACATATAGGAAAACAA 57.306 29.630 0.00 0.00 39.17 2.83
2229 2405 8.248945 ACGCAGTTACTGTATTCTACACTAAAT 58.751 33.333 14.23 0.00 37.78 1.40
2230 2406 7.596494 ACGCAGTTACTGTATTCTACACTAAA 58.404 34.615 14.23 0.00 37.78 1.85
2232 2408 6.748333 ACGCAGTTACTGTATTCTACACTA 57.252 37.500 14.23 0.00 37.78 2.74
2233 2409 5.640189 ACGCAGTTACTGTATTCTACACT 57.360 39.130 14.23 0.00 37.78 3.55
2251 2427 3.196901 AGAAGTACCCAATATGTGACGCA 59.803 43.478 0.00 0.00 0.00 5.24
2252 2428 3.793559 AGAAGTACCCAATATGTGACGC 58.206 45.455 0.00 0.00 0.00 5.19
2253 2429 6.015350 AGGATAGAAGTACCCAATATGTGACG 60.015 42.308 0.00 0.00 0.00 4.35
2254 2430 7.304497 AGGATAGAAGTACCCAATATGTGAC 57.696 40.000 0.00 0.00 0.00 3.67
2255 2431 7.931015 AAGGATAGAAGTACCCAATATGTGA 57.069 36.000 0.00 0.00 0.00 3.58
2261 2437 7.125356 ACGAGTTAAAGGATAGAAGTACCCAAT 59.875 37.037 0.00 0.00 0.00 3.16
2262 2438 6.438425 ACGAGTTAAAGGATAGAAGTACCCAA 59.562 38.462 0.00 0.00 0.00 4.12
2263 2439 5.954150 ACGAGTTAAAGGATAGAAGTACCCA 59.046 40.000 0.00 0.00 0.00 4.51
2264 2440 6.460814 GGACGAGTTAAAGGATAGAAGTACCC 60.461 46.154 0.00 0.00 0.00 3.69
2265 2441 6.096001 TGGACGAGTTAAAGGATAGAAGTACC 59.904 42.308 0.00 0.00 0.00 3.34
2266 2442 7.093322 TGGACGAGTTAAAGGATAGAAGTAC 57.907 40.000 0.00 0.00 0.00 2.73
2267 2443 7.893124 ATGGACGAGTTAAAGGATAGAAGTA 57.107 36.000 0.00 0.00 0.00 2.24
2268 2444 6.793505 ATGGACGAGTTAAAGGATAGAAGT 57.206 37.500 0.00 0.00 0.00 3.01
2269 2445 7.329717 GCATATGGACGAGTTAAAGGATAGAAG 59.670 40.741 4.56 0.00 0.00 2.85
2270 2446 7.015292 AGCATATGGACGAGTTAAAGGATAGAA 59.985 37.037 4.56 0.00 0.00 2.10
2271 2447 6.493802 AGCATATGGACGAGTTAAAGGATAGA 59.506 38.462 4.56 0.00 0.00 1.98
2272 2448 6.692486 AGCATATGGACGAGTTAAAGGATAG 58.308 40.000 4.56 0.00 0.00 2.08
2273 2449 6.493802 AGAGCATATGGACGAGTTAAAGGATA 59.506 38.462 4.56 0.00 0.00 2.59
2274 2450 5.305644 AGAGCATATGGACGAGTTAAAGGAT 59.694 40.000 4.56 0.00 0.00 3.24
2275 2451 4.649674 AGAGCATATGGACGAGTTAAAGGA 59.350 41.667 4.56 0.00 0.00 3.36
2276 2452 4.950050 AGAGCATATGGACGAGTTAAAGG 58.050 43.478 4.56 0.00 0.00 3.11
2277 2453 6.758886 AGAAAGAGCATATGGACGAGTTAAAG 59.241 38.462 4.56 0.00 0.00 1.85
2278 2454 6.640518 AGAAAGAGCATATGGACGAGTTAAA 58.359 36.000 4.56 0.00 0.00 1.52
2279 2455 6.222038 AGAAAGAGCATATGGACGAGTTAA 57.778 37.500 4.56 0.00 0.00 2.01
2280 2456 5.854010 AGAAAGAGCATATGGACGAGTTA 57.146 39.130 4.56 0.00 0.00 2.24
2281 2457 4.744795 AGAAAGAGCATATGGACGAGTT 57.255 40.909 4.56 0.00 0.00 3.01
2282 2458 4.160439 TGAAGAAAGAGCATATGGACGAGT 59.840 41.667 4.56 0.00 0.00 4.18
2283 2459 4.505922 GTGAAGAAAGAGCATATGGACGAG 59.494 45.833 4.56 0.00 0.00 4.18
2284 2460 4.081697 TGTGAAGAAAGAGCATATGGACGA 60.082 41.667 4.56 0.00 0.00 4.20
2285 2461 4.183865 TGTGAAGAAAGAGCATATGGACG 58.816 43.478 4.56 0.00 0.00 4.79
2286 2462 4.574013 CCTGTGAAGAAAGAGCATATGGAC 59.426 45.833 4.56 0.00 0.00 4.02
2287 2463 4.471025 TCCTGTGAAGAAAGAGCATATGGA 59.529 41.667 4.56 0.00 0.00 3.41
2288 2464 4.774124 TCCTGTGAAGAAAGAGCATATGG 58.226 43.478 4.56 0.00 0.00 2.74
2289 2465 6.748333 TTTCCTGTGAAGAAAGAGCATATG 57.252 37.500 0.00 0.00 0.00 1.78
2290 2466 6.545298 GGATTTCCTGTGAAGAAAGAGCATAT 59.455 38.462 0.00 0.00 36.71 1.78
2291 2467 5.882557 GGATTTCCTGTGAAGAAAGAGCATA 59.117 40.000 0.00 0.00 36.71 3.14
2292 2468 4.704057 GGATTTCCTGTGAAGAAAGAGCAT 59.296 41.667 0.00 0.00 36.71 3.79
2293 2469 4.074970 GGATTTCCTGTGAAGAAAGAGCA 58.925 43.478 0.00 0.00 36.71 4.26
2294 2470 4.074970 TGGATTTCCTGTGAAGAAAGAGC 58.925 43.478 0.00 0.00 36.71 4.09
2295 2471 8.517062 AATATGGATTTCCTGTGAAGAAAGAG 57.483 34.615 0.00 0.00 36.71 2.85
2296 2472 8.742777 CAAATATGGATTTCCTGTGAAGAAAGA 58.257 33.333 0.00 0.00 36.71 2.52
2297 2473 8.526147 ACAAATATGGATTTCCTGTGAAGAAAG 58.474 33.333 0.00 0.00 36.71 2.62
2298 2474 8.306038 CACAAATATGGATTTCCTGTGAAGAAA 58.694 33.333 9.25 0.00 34.98 2.52
2299 2475 7.669304 TCACAAATATGGATTTCCTGTGAAGAA 59.331 33.333 13.31 0.00 37.37 2.52
2300 2476 7.174413 TCACAAATATGGATTTCCTGTGAAGA 58.826 34.615 13.31 0.00 37.37 2.87
2301 2477 7.395190 TCACAAATATGGATTTCCTGTGAAG 57.605 36.000 13.31 0.00 37.37 3.02
2302 2478 7.631161 GCATCACAAATATGGATTTCCTGTGAA 60.631 37.037 17.42 6.62 40.83 3.18
2303 2479 6.183360 GCATCACAAATATGGATTTCCTGTGA 60.183 38.462 16.38 16.38 41.31 3.58
2304 2480 5.981315 GCATCACAAATATGGATTTCCTGTG 59.019 40.000 8.78 8.78 34.60 3.66
2305 2481 5.069516 GGCATCACAAATATGGATTTCCTGT 59.930 40.000 0.00 0.00 32.73 4.00
2306 2482 5.069383 TGGCATCACAAATATGGATTTCCTG 59.931 40.000 0.00 0.00 32.73 3.86
2307 2483 5.210430 TGGCATCACAAATATGGATTTCCT 58.790 37.500 0.00 0.00 32.73 3.36
2308 2484 5.534207 TGGCATCACAAATATGGATTTCC 57.466 39.130 0.00 0.00 32.73 3.13
2317 2493 9.171877 TGCGATTAATATATGGCATCACAAATA 57.828 29.630 1.65 0.00 34.85 1.40
2341 2517 5.519927 ACAAAATTTGCTAAGTCAGTTGTGC 59.480 36.000 5.52 0.00 0.00 4.57
2348 2524 7.939782 TGATCTGAACAAAATTTGCTAAGTCA 58.060 30.769 5.52 1.60 0.00 3.41
2349 2525 8.976986 ATGATCTGAACAAAATTTGCTAAGTC 57.023 30.769 5.52 0.00 0.00 3.01
2373 2550 8.761689 ACATTAGCCACAAAAGGAAATGATAAT 58.238 29.630 12.49 0.00 37.18 1.28
2376 2553 6.211184 TCACATTAGCCACAAAAGGAAATGAT 59.789 34.615 12.49 0.16 37.18 2.45
2377 2554 5.538053 TCACATTAGCCACAAAAGGAAATGA 59.462 36.000 12.49 0.00 37.18 2.57
2449 2630 0.321653 ACAACGACAATCCTGCCTCC 60.322 55.000 0.00 0.00 0.00 4.30
2461 2642 1.422388 GTACCTTCCGGAACAACGAC 58.578 55.000 14.35 3.57 35.47 4.34
2463 2644 0.033781 TGGTACCTTCCGGAACAACG 59.966 55.000 14.35 3.14 0.00 4.10
2473 2654 7.393515 ACAAGGATTCTAAAATGTGGTACCTTC 59.606 37.037 14.36 7.07 32.74 3.46
2488 2669 1.338674 CCGCCACACACAAGGATTCTA 60.339 52.381 0.00 0.00 0.00 2.10
2506 2687 0.672401 AACCAACAGTACCATCGCCG 60.672 55.000 0.00 0.00 0.00 6.46
2512 2693 1.847737 AGAACCCAACCAACAGTACCA 59.152 47.619 0.00 0.00 0.00 3.25
2785 2966 8.897872 ATAAAAGTAAATATCCACACCTACCG 57.102 34.615 0.00 0.00 0.00 4.02
2815 3027 5.568620 AGTAAGTTCCTTGGATCAACTGT 57.431 39.130 0.00 0.00 30.63 3.55
2836 3048 4.094887 CCGATACCTGTCAACATGGAAAAG 59.905 45.833 0.00 0.00 0.00 2.27
2881 3097 3.499918 CCTTGCGGAGATTATGAATGTCC 59.500 47.826 5.50 5.50 45.35 4.02
2900 3116 6.601332 TGTAGAACTTGTCTGGATTTTCCTT 58.399 36.000 0.00 0.00 37.46 3.36
2939 3155 7.045126 AGACTGCTATATGTGGTAGAGAAAC 57.955 40.000 0.00 0.00 0.00 2.78
2940 3156 6.833933 TGAGACTGCTATATGTGGTAGAGAAA 59.166 38.462 0.00 0.00 0.00 2.52
2941 3157 6.365520 TGAGACTGCTATATGTGGTAGAGAA 58.634 40.000 0.00 0.00 0.00 2.87
2942 3158 5.941788 TGAGACTGCTATATGTGGTAGAGA 58.058 41.667 0.00 0.00 0.00 3.10
2943 3159 6.832520 ATGAGACTGCTATATGTGGTAGAG 57.167 41.667 0.00 0.00 0.00 2.43
2944 3160 7.231467 TGTATGAGACTGCTATATGTGGTAGA 58.769 38.462 0.00 0.00 0.00 2.59
2977 3193 7.446625 GGACAATGTAAATATCCTGATCAGCTT 59.553 37.037 17.76 8.86 0.00 3.74
2978 3194 6.939163 GGACAATGTAAATATCCTGATCAGCT 59.061 38.462 17.76 9.05 0.00 4.24
2979 3195 6.939163 AGGACAATGTAAATATCCTGATCAGC 59.061 38.462 17.76 1.53 38.40 4.26
2980 3196 8.373981 AGAGGACAATGTAAATATCCTGATCAG 58.626 37.037 16.24 16.24 39.96 2.90
2981 3197 8.267620 AGAGGACAATGTAAATATCCTGATCA 57.732 34.615 3.75 0.00 39.96 2.92
2982 3198 9.566432 AAAGAGGACAATGTAAATATCCTGATC 57.434 33.333 3.75 0.00 39.96 2.92
2983 3199 9.566432 GAAAGAGGACAATGTAAATATCCTGAT 57.434 33.333 3.75 0.00 39.96 2.90
2984 3200 7.710907 CGAAAGAGGACAATGTAAATATCCTGA 59.289 37.037 3.75 0.00 39.96 3.86
2985 3201 7.041780 CCGAAAGAGGACAATGTAAATATCCTG 60.042 40.741 3.75 0.00 39.96 3.86
2986 3202 6.992715 CCGAAAGAGGACAATGTAAATATCCT 59.007 38.462 0.00 0.00 42.62 3.24
2987 3203 6.766467 ACCGAAAGAGGACAATGTAAATATCC 59.234 38.462 0.00 0.00 34.73 2.59
2988 3204 7.280205 ACACCGAAAGAGGACAATGTAAATATC 59.720 37.037 0.00 0.00 34.73 1.63
2989 3205 7.110155 ACACCGAAAGAGGACAATGTAAATAT 58.890 34.615 0.00 0.00 34.73 1.28
2990 3206 6.469410 ACACCGAAAGAGGACAATGTAAATA 58.531 36.000 0.00 0.00 34.73 1.40
2991 3207 5.313712 ACACCGAAAGAGGACAATGTAAAT 58.686 37.500 0.00 0.00 34.73 1.40
3069 3296 6.937436 AAACGACCTTGTAAAATGAGAAGT 57.063 33.333 0.00 0.00 0.00 3.01
3194 3421 0.690762 TGACTTGCCAAGGTAGGTCC 59.309 55.000 14.90 1.02 36.36 4.46
3212 3439 0.457851 CTCCGTCAACCTCTAGCCTG 59.542 60.000 0.00 0.00 0.00 4.85
3273 3500 8.930846 AGATAGTGGTGGTACGTATAATAGTT 57.069 34.615 0.00 0.00 0.00 2.24
3381 3608 0.250295 TCCTCCTCGTTTTGCCACAG 60.250 55.000 0.00 0.00 0.00 3.66
3532 3761 2.910688 TATCCATCCTCCAGCGTTTC 57.089 50.000 0.00 0.00 0.00 2.78
3569 3799 4.159879 ACGAGAAAGACCGACCTGATAAAT 59.840 41.667 0.00 0.00 0.00 1.40
3604 3834 1.146930 GATCGATTGGCCCTGAGCA 59.853 57.895 0.00 0.00 46.50 4.26
3640 3870 1.971695 CACCTGAACCGGGAAAGGC 60.972 63.158 16.15 0.00 33.36 4.35
3706 3936 1.993956 TGAACCAAACCTGTCCATGG 58.006 50.000 4.97 4.97 38.91 3.66
3718 3948 9.495572 AAAACAAAAACTACAAGAATGAACCAA 57.504 25.926 0.00 0.00 0.00 3.67
3719 3949 9.495572 AAAAACAAAAACTACAAGAATGAACCA 57.504 25.926 0.00 0.00 0.00 3.67
3759 3989 5.298777 AGAGCAGTTTCCAAATCATCATAGC 59.701 40.000 0.00 0.00 0.00 2.97
3811 4041 1.470098 GCATGAAAGCCTGAACGACAT 59.530 47.619 0.00 0.00 0.00 3.06
3884 4114 1.266718 GTCTCGGCATTTTCAAGCACA 59.733 47.619 0.00 0.00 0.00 4.57
3921 4151 2.202676 GGCTCTCTTCTGCGACGG 60.203 66.667 0.00 0.00 0.00 4.79
4054 4285 1.636988 GGTTTCATACCACCGTCGAG 58.363 55.000 0.00 0.00 46.92 4.04
4095 4326 2.625314 AGAAAAAGAAACTGCCTGCCTC 59.375 45.455 0.00 0.00 0.00 4.70
4096 4327 2.670939 AGAAAAAGAAACTGCCTGCCT 58.329 42.857 0.00 0.00 0.00 4.75
4097 4328 3.459232 AAGAAAAAGAAACTGCCTGCC 57.541 42.857 0.00 0.00 0.00 4.85
4099 4330 7.601073 AAAGAAAAGAAAAAGAAACTGCCTG 57.399 32.000 0.00 0.00 0.00 4.85
4100 4331 8.621532 AAAAAGAAAAGAAAAAGAAACTGCCT 57.378 26.923 0.00 0.00 0.00 4.75
4128 4359 0.322098 CCAACACCTTCCGGCATGTA 60.322 55.000 0.00 0.00 0.00 2.29
4135 4366 2.162208 CACATTCATCCAACACCTTCCG 59.838 50.000 0.00 0.00 0.00 4.30
4180 4412 4.036262 ACATCATGTACACACAACACAACC 59.964 41.667 0.00 0.00 38.42 3.77
4221 4453 0.827089 CAACACCCAGTGGCATTCCA 60.827 55.000 2.61 0.00 40.85 3.53
4298 4541 3.989595 GCGCGCGTCTATTGGAGC 61.990 66.667 32.35 6.21 0.00 4.70
4302 4545 2.994533 TTTTTGCGCGCGTCTATTG 58.005 47.368 32.35 0.92 0.00 1.90
4320 4563 5.407502 GGCTATTTCGGTGCTGTAATTTTT 58.592 37.500 0.00 0.00 0.00 1.94
4321 4564 4.142249 GGGCTATTTCGGTGCTGTAATTTT 60.142 41.667 0.00 0.00 0.00 1.82
4322 4565 3.380320 GGGCTATTTCGGTGCTGTAATTT 59.620 43.478 0.00 0.00 0.00 1.82
4323 4566 2.949644 GGGCTATTTCGGTGCTGTAATT 59.050 45.455 0.00 0.00 0.00 1.40
4324 4567 2.172717 AGGGCTATTTCGGTGCTGTAAT 59.827 45.455 0.00 0.00 0.00 1.89
4332 4588 0.808755 CGCAAAAGGGCTATTTCGGT 59.191 50.000 0.00 0.00 0.00 4.69
4444 4700 1.393603 TTGATGTTGTTTGTGCCGGA 58.606 45.000 5.05 0.00 0.00 5.14
4447 4703 7.009540 GCTCTATATTTTGATGTTGTTTGTGCC 59.990 37.037 0.00 0.00 0.00 5.01
4455 4711 3.902465 GCGCGCTCTATATTTTGATGTTG 59.098 43.478 26.67 0.00 0.00 3.33
4457 4713 2.155732 CGCGCGCTCTATATTTTGATGT 59.844 45.455 30.48 0.00 0.00 3.06
4458 4714 2.751072 CGCGCGCTCTATATTTTGATG 58.249 47.619 30.48 3.74 0.00 3.07
4461 4717 2.973674 GCGCGCGCTCTATATTTTG 58.026 52.632 44.38 10.35 38.26 2.44
4465 4721 4.778415 CGGGCGCGCGCTCTATAT 62.778 66.667 46.35 0.00 39.97 0.86
4476 4732 4.337060 GTTGTTTGTCCCGGGCGC 62.337 66.667 18.49 12.13 0.00 6.53
4477 4733 1.801309 AATGTTGTTTGTCCCGGGCG 61.801 55.000 18.49 0.00 0.00 6.13
4478 4734 0.391228 AAATGTTGTTTGTCCCGGGC 59.609 50.000 18.49 12.24 0.00 6.13
4479 4735 2.478831 CAAAATGTTGTTTGTCCCGGG 58.521 47.619 16.85 16.85 34.43 5.73
4480 4736 1.864082 GCAAAATGTTGTTTGTCCCGG 59.136 47.619 0.00 0.00 40.06 5.73
4481 4737 2.544685 TGCAAAATGTTGTTTGTCCCG 58.455 42.857 0.00 0.00 40.06 5.14
4482 4738 5.497635 AAATGCAAAATGTTGTTTGTCCC 57.502 34.783 0.00 0.00 40.06 4.46
4483 4739 8.127954 ACATTAAATGCAAAATGTTGTTTGTCC 58.872 29.630 15.71 0.00 42.22 4.02
4484 4740 8.945930 CACATTAAATGCAAAATGTTGTTTGTC 58.054 29.630 17.79 0.00 42.22 3.18
4485 4741 7.914346 CCACATTAAATGCAAAATGTTGTTTGT 59.086 29.630 17.79 0.49 42.22 2.83
4486 4742 8.127327 TCCACATTAAATGCAAAATGTTGTTTG 58.873 29.630 17.79 9.81 42.22 2.93
4487 4743 8.218338 TCCACATTAAATGCAAAATGTTGTTT 57.782 26.923 17.79 3.45 42.22 2.83
4488 4744 7.798596 TCCACATTAAATGCAAAATGTTGTT 57.201 28.000 17.79 0.81 42.22 2.83
4489 4745 7.281774 TGTTCCACATTAAATGCAAAATGTTGT 59.718 29.630 17.79 4.72 42.22 3.32
4490 4746 7.637229 TGTTCCACATTAAATGCAAAATGTTG 58.363 30.769 17.79 15.50 42.22 3.33
4491 4747 7.798596 TGTTCCACATTAAATGCAAAATGTT 57.201 28.000 17.79 6.12 42.22 2.71
4492 4748 7.798596 TTGTTCCACATTAAATGCAAAATGT 57.201 28.000 15.71 15.71 44.94 2.71
4493 4749 8.557864 TCTTTGTTCCACATTAAATGCAAAATG 58.442 29.630 14.71 14.71 38.71 2.32
4494 4750 8.674263 TCTTTGTTCCACATTAAATGCAAAAT 57.326 26.923 0.00 0.00 0.00 1.82
4495 4751 8.498054 TTCTTTGTTCCACATTAAATGCAAAA 57.502 26.923 0.00 0.00 0.00 2.44
4496 4752 7.984050 TCTTCTTTGTTCCACATTAAATGCAAA 59.016 29.630 0.00 0.00 0.00 3.68
4497 4753 7.495901 TCTTCTTTGTTCCACATTAAATGCAA 58.504 30.769 0.00 0.00 0.00 4.08
4498 4754 7.048629 TCTTCTTTGTTCCACATTAAATGCA 57.951 32.000 0.00 0.00 0.00 3.96
4499 4755 7.814107 TGATCTTCTTTGTTCCACATTAAATGC 59.186 33.333 0.00 0.00 0.00 3.56
4500 4756 9.695526 TTGATCTTCTTTGTTCCACATTAAATG 57.304 29.630 0.00 0.00 0.00 2.32
4504 4760 8.134895 GTGTTTGATCTTCTTTGTTCCACATTA 58.865 33.333 0.00 0.00 0.00 1.90
4644 4927 1.922447 AGGAGTGGTGGGCATGAAATA 59.078 47.619 0.00 0.00 0.00 1.40
4646 4929 0.038166 GAGGAGTGGTGGGCATGAAA 59.962 55.000 0.00 0.00 0.00 2.69
4648 4931 2.659063 CGAGGAGTGGTGGGCATGA 61.659 63.158 0.00 0.00 0.00 3.07
4651 4934 2.435120 TAGTCGAGGAGTGGTGGGCA 62.435 60.000 0.00 0.00 0.00 5.36
4668 4951 7.438757 CACATGATGAACTTCAGAAGGATCTAG 59.561 40.741 14.90 10.63 33.50 2.43
4678 4961 4.715896 CCGAAACACATGATGAACTTCAG 58.284 43.478 0.00 0.00 0.00 3.02
4707 4990 2.555757 GTTGCCTCCTATCATGCCATTC 59.444 50.000 0.00 0.00 0.00 2.67
4711 4994 2.057137 TTGTTGCCTCCTATCATGCC 57.943 50.000 0.00 0.00 0.00 4.40
4757 5040 3.958822 GACACCCCGCACGAGTACG 62.959 68.421 0.00 0.00 45.75 3.67
4759 5042 3.376078 GGACACCCCGCACGAGTA 61.376 66.667 0.00 0.00 0.00 2.59
4785 5068 8.954950 ACAAGATTTGGACTATTCTCAGTATG 57.045 34.615 0.00 0.00 34.12 2.39
4795 5078 5.121380 AGCATGGACAAGATTTGGACTAT 57.879 39.130 0.00 0.00 34.12 2.12
4810 5093 2.032634 GTCGGCGAACAAGCATGGA 61.033 57.895 12.92 0.00 39.27 3.41
4814 5097 3.793775 TTCCGTCGGCGAACAAGCA 62.794 57.895 12.93 0.00 41.33 3.91
4852 5135 3.452786 CTGCTTCCTCCTCCGCGA 61.453 66.667 8.23 0.00 0.00 5.87
4881 5164 1.923909 CCGTTTCCCCCTCTTCCCT 60.924 63.158 0.00 0.00 0.00 4.20
4900 5183 4.360964 CGTTCCCCACCGCACGTA 62.361 66.667 0.00 0.00 0.00 3.57
4937 5220 2.107141 CATCCTCTTCGGCGACCC 59.893 66.667 10.16 0.00 0.00 4.46
4944 5227 2.478709 CGTGACTTCCTCATCCTCTTCG 60.479 54.545 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.