Multiple sequence alignment - TraesCS6D01G117000

Loading Multiple Alignment...

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 TraesCS6D01G117000 chr6D 100.000 2711 0 0 1 2711 83056279 83058989 0.000000e+00 5007.0
1 TraesCS6D01G117000 chr6D 86.542 1709 217 11 1 1706 83542248 83540550 0.000000e+00 1869.0
2 TraesCS6D01G117000 chr6D 86.358 1708 222 10 1 1706 83123084 83124782 0.000000e+00 1853.0
3 TraesCS6D01G117000 chr6D 87.484 1590 192 7 1 1587 83045222 83046807 0.000000e+00 1827.0
4 TraesCS6D01G117000 chr6B 94.177 2284 124 6 1 2284 158102238 158104512 0.000000e+00 3472.0
5 TraesCS6D01G117000 chr6B 86.140 1710 222 14 1 1706 158148153 158149851 0.000000e+00 1831.0
6 TraesCS6D01G117000 chr6B 86.007 1708 228 7 1 1706 159403716 159402018 0.000000e+00 1820.0
7 TraesCS6D01G117000 chr6B 84.507 213 26 6 2502 2711 229671971 229671763 1.270000e-48 204.0
8 TraesCS6D01G117000 chr6A 91.516 2157 117 16 1 2138 100086229 100088338 0.000000e+00 2909.0
9 TraesCS6D01G117000 chr6A 86.132 1709 224 10 1 1706 100762622 100760924 0.000000e+00 1831.0
10 TraesCS6D01G117000 chr6A 85.664 1709 233 9 1 1706 100183441 100185140 0.000000e+00 1788.0
11 TraesCS6D01G117000 chr6A 84.964 419 32 13 2320 2711 100094245 100094659 1.960000e-106 396.0
12 TraesCS6D01G117000 chr6A 89.764 127 12 1 2185 2311 100088353 100088478 7.770000e-36 161.0
13 TraesCS6D01G117000 chr5A 82.906 234 31 7 2476 2706 366760002 366759775 4.580000e-48 202.0
14 TraesCS6D01G117000 chr5B 83.810 210 28 5 2502 2711 420009895 420009692 7.660000e-46 195.0
15 TraesCS6D01G117000 chr4D 85.217 115 17 0 2594 2708 507667542 507667656 4.740000e-23 119.0
16 TraesCS6D01G117000 chr4D 94.737 38 1 1 2523 2560 507667506 507667542 1.050000e-04 58.4


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 TraesCS6D01G117000 chr6D 83056279 83058989 2710 False 5007 5007 100.000 1 2711 1 chr6D.!!$F2 2710
1 TraesCS6D01G117000 chr6D 83540550 83542248 1698 True 1869 1869 86.542 1 1706 1 chr6D.!!$R1 1705
2 TraesCS6D01G117000 chr6D 83123084 83124782 1698 False 1853 1853 86.358 1 1706 1 chr6D.!!$F3 1705
3 TraesCS6D01G117000 chr6D 83045222 83046807 1585 False 1827 1827 87.484 1 1587 1 chr6D.!!$F1 1586
4 TraesCS6D01G117000 chr6B 158102238 158104512 2274 False 3472 3472 94.177 1 2284 1 chr6B.!!$F1 2283
5 TraesCS6D01G117000 chr6B 158148153 158149851 1698 False 1831 1831 86.140 1 1706 1 chr6B.!!$F2 1705
6 TraesCS6D01G117000 chr6B 159402018 159403716 1698 True 1820 1820 86.007 1 1706 1 chr6B.!!$R1 1705
7 TraesCS6D01G117000 chr6A 100760924 100762622 1698 True 1831 1831 86.132 1 1706 1 chr6A.!!$R1 1705
8 TraesCS6D01G117000 chr6A 100183441 100185140 1699 False 1788 1788 85.664 1 1706 1 chr6A.!!$F2 1705
9 TraesCS6D01G117000 chr6A 100086229 100088478 2249 False 1535 2909 90.640 1 2311 2 chr6A.!!$F3 2310

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
950 952 0.368227 GTGACATTGAAGAGCTCGCG 59.632 55.0 8.37 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2431 2452 0.108138 GGTAGAAGCCGCACAGTGAT 60.108 55.0 4.15 0.0 0.0 3.06 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
480 481 5.924475 TTGTAAGAGAGTTGTTAGCAAGC 57.076 39.130 0.00 0.00 34.94 4.01
567 568 0.747255 ATAGCCGTAGTGCAGTCAGG 59.253 55.000 0.00 3.89 0.00 3.86
875 876 2.159517 CCAGATTTGTTAGCTTGCCGAC 60.160 50.000 0.00 0.00 0.00 4.79
885 886 3.039202 CTTGCCGACGCCATTGACC 62.039 63.158 0.00 0.00 0.00 4.02
950 952 0.368227 GTGACATTGAAGAGCTCGCG 59.632 55.000 8.37 0.00 0.00 5.87
965 967 1.811266 CGCGTGGAAGAGTCCCATG 60.811 63.158 0.00 3.84 44.23 3.66
1024 1026 0.393808 GCAATTACCGAGCCCTGGAA 60.394 55.000 0.00 0.00 0.00 3.53
1225 1227 0.610687 GTTGAGTACCTGCAGAGGCT 59.389 55.000 17.39 9.46 44.33 4.58
1329 1331 2.192861 CACCAACTCCAGCGGCAAA 61.193 57.895 1.45 0.00 0.00 3.68
1331 1333 1.898574 CCAACTCCAGCGGCAAAGT 60.899 57.895 1.45 0.00 0.00 2.66
1347 1349 1.812686 AAGTGCCGGACAGCGAGTTA 61.813 55.000 5.05 0.00 34.65 2.24
1450 1452 3.615592 CGAAACATCGGTGACCTTCCTAA 60.616 47.826 0.65 0.00 0.00 2.69
1559 1561 2.741055 GGAGCTGGAGAAGGGAGCC 61.741 68.421 0.00 0.00 32.86 4.70
1601 1603 1.205893 GCTGGTCGGAGAGATCAAAGT 59.794 52.381 0.00 0.00 39.92 2.66
1658 1660 4.177537 TGTGGAAGGAATTTCTTGGTGA 57.822 40.909 2.93 0.00 36.03 4.02
1730 1738 1.880027 GCGTGGAAACCAGATTCTTGT 59.120 47.619 0.00 0.00 32.34 3.16
1781 1792 1.197721 GCATGACAAGTTGAGAACGGG 59.802 52.381 10.54 0.00 36.23 5.28
1801 1817 2.941720 GGAGTGCTCATTCTGATCCAAC 59.058 50.000 1.41 0.00 0.00 3.77
1808 1824 4.338879 CTCATTCTGATCCAACCAAACCT 58.661 43.478 0.00 0.00 0.00 3.50
1809 1825 4.335416 TCATTCTGATCCAACCAAACCTC 58.665 43.478 0.00 0.00 0.00 3.85
1810 1826 4.043310 TCATTCTGATCCAACCAAACCTCT 59.957 41.667 0.00 0.00 0.00 3.69
1811 1827 5.250543 TCATTCTGATCCAACCAAACCTCTA 59.749 40.000 0.00 0.00 0.00 2.43
1822 1838 2.432444 CAAACCTCTATCGTGGGCAAA 58.568 47.619 0.00 0.00 0.00 3.68
1873 1889 2.942710 TCTTCGGTGATGTCGTCTTTC 58.057 47.619 0.00 0.00 0.00 2.62
1885 1901 0.944311 CGTCTTTCTGGTGGTCGTGG 60.944 60.000 0.00 0.00 0.00 4.94
1925 1941 1.674057 CCAGGCAGGAAAGTCTCGT 59.326 57.895 0.00 0.00 41.22 4.18
1987 2008 2.591715 GTCGTTGGCTGTGGCTGT 60.592 61.111 0.00 0.00 38.73 4.40
1988 2009 2.591429 TCGTTGGCTGTGGCTGTG 60.591 61.111 0.00 0.00 38.73 3.66
1999 2020 2.519302 GGCTGTGGCTGTTGGTGT 60.519 61.111 0.00 0.00 38.73 4.16
2002 2023 1.028905 GCTGTGGCTGTTGGTGTAAA 58.971 50.000 0.00 0.00 35.22 2.01
2003 2024 1.407258 GCTGTGGCTGTTGGTGTAAAA 59.593 47.619 0.00 0.00 35.22 1.52
2004 2025 2.159170 GCTGTGGCTGTTGGTGTAAAAA 60.159 45.455 0.00 0.00 35.22 1.94
2014 2035 3.172229 TGGTGTAAAAAGTTTGCTGCC 57.828 42.857 0.00 0.00 0.00 4.85
2016 2037 2.863740 GGTGTAAAAAGTTTGCTGCCAC 59.136 45.455 0.00 0.00 0.00 5.01
2127 2148 0.773644 TTTTTGGAGGCCTGAGAGCT 59.226 50.000 12.00 0.00 0.00 4.09
2166 2187 2.159028 GCCGAGCTACTCCAAATCTTCT 60.159 50.000 0.00 0.00 0.00 2.85
2219 2240 2.601367 CCCACTTGGCCACTTGGG 60.601 66.667 28.96 28.96 42.92 4.12
2257 2278 1.272536 TGACGGGCTCCTACTTCTCTT 60.273 52.381 0.00 0.00 0.00 2.85
2288 2309 0.531090 AGTCACTTTGCGCGGTAACA 60.531 50.000 8.83 0.00 0.00 2.41
2292 2313 2.158058 TCACTTTGCGCGGTAACATTAC 59.842 45.455 8.83 0.00 0.00 1.89
2313 2334 2.714259 TTTTTCTCTGGGGTGCACG 58.286 52.632 11.45 0.00 0.00 5.34
2314 2335 0.821711 TTTTTCTCTGGGGTGCACGG 60.822 55.000 11.45 1.10 0.00 4.94
2315 2336 1.990160 TTTTCTCTGGGGTGCACGGT 61.990 55.000 11.45 0.00 0.00 4.83
2316 2337 1.122632 TTTCTCTGGGGTGCACGGTA 61.123 55.000 11.45 0.00 0.00 4.02
2317 2338 1.122632 TTCTCTGGGGTGCACGGTAA 61.123 55.000 11.45 0.00 0.00 2.85
2318 2339 1.375523 CTCTGGGGTGCACGGTAAC 60.376 63.158 11.45 0.00 0.00 2.50
2319 2340 2.107041 CTCTGGGGTGCACGGTAACA 62.107 60.000 11.45 4.21 0.00 2.41
2320 2341 1.002624 CTGGGGTGCACGGTAACAT 60.003 57.895 11.45 0.00 0.00 2.71
2321 2342 0.608035 CTGGGGTGCACGGTAACATT 60.608 55.000 11.45 0.00 0.00 2.71
2322 2343 0.691332 TGGGGTGCACGGTAACATTA 59.309 50.000 11.45 0.00 0.00 1.90
2323 2344 1.089112 GGGGTGCACGGTAACATTAC 58.911 55.000 11.45 0.00 0.00 1.89
2340 2361 9.189723 GTAACATTACCTATCGGTACATCTTTC 57.810 37.037 0.00 0.00 45.29 2.62
2341 2362 7.356089 ACATTACCTATCGGTACATCTTTCA 57.644 36.000 0.00 0.00 45.29 2.69
2342 2363 7.963532 ACATTACCTATCGGTACATCTTTCAT 58.036 34.615 0.00 0.00 45.29 2.57
2343 2364 8.088981 ACATTACCTATCGGTACATCTTTCATC 58.911 37.037 0.00 0.00 45.29 2.92
2344 2365 7.591421 TTACCTATCGGTACATCTTTCATCA 57.409 36.000 0.00 0.00 45.29 3.07
2345 2366 6.672266 ACCTATCGGTACATCTTTCATCAT 57.328 37.500 0.00 0.00 43.29 2.45
2346 2367 7.067496 ACCTATCGGTACATCTTTCATCATT 57.933 36.000 0.00 0.00 43.29 2.57
2347 2368 7.155328 ACCTATCGGTACATCTTTCATCATTC 58.845 38.462 0.00 0.00 43.29 2.67
2348 2369 7.154656 CCTATCGGTACATCTTTCATCATTCA 58.845 38.462 0.00 0.00 0.00 2.57
2349 2370 7.821359 CCTATCGGTACATCTTTCATCATTCAT 59.179 37.037 0.00 0.00 0.00 2.57
2350 2371 9.212641 CTATCGGTACATCTTTCATCATTCATT 57.787 33.333 0.00 0.00 0.00 2.57
2351 2372 7.864108 TCGGTACATCTTTCATCATTCATTT 57.136 32.000 0.00 0.00 0.00 2.32
2352 2373 8.279970 TCGGTACATCTTTCATCATTCATTTT 57.720 30.769 0.00 0.00 0.00 1.82
2353 2374 8.397906 TCGGTACATCTTTCATCATTCATTTTC 58.602 33.333 0.00 0.00 0.00 2.29
2354 2375 8.400947 CGGTACATCTTTCATCATTCATTTTCT 58.599 33.333 0.00 0.00 0.00 2.52
2355 2376 9.727627 GGTACATCTTTCATCATTCATTTTCTC 57.272 33.333 0.00 0.00 0.00 2.87
2367 2388 8.206325 TCATTCATTTTCTCTAAGATCTGTGC 57.794 34.615 0.00 0.00 0.00 4.57
2368 2389 6.653273 TTCATTTTCTCTAAGATCTGTGCG 57.347 37.500 0.00 0.00 0.00 5.34
2369 2390 5.965922 TCATTTTCTCTAAGATCTGTGCGA 58.034 37.500 0.00 0.00 0.00 5.10
2370 2391 6.577103 TCATTTTCTCTAAGATCTGTGCGAT 58.423 36.000 0.00 0.00 34.25 4.58
2371 2392 7.044181 TCATTTTCTCTAAGATCTGTGCGATT 58.956 34.615 0.00 0.00 30.84 3.34
2372 2393 6.653273 TTTTCTCTAAGATCTGTGCGATTG 57.347 37.500 0.00 0.00 30.84 2.67
2373 2394 4.313277 TCTCTAAGATCTGTGCGATTGG 57.687 45.455 0.00 0.00 30.84 3.16
2374 2395 3.068732 TCTCTAAGATCTGTGCGATTGGG 59.931 47.826 0.00 0.00 30.84 4.12
2375 2396 2.103094 TCTAAGATCTGTGCGATTGGGG 59.897 50.000 0.00 0.00 30.84 4.96
2376 2397 0.620556 AAGATCTGTGCGATTGGGGT 59.379 50.000 0.00 0.00 30.84 4.95
2377 2398 0.179000 AGATCTGTGCGATTGGGGTC 59.821 55.000 0.00 0.00 30.84 4.46
2378 2399 0.815615 GATCTGTGCGATTGGGGTCC 60.816 60.000 0.00 0.00 30.84 4.46
2379 2400 1.561769 ATCTGTGCGATTGGGGTCCA 61.562 55.000 0.00 0.00 0.00 4.02
2380 2401 2.033448 TGTGCGATTGGGGTCCAC 59.967 61.111 0.00 0.00 30.78 4.02
2381 2402 2.351276 GTGCGATTGGGGTCCACT 59.649 61.111 0.00 0.00 30.78 4.00
2382 2403 2.040544 GTGCGATTGGGGTCCACTG 61.041 63.158 0.00 0.00 30.78 3.66
2383 2404 2.351276 GCGATTGGGGTCCACTGT 59.649 61.111 0.00 0.00 30.78 3.55
2384 2405 1.195442 TGCGATTGGGGTCCACTGTA 61.195 55.000 0.00 0.00 30.78 2.74
2385 2406 0.180406 GCGATTGGGGTCCACTGTAT 59.820 55.000 0.00 0.00 30.78 2.29
2386 2407 1.414919 GCGATTGGGGTCCACTGTATA 59.585 52.381 0.00 0.00 30.78 1.47
2387 2408 2.038557 GCGATTGGGGTCCACTGTATAT 59.961 50.000 0.00 0.00 30.78 0.86
2388 2409 3.259876 GCGATTGGGGTCCACTGTATATA 59.740 47.826 0.00 0.00 30.78 0.86
2389 2410 4.081087 GCGATTGGGGTCCACTGTATATAT 60.081 45.833 0.00 0.00 30.78 0.86
2390 2411 5.128171 GCGATTGGGGTCCACTGTATATATA 59.872 44.000 0.00 0.00 30.78 0.86
2391 2412 6.183360 GCGATTGGGGTCCACTGTATATATAT 60.183 42.308 0.00 0.00 30.78 0.86
2392 2413 7.014905 GCGATTGGGGTCCACTGTATATATATA 59.985 40.741 0.00 0.00 30.78 0.86
2393 2414 9.090103 CGATTGGGGTCCACTGTATATATATAT 57.910 37.037 10.10 10.10 30.78 0.86
2395 2416 9.744125 ATTGGGGTCCACTGTATATATATATGT 57.256 33.333 14.42 1.27 30.78 2.29
2402 2423 9.908152 TCCACTGTATATATATATGTATTGCGC 57.092 33.333 14.42 0.00 0.00 6.09
2403 2424 9.691362 CCACTGTATATATATATGTATTGCGCA 57.309 33.333 5.66 5.66 0.00 6.09
2411 2432 8.737168 ATATATATGTATTGCGCATTTCACCT 57.263 30.769 12.75 5.69 0.00 4.00
2412 2433 5.772825 ATATGTATTGCGCATTTCACCTT 57.227 34.783 12.75 0.00 0.00 3.50
2413 2434 3.214697 TGTATTGCGCATTTCACCTTG 57.785 42.857 12.75 0.00 0.00 3.61
2414 2435 2.556189 TGTATTGCGCATTTCACCTTGT 59.444 40.909 12.75 0.00 0.00 3.16
2415 2436 3.753797 TGTATTGCGCATTTCACCTTGTA 59.246 39.130 12.75 0.00 0.00 2.41
2416 2437 2.697431 TTGCGCATTTCACCTTGTAC 57.303 45.000 12.75 0.00 0.00 2.90
2417 2438 0.515127 TGCGCATTTCACCTTGTACG 59.485 50.000 5.66 0.00 0.00 3.67
2418 2439 0.515564 GCGCATTTCACCTTGTACGT 59.484 50.000 0.30 0.00 0.00 3.57
2419 2440 1.727880 GCGCATTTCACCTTGTACGTA 59.272 47.619 0.30 0.00 0.00 3.57
2420 2441 2.350498 GCGCATTTCACCTTGTACGTAT 59.650 45.455 0.30 0.00 0.00 3.06
2421 2442 3.181514 GCGCATTTCACCTTGTACGTATT 60.182 43.478 0.30 0.00 0.00 1.89
2422 2443 4.670735 GCGCATTTCACCTTGTACGTATTT 60.671 41.667 0.30 0.00 0.00 1.40
2423 2444 5.019498 CGCATTTCACCTTGTACGTATTTC 58.981 41.667 0.00 0.00 0.00 2.17
2424 2445 5.390040 CGCATTTCACCTTGTACGTATTTCA 60.390 40.000 0.00 0.00 0.00 2.69
2425 2446 6.375377 GCATTTCACCTTGTACGTATTTCAA 58.625 36.000 0.00 0.00 0.00 2.69
2426 2447 6.523201 GCATTTCACCTTGTACGTATTTCAAG 59.477 38.462 14.40 14.40 38.45 3.02
2427 2448 7.581476 CATTTCACCTTGTACGTATTTCAAGT 58.419 34.615 17.97 7.97 37.45 3.16
2428 2449 6.774354 TTCACCTTGTACGTATTTCAAGTC 57.226 37.500 17.97 0.00 37.45 3.01
2429 2450 5.845103 TCACCTTGTACGTATTTCAAGTCA 58.155 37.500 17.97 0.12 37.45 3.41
2430 2451 6.282167 TCACCTTGTACGTATTTCAAGTCAA 58.718 36.000 17.97 7.08 37.45 3.18
2431 2452 6.762187 TCACCTTGTACGTATTTCAAGTCAAA 59.238 34.615 17.97 4.06 37.45 2.69
2432 2453 7.442969 TCACCTTGTACGTATTTCAAGTCAAAT 59.557 33.333 17.97 2.25 37.45 2.32
2433 2454 7.744715 CACCTTGTACGTATTTCAAGTCAAATC 59.255 37.037 17.97 0.00 37.45 2.17
2434 2455 7.442969 ACCTTGTACGTATTTCAAGTCAAATCA 59.557 33.333 17.97 0.00 37.45 2.57
2435 2456 7.744715 CCTTGTACGTATTTCAAGTCAAATCAC 59.255 37.037 17.97 0.00 37.45 3.06
2436 2457 7.956420 TGTACGTATTTCAAGTCAAATCACT 57.044 32.000 0.00 0.00 0.00 3.41
2437 2458 7.792925 TGTACGTATTTCAAGTCAAATCACTG 58.207 34.615 0.00 0.00 0.00 3.66
2438 2459 6.861065 ACGTATTTCAAGTCAAATCACTGT 57.139 33.333 0.00 0.00 0.00 3.55
2439 2460 6.658831 ACGTATTTCAAGTCAAATCACTGTG 58.341 36.000 0.17 0.17 0.00 3.66
2440 2461 5.565259 CGTATTTCAAGTCAAATCACTGTGC 59.435 40.000 2.12 0.00 0.00 4.57
2441 2462 3.607422 TTCAAGTCAAATCACTGTGCG 57.393 42.857 2.12 0.00 0.00 5.34
2442 2463 1.872952 TCAAGTCAAATCACTGTGCGG 59.127 47.619 2.12 0.00 0.00 5.69
2443 2464 0.593128 AAGTCAAATCACTGTGCGGC 59.407 50.000 2.12 0.00 0.00 6.53
2444 2465 0.250467 AGTCAAATCACTGTGCGGCT 60.250 50.000 2.12 0.00 0.00 5.52
2445 2466 0.593128 GTCAAATCACTGTGCGGCTT 59.407 50.000 2.12 0.00 0.00 4.35
2446 2467 0.874390 TCAAATCACTGTGCGGCTTC 59.126 50.000 2.12 0.00 0.00 3.86
2447 2468 0.877071 CAAATCACTGTGCGGCTTCT 59.123 50.000 2.12 0.00 0.00 2.85
2448 2469 2.076100 CAAATCACTGTGCGGCTTCTA 58.924 47.619 2.12 0.00 0.00 2.10
2449 2470 1.726853 AATCACTGTGCGGCTTCTAC 58.273 50.000 2.12 0.00 0.00 2.59
2450 2471 0.108138 ATCACTGTGCGGCTTCTACC 60.108 55.000 2.12 0.00 0.00 3.18
2451 2472 1.005037 CACTGTGCGGCTTCTACCA 60.005 57.895 0.00 0.00 0.00 3.25
2452 2473 0.391661 CACTGTGCGGCTTCTACCAT 60.392 55.000 0.00 0.00 0.00 3.55
2453 2474 1.134818 CACTGTGCGGCTTCTACCATA 60.135 52.381 0.00 0.00 0.00 2.74
2454 2475 1.137086 ACTGTGCGGCTTCTACCATAG 59.863 52.381 0.00 0.00 0.00 2.23
2455 2476 1.137086 CTGTGCGGCTTCTACCATAGT 59.863 52.381 0.00 0.00 0.00 2.12
2456 2477 1.136305 TGTGCGGCTTCTACCATAGTC 59.864 52.381 0.00 0.00 0.00 2.59
2457 2478 1.136305 GTGCGGCTTCTACCATAGTCA 59.864 52.381 0.00 0.00 0.00 3.41
2458 2479 1.409064 TGCGGCTTCTACCATAGTCAG 59.591 52.381 0.00 0.00 0.00 3.51
2459 2480 1.681793 GCGGCTTCTACCATAGTCAGA 59.318 52.381 0.00 0.00 0.00 3.27
2460 2481 2.100916 GCGGCTTCTACCATAGTCAGAA 59.899 50.000 0.00 0.00 0.00 3.02
2461 2482 3.430374 GCGGCTTCTACCATAGTCAGAAA 60.430 47.826 0.00 0.00 0.00 2.52
2462 2483 4.755411 CGGCTTCTACCATAGTCAGAAAA 58.245 43.478 0.00 0.00 0.00 2.29
2463 2484 5.175859 CGGCTTCTACCATAGTCAGAAAAA 58.824 41.667 0.00 0.00 0.00 1.94
2489 2510 8.093659 AGACACATTTTTCTCTCTTTTCTAGC 57.906 34.615 0.00 0.00 0.00 3.42
2490 2511 7.936301 AGACACATTTTTCTCTCTTTTCTAGCT 59.064 33.333 0.00 0.00 0.00 3.32
2491 2512 7.869800 ACACATTTTTCTCTCTTTTCTAGCTG 58.130 34.615 0.00 0.00 0.00 4.24
2492 2513 7.716998 ACACATTTTTCTCTCTTTTCTAGCTGA 59.283 33.333 0.00 0.00 0.00 4.26
2493 2514 8.562892 CACATTTTTCTCTCTTTTCTAGCTGAA 58.437 33.333 0.00 0.00 0.00 3.02
2494 2515 8.782144 ACATTTTTCTCTCTTTTCTAGCTGAAG 58.218 33.333 0.00 0.00 35.89 3.02
2495 2516 6.793492 TTTTCTCTCTTTTCTAGCTGAAGC 57.207 37.500 0.00 0.00 42.49 3.86
2496 2517 5.474578 TTCTCTCTTTTCTAGCTGAAGCA 57.525 39.130 4.90 0.00 45.16 3.91
2497 2518 4.815269 TCTCTCTTTTCTAGCTGAAGCAC 58.185 43.478 4.90 0.00 45.16 4.40
2498 2519 4.281941 TCTCTCTTTTCTAGCTGAAGCACA 59.718 41.667 4.90 0.00 45.16 4.57
2507 2528 4.974792 TGAAGCACAGACTCTCGC 57.025 55.556 0.00 0.00 0.00 5.03
2508 2529 2.345565 TGAAGCACAGACTCTCGCT 58.654 52.632 0.00 0.00 35.90 4.93
2509 2530 0.242286 TGAAGCACAGACTCTCGCTC 59.758 55.000 0.85 0.00 32.37 5.03
2510 2531 0.525761 GAAGCACAGACTCTCGCTCT 59.474 55.000 0.85 0.00 32.37 4.09
2511 2532 0.525761 AAGCACAGACTCTCGCTCTC 59.474 55.000 0.85 0.00 32.37 3.20
2512 2533 0.322456 AGCACAGACTCTCGCTCTCT 60.322 55.000 0.00 0.00 0.00 3.10
2513 2534 0.525761 GCACAGACTCTCGCTCTCTT 59.474 55.000 0.00 0.00 0.00 2.85
2514 2535 1.067915 GCACAGACTCTCGCTCTCTTT 60.068 52.381 0.00 0.00 0.00 2.52
2515 2536 2.594321 CACAGACTCTCGCTCTCTTTG 58.406 52.381 0.00 0.00 0.00 2.77
2516 2537 2.030363 CACAGACTCTCGCTCTCTTTGT 60.030 50.000 0.00 0.00 0.00 2.83
2517 2538 2.030363 ACAGACTCTCGCTCTCTTTGTG 60.030 50.000 0.00 0.00 0.00 3.33
2518 2539 2.227626 CAGACTCTCGCTCTCTTTGTGA 59.772 50.000 0.00 0.00 0.00 3.58
2519 2540 2.887783 AGACTCTCGCTCTCTTTGTGAA 59.112 45.455 0.00 0.00 0.00 3.18
2520 2541 3.319405 AGACTCTCGCTCTCTTTGTGAAA 59.681 43.478 0.00 0.00 0.00 2.69
2521 2542 4.021544 AGACTCTCGCTCTCTTTGTGAAAT 60.022 41.667 0.00 0.00 0.00 2.17
2522 2543 4.241681 ACTCTCGCTCTCTTTGTGAAATC 58.758 43.478 0.00 0.00 0.00 2.17
2523 2544 3.589988 TCTCGCTCTCTTTGTGAAATCC 58.410 45.455 0.00 0.00 0.00 3.01
2524 2545 3.006859 TCTCGCTCTCTTTGTGAAATCCA 59.993 43.478 0.00 0.00 0.00 3.41
2525 2546 3.937706 CTCGCTCTCTTTGTGAAATCCAT 59.062 43.478 0.00 0.00 0.00 3.41
2526 2547 3.935203 TCGCTCTCTTTGTGAAATCCATC 59.065 43.478 0.00 0.00 0.00 3.51
2527 2548 3.686241 CGCTCTCTTTGTGAAATCCATCA 59.314 43.478 0.00 0.00 0.00 3.07
2570 2591 9.650539 CATATTTTGGATGATTCGTATCTCTCT 57.349 33.333 3.59 0.00 0.00 3.10
2574 2595 9.884636 TTTTGGATGATTCGTATCTCTCTTAAA 57.115 29.630 3.59 4.70 0.00 1.52
2575 2596 8.873215 TTGGATGATTCGTATCTCTCTTAAAC 57.127 34.615 3.59 0.00 0.00 2.01
2576 2597 8.007405 TGGATGATTCGTATCTCTCTTAAACA 57.993 34.615 3.59 0.00 0.00 2.83
2577 2598 8.474831 TGGATGATTCGTATCTCTCTTAAACAA 58.525 33.333 3.59 0.00 0.00 2.83
2578 2599 9.314321 GGATGATTCGTATCTCTCTTAAACAAA 57.686 33.333 3.59 0.00 0.00 2.83
2622 2643 8.759481 TTTATATATTTGAACTCCATGTGCCA 57.241 30.769 0.00 0.00 0.00 4.92
2623 2644 8.759481 TTATATATTTGAACTCCATGTGCCAA 57.241 30.769 0.00 0.00 0.00 4.52
2624 2645 3.947910 ATTTGAACTCCATGTGCCAAG 57.052 42.857 0.00 0.00 0.00 3.61
2625 2646 2.655090 TTGAACTCCATGTGCCAAGA 57.345 45.000 0.00 0.00 0.00 3.02
2626 2647 1.896220 TGAACTCCATGTGCCAAGAC 58.104 50.000 0.00 0.00 0.00 3.01
2627 2648 1.168714 GAACTCCATGTGCCAAGACC 58.831 55.000 0.00 0.00 0.00 3.85
2628 2649 0.606401 AACTCCATGTGCCAAGACCG 60.606 55.000 0.00 0.00 0.00 4.79
2629 2650 1.003355 CTCCATGTGCCAAGACCGT 60.003 57.895 0.00 0.00 0.00 4.83
2630 2651 1.003839 TCCATGTGCCAAGACCGTC 60.004 57.895 0.00 0.00 0.00 4.79
2631 2652 1.302431 CCATGTGCCAAGACCGTCA 60.302 57.895 0.40 0.00 0.00 4.35
2632 2653 1.300971 CCATGTGCCAAGACCGTCAG 61.301 60.000 0.40 0.00 0.00 3.51
2633 2654 0.320683 CATGTGCCAAGACCGTCAGA 60.321 55.000 0.40 0.00 0.00 3.27
2634 2655 0.396435 ATGTGCCAAGACCGTCAGAA 59.604 50.000 0.40 0.00 0.00 3.02
2635 2656 0.396435 TGTGCCAAGACCGTCAGAAT 59.604 50.000 0.40 0.00 0.00 2.40
2636 2657 1.621317 TGTGCCAAGACCGTCAGAATA 59.379 47.619 0.40 0.00 0.00 1.75
2637 2658 2.037902 TGTGCCAAGACCGTCAGAATAA 59.962 45.455 0.40 0.00 0.00 1.40
2638 2659 2.673368 GTGCCAAGACCGTCAGAATAAG 59.327 50.000 0.40 0.00 0.00 1.73
2639 2660 2.565391 TGCCAAGACCGTCAGAATAAGA 59.435 45.455 0.40 0.00 0.00 2.10
2640 2661 3.197766 TGCCAAGACCGTCAGAATAAGAT 59.802 43.478 0.40 0.00 0.00 2.40
2641 2662 3.804873 GCCAAGACCGTCAGAATAAGATC 59.195 47.826 0.40 0.00 0.00 2.75
2642 2663 4.680708 GCCAAGACCGTCAGAATAAGATCA 60.681 45.833 0.40 0.00 0.00 2.92
2643 2664 5.419542 CCAAGACCGTCAGAATAAGATCAA 58.580 41.667 0.40 0.00 0.00 2.57
2644 2665 6.051717 CCAAGACCGTCAGAATAAGATCAAT 58.948 40.000 0.40 0.00 0.00 2.57
2645 2666 6.201806 CCAAGACCGTCAGAATAAGATCAATC 59.798 42.308 0.40 0.00 0.00 2.67
2646 2667 5.848406 AGACCGTCAGAATAAGATCAATCC 58.152 41.667 0.40 0.00 0.00 3.01
2647 2668 5.600484 AGACCGTCAGAATAAGATCAATCCT 59.400 40.000 0.40 0.00 0.00 3.24
2648 2669 6.098982 AGACCGTCAGAATAAGATCAATCCTT 59.901 38.462 0.40 0.00 0.00 3.36
2649 2670 6.051717 ACCGTCAGAATAAGATCAATCCTTG 58.948 40.000 0.00 0.00 0.00 3.61
2650 2671 6.127054 ACCGTCAGAATAAGATCAATCCTTGA 60.127 38.462 0.00 0.00 45.01 3.02
2665 2686 7.304735 TCAATCCTTGATACATTTGAAACACG 58.695 34.615 0.00 0.00 34.08 4.49
2666 2687 6.817765 ATCCTTGATACATTTGAAACACGT 57.182 33.333 0.00 0.00 0.00 4.49
2667 2688 6.627395 TCCTTGATACATTTGAAACACGTT 57.373 33.333 0.00 0.00 0.00 3.99
2668 2689 7.033530 TCCTTGATACATTTGAAACACGTTT 57.966 32.000 0.00 0.00 35.14 3.60
2669 2690 8.155821 TCCTTGATACATTTGAAACACGTTTA 57.844 30.769 0.00 0.00 32.11 2.01
2670 2691 8.622157 TCCTTGATACATTTGAAACACGTTTAA 58.378 29.630 0.00 0.00 32.11 1.52
2671 2692 9.405587 CCTTGATACATTTGAAACACGTTTAAT 57.594 29.630 0.00 0.00 32.11 1.40
2678 2699 9.748100 ACATTTGAAACACGTTTAATTTTTGAC 57.252 25.926 0.00 0.00 32.11 3.18
2679 2700 9.746711 CATTTGAAACACGTTTAATTTTTGACA 57.253 25.926 0.00 0.00 32.11 3.58
2683 2704 9.959775 TGAAACACGTTTAATTTTTGACATTTC 57.040 25.926 0.00 0.00 32.11 2.17
2684 2705 9.959775 GAAACACGTTTAATTTTTGACATTTCA 57.040 25.926 0.00 0.00 32.11 2.69
2685 2706 9.748100 AAACACGTTTAATTTTTGACATTTCAC 57.252 25.926 0.00 0.00 0.00 3.18
2686 2707 8.467402 ACACGTTTAATTTTTGACATTTCACA 57.533 26.923 0.00 0.00 0.00 3.58
2687 2708 9.092876 ACACGTTTAATTTTTGACATTTCACAT 57.907 25.926 0.00 0.00 0.00 3.21
2688 2709 9.913451 CACGTTTAATTTTTGACATTTCACATT 57.087 25.926 0.00 0.00 0.00 2.71
2697 2718 9.605955 TTTTTGACATTTCACATTCTATACGTG 57.394 29.630 0.00 0.00 0.00 4.49
2698 2719 8.541133 TTTGACATTTCACATTCTATACGTGA 57.459 30.769 0.00 0.00 37.87 4.35
2699 2720 8.541133 TTGACATTTCACATTCTATACGTGAA 57.459 30.769 0.00 0.00 45.34 3.18
2706 2727 7.124347 TCACATTCTATACGTGAAACAAACC 57.876 36.000 0.00 0.00 36.75 3.27
2707 2728 6.932400 TCACATTCTATACGTGAAACAAACCT 59.068 34.615 0.00 0.00 36.75 3.50
2708 2729 8.089597 TCACATTCTATACGTGAAACAAACCTA 58.910 33.333 0.00 0.00 36.75 3.08
2709 2730 8.879759 CACATTCTATACGTGAAACAAACCTAT 58.120 33.333 0.00 0.00 35.74 2.57
2710 2731 9.444600 ACATTCTATACGTGAAACAAACCTATT 57.555 29.630 0.00 0.00 35.74 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 5.220472 CGAGAACACATTTATGCAGTACCTG 60.220 44.000 0.00 0.00 34.12 4.00
102 103 2.479389 GCTGAGATCAGACAAGACTCCG 60.479 54.545 13.98 0.00 46.59 4.63
480 481 1.970092 AGTCCCTCTCGTTCCTATCG 58.030 55.000 0.00 0.00 0.00 2.92
567 568 3.199880 AGCATATACTCCTGCACCAAC 57.800 47.619 0.00 0.00 40.88 3.77
864 865 2.106074 CAATGGCGTCGGCAAGCTA 61.106 57.895 26.08 1.32 42.43 3.32
885 886 1.722011 ACAATTGGTTAGACGGAGCG 58.278 50.000 10.83 0.00 0.00 5.03
950 952 0.543749 CCTCCATGGGACTCTTCCAC 59.456 60.000 13.02 0.00 44.98 4.02
965 967 1.298859 CGCTGGCTACAACAACCTCC 61.299 60.000 0.00 0.00 0.00 4.30
1001 1003 1.223487 GGGCTCGGTAATTGCTCCA 59.777 57.895 0.00 0.00 0.00 3.86
1086 1088 0.810031 AGATACCAACGACGCCATGC 60.810 55.000 0.00 0.00 0.00 4.06
1142 1144 5.246656 ACATGGAAAGCAATGGAGAATTTGA 59.753 36.000 0.00 0.00 0.00 2.69
1225 1227 3.329889 ATCCTCAACCCCTGCGCA 61.330 61.111 10.98 10.98 0.00 6.09
1329 1331 2.273179 TAACTCGCTGTCCGGCACT 61.273 57.895 0.00 0.00 37.59 4.40
1331 1333 2.260434 GTAACTCGCTGTCCGGCA 59.740 61.111 0.00 0.00 37.59 5.69
1388 1390 4.570663 GGTCCATCTCGCCGTCCG 62.571 72.222 0.00 0.00 38.61 4.79
1450 1452 0.251341 GGGATCACCTGCAACCAAGT 60.251 55.000 0.00 0.00 35.85 3.16
1559 1561 2.125350 GCACCGAGCAGGAGAAGG 60.125 66.667 5.19 0.00 45.00 3.46
1601 1603 2.271173 CTCTGATGCTGCTGGCCA 59.729 61.111 4.71 4.71 40.92 5.36
1658 1660 0.181114 TGCTCTCCACACAGCAGTTT 59.819 50.000 0.00 0.00 40.80 2.66
1730 1738 1.621317 TCATTAGACCTCACCGCACAA 59.379 47.619 0.00 0.00 0.00 3.33
1801 1817 0.251916 TGCCCACGATAGAGGTTTGG 59.748 55.000 0.00 0.00 46.28 3.28
1808 1824 1.065709 GTTCCCTTTGCCCACGATAGA 60.066 52.381 0.00 0.00 41.38 1.98
1809 1825 1.065418 AGTTCCCTTTGCCCACGATAG 60.065 52.381 0.00 0.00 46.19 2.08
1810 1826 0.988832 AGTTCCCTTTGCCCACGATA 59.011 50.000 0.00 0.00 0.00 2.92
1811 1827 0.112412 AAGTTCCCTTTGCCCACGAT 59.888 50.000 0.00 0.00 0.00 3.73
1822 1838 2.629617 CAACAGAAATGGCAAGTTCCCT 59.370 45.455 9.85 0.00 30.59 4.20
1873 1889 4.704833 CTGGGCCACGACCACCAG 62.705 72.222 0.00 0.00 43.87 4.00
1885 1901 3.793144 CGCGAGACTTTGCTGGGC 61.793 66.667 0.00 0.00 0.00 5.36
1925 1941 1.772156 TGATCCACACCCACCCACA 60.772 57.895 0.00 0.00 0.00 4.17
1987 2008 4.499183 CAAACTTTTTACACCAACAGCCA 58.501 39.130 0.00 0.00 0.00 4.75
1988 2009 3.308595 GCAAACTTTTTACACCAACAGCC 59.691 43.478 0.00 0.00 0.00 4.85
1999 2020 2.364002 GAGGGTGGCAGCAAACTTTTTA 59.636 45.455 19.48 0.00 0.00 1.52
2002 2023 1.115326 GGAGGGTGGCAGCAAACTTT 61.115 55.000 19.48 0.00 0.00 2.66
2003 2024 1.531602 GGAGGGTGGCAGCAAACTT 60.532 57.895 19.48 0.00 0.00 2.66
2004 2025 2.011617 AAGGAGGGTGGCAGCAAACT 62.012 55.000 19.48 9.54 0.00 2.66
2014 2035 2.506065 CCGAGTAGGAAGGAGGGTG 58.494 63.158 0.00 0.00 45.00 4.61
2111 2132 0.975040 GAGAGCTCTCAGGCCTCCAA 60.975 60.000 33.99 0.00 42.42 3.53
2127 2148 0.663688 GCGGCTCTCAGATAACGAGA 59.336 55.000 0.00 0.00 37.18 4.04
2145 2166 2.159028 AGAAGATTTGGAGTAGCTCGGC 60.159 50.000 0.00 0.00 0.00 5.54
2166 2187 7.190871 GTGGACTTTTCATAGAAAACAAACGA 58.809 34.615 1.09 0.00 0.00 3.85
2300 2321 1.375523 GTTACCGTGCACCCCAGAG 60.376 63.158 12.15 0.00 0.00 3.35
2303 2324 0.691332 TAATGTTACCGTGCACCCCA 59.309 50.000 12.15 1.10 0.00 4.96
2324 2345 8.768957 ATGAATGATGAAAGATGTACCGATAG 57.231 34.615 0.00 0.00 0.00 2.08
2325 2346 9.559732 AAATGAATGATGAAAGATGTACCGATA 57.440 29.630 0.00 0.00 0.00 2.92
2326 2347 8.455903 AAATGAATGATGAAAGATGTACCGAT 57.544 30.769 0.00 0.00 0.00 4.18
2327 2348 7.864108 AAATGAATGATGAAAGATGTACCGA 57.136 32.000 0.00 0.00 0.00 4.69
2328 2349 8.400947 AGAAAATGAATGATGAAAGATGTACCG 58.599 33.333 0.00 0.00 0.00 4.02
2329 2350 9.727627 GAGAAAATGAATGATGAAAGATGTACC 57.272 33.333 0.00 0.00 0.00 3.34
2341 2362 8.838365 GCACAGATCTTAGAGAAAATGAATGAT 58.162 33.333 0.00 0.00 0.00 2.45
2342 2363 7.010830 CGCACAGATCTTAGAGAAAATGAATGA 59.989 37.037 0.00 0.00 0.00 2.57
2343 2364 7.010830 TCGCACAGATCTTAGAGAAAATGAATG 59.989 37.037 0.00 0.00 0.00 2.67
2344 2365 7.044181 TCGCACAGATCTTAGAGAAAATGAAT 58.956 34.615 0.00 0.00 0.00 2.57
2345 2366 6.398095 TCGCACAGATCTTAGAGAAAATGAA 58.602 36.000 0.00 0.00 0.00 2.57
2346 2367 5.965922 TCGCACAGATCTTAGAGAAAATGA 58.034 37.500 0.00 0.00 0.00 2.57
2347 2368 6.841443 ATCGCACAGATCTTAGAGAAAATG 57.159 37.500 0.00 0.00 33.45 2.32
2348 2369 6.259608 CCAATCGCACAGATCTTAGAGAAAAT 59.740 38.462 0.00 0.00 38.98 1.82
2349 2370 5.582269 CCAATCGCACAGATCTTAGAGAAAA 59.418 40.000 0.00 0.00 38.98 2.29
2350 2371 5.111989 CCAATCGCACAGATCTTAGAGAAA 58.888 41.667 0.00 0.00 38.98 2.52
2351 2372 4.442052 CCCAATCGCACAGATCTTAGAGAA 60.442 45.833 0.00 0.00 38.98 2.87
2352 2373 3.068732 CCCAATCGCACAGATCTTAGAGA 59.931 47.826 0.00 0.00 38.98 3.10
2353 2374 3.388308 CCCAATCGCACAGATCTTAGAG 58.612 50.000 0.00 0.00 38.98 2.43
2354 2375 2.103094 CCCCAATCGCACAGATCTTAGA 59.897 50.000 0.00 0.00 38.98 2.10
2355 2376 2.158900 ACCCCAATCGCACAGATCTTAG 60.159 50.000 0.00 0.00 38.98 2.18
2356 2377 1.837439 ACCCCAATCGCACAGATCTTA 59.163 47.619 0.00 0.00 38.98 2.10
2357 2378 0.620556 ACCCCAATCGCACAGATCTT 59.379 50.000 0.00 0.00 38.98 2.40
2358 2379 0.179000 GACCCCAATCGCACAGATCT 59.821 55.000 0.00 0.00 38.98 2.75
2359 2380 0.815615 GGACCCCAATCGCACAGATC 60.816 60.000 0.00 0.00 38.98 2.75
2360 2381 1.224592 GGACCCCAATCGCACAGAT 59.775 57.895 0.00 0.00 42.43 2.90
2361 2382 2.220586 TGGACCCCAATCGCACAGA 61.221 57.895 0.00 0.00 0.00 3.41
2362 2383 2.040544 GTGGACCCCAATCGCACAG 61.041 63.158 0.00 0.00 34.18 3.66
2363 2384 2.033448 GTGGACCCCAATCGCACA 59.967 61.111 0.00 0.00 34.18 4.57
2364 2385 2.040544 CAGTGGACCCCAATCGCAC 61.041 63.158 0.00 0.00 34.18 5.34
2365 2386 1.195442 TACAGTGGACCCCAATCGCA 61.195 55.000 0.00 0.00 34.18 5.10
2366 2387 0.180406 ATACAGTGGACCCCAATCGC 59.820 55.000 0.00 0.00 34.18 4.58
2367 2388 5.677319 ATATATACAGTGGACCCCAATCG 57.323 43.478 0.00 0.00 34.18 3.34
2369 2390 9.744125 ACATATATATATACAGTGGACCCCAAT 57.256 33.333 4.54 0.00 34.18 3.16
2376 2397 9.908152 GCGCAATACATATATATATACAGTGGA 57.092 33.333 0.30 5.11 0.00 4.02
2377 2398 9.691362 TGCGCAATACATATATATATACAGTGG 57.309 33.333 8.16 8.87 0.00 4.00
2385 2406 9.830975 AGGTGAAATGCGCAATACATATATATA 57.169 29.630 17.11 0.00 0.00 0.86
2386 2407 8.737168 AGGTGAAATGCGCAATACATATATAT 57.263 30.769 17.11 0.00 0.00 0.86
2387 2408 8.450180 CAAGGTGAAATGCGCAATACATATATA 58.550 33.333 17.11 0.00 0.00 0.86
2388 2409 7.040478 ACAAGGTGAAATGCGCAATACATATAT 60.040 33.333 17.11 0.00 0.00 0.86
2389 2410 6.262049 ACAAGGTGAAATGCGCAATACATATA 59.738 34.615 17.11 0.00 0.00 0.86
2390 2411 5.067674 ACAAGGTGAAATGCGCAATACATAT 59.932 36.000 17.11 4.84 0.00 1.78
2391 2412 4.397730 ACAAGGTGAAATGCGCAATACATA 59.602 37.500 17.11 0.00 0.00 2.29
2392 2413 3.193267 ACAAGGTGAAATGCGCAATACAT 59.807 39.130 17.11 6.08 0.00 2.29
2393 2414 2.556189 ACAAGGTGAAATGCGCAATACA 59.444 40.909 17.11 12.07 0.00 2.29
2394 2415 3.216147 ACAAGGTGAAATGCGCAATAC 57.784 42.857 17.11 11.14 0.00 1.89
2395 2416 3.181515 CGTACAAGGTGAAATGCGCAATA 60.182 43.478 17.11 0.00 0.00 1.90
2396 2417 2.414029 CGTACAAGGTGAAATGCGCAAT 60.414 45.455 17.11 1.49 0.00 3.56
2397 2418 1.069568 CGTACAAGGTGAAATGCGCAA 60.070 47.619 17.11 0.00 0.00 4.85
2398 2419 0.515127 CGTACAAGGTGAAATGCGCA 59.485 50.000 14.96 14.96 0.00 6.09
2399 2420 0.515564 ACGTACAAGGTGAAATGCGC 59.484 50.000 0.00 0.00 0.00 6.09
2400 2421 4.593597 AATACGTACAAGGTGAAATGCG 57.406 40.909 0.00 0.00 0.00 4.73
2401 2422 5.933790 TGAAATACGTACAAGGTGAAATGC 58.066 37.500 0.00 0.00 0.00 3.56
2402 2423 7.581476 ACTTGAAATACGTACAAGGTGAAATG 58.419 34.615 21.54 3.29 43.28 2.32
2403 2424 7.442969 TGACTTGAAATACGTACAAGGTGAAAT 59.557 33.333 21.54 6.19 43.28 2.17
2404 2425 6.762187 TGACTTGAAATACGTACAAGGTGAAA 59.238 34.615 21.54 6.22 43.28 2.69
2405 2426 6.282167 TGACTTGAAATACGTACAAGGTGAA 58.718 36.000 21.54 7.48 43.28 3.18
2406 2427 5.845103 TGACTTGAAATACGTACAAGGTGA 58.155 37.500 21.54 8.06 43.28 4.02
2407 2428 6.533819 TTGACTTGAAATACGTACAAGGTG 57.466 37.500 21.54 6.24 43.28 4.00
2408 2429 7.442969 TGATTTGACTTGAAATACGTACAAGGT 59.557 33.333 21.54 11.62 43.28 3.50
2409 2430 7.744715 GTGATTTGACTTGAAATACGTACAAGG 59.255 37.037 21.54 9.37 43.28 3.61
2410 2431 8.495949 AGTGATTTGACTTGAAATACGTACAAG 58.504 33.333 17.99 17.99 44.16 3.16
2411 2432 8.279800 CAGTGATTTGACTTGAAATACGTACAA 58.720 33.333 0.00 0.00 0.00 2.41
2412 2433 7.439955 ACAGTGATTTGACTTGAAATACGTACA 59.560 33.333 0.00 0.00 0.00 2.90
2413 2434 7.740346 CACAGTGATTTGACTTGAAATACGTAC 59.260 37.037 0.00 0.00 0.00 3.67
2414 2435 7.570507 GCACAGTGATTTGACTTGAAATACGTA 60.571 37.037 4.15 0.00 0.00 3.57
2415 2436 6.658831 CACAGTGATTTGACTTGAAATACGT 58.341 36.000 0.00 0.00 0.00 3.57
2416 2437 5.565259 GCACAGTGATTTGACTTGAAATACG 59.435 40.000 4.15 0.00 0.00 3.06
2417 2438 5.565259 CGCACAGTGATTTGACTTGAAATAC 59.435 40.000 4.15 0.00 0.00 1.89
2418 2439 5.334802 CCGCACAGTGATTTGACTTGAAATA 60.335 40.000 4.15 0.00 0.00 1.40
2419 2440 4.539870 CGCACAGTGATTTGACTTGAAAT 58.460 39.130 4.15 0.00 0.00 2.17
2420 2441 3.243035 CCGCACAGTGATTTGACTTGAAA 60.243 43.478 4.15 0.00 0.00 2.69
2421 2442 2.290367 CCGCACAGTGATTTGACTTGAA 59.710 45.455 4.15 0.00 0.00 2.69
2422 2443 1.872952 CCGCACAGTGATTTGACTTGA 59.127 47.619 4.15 0.00 0.00 3.02
2423 2444 1.664016 GCCGCACAGTGATTTGACTTG 60.664 52.381 4.15 0.00 0.00 3.16
2424 2445 0.593128 GCCGCACAGTGATTTGACTT 59.407 50.000 4.15 0.00 0.00 3.01
2425 2446 0.250467 AGCCGCACAGTGATTTGACT 60.250 50.000 4.15 0.00 0.00 3.41
2426 2447 0.593128 AAGCCGCACAGTGATTTGAC 59.407 50.000 4.15 0.00 0.00 3.18
2427 2448 0.874390 GAAGCCGCACAGTGATTTGA 59.126 50.000 4.15 0.00 0.00 2.69
2428 2449 0.877071 AGAAGCCGCACAGTGATTTG 59.123 50.000 4.15 0.00 0.00 2.32
2429 2450 2.076863 GTAGAAGCCGCACAGTGATTT 58.923 47.619 4.15 0.00 0.00 2.17
2430 2451 1.676014 GGTAGAAGCCGCACAGTGATT 60.676 52.381 4.15 0.00 0.00 2.57
2431 2452 0.108138 GGTAGAAGCCGCACAGTGAT 60.108 55.000 4.15 0.00 0.00 3.06
2432 2453 1.292223 GGTAGAAGCCGCACAGTGA 59.708 57.895 4.15 0.00 0.00 3.41
2433 2454 0.391661 ATGGTAGAAGCCGCACAGTG 60.392 55.000 0.00 0.00 0.00 3.66
2434 2455 1.137086 CTATGGTAGAAGCCGCACAGT 59.863 52.381 0.00 0.00 0.00 3.55
2435 2456 1.137086 ACTATGGTAGAAGCCGCACAG 59.863 52.381 0.00 0.00 0.00 3.66
2436 2457 1.136305 GACTATGGTAGAAGCCGCACA 59.864 52.381 0.00 0.00 0.00 4.57
2437 2458 1.136305 TGACTATGGTAGAAGCCGCAC 59.864 52.381 0.00 0.00 0.00 5.34
2438 2459 1.409064 CTGACTATGGTAGAAGCCGCA 59.591 52.381 0.00 0.00 0.00 5.69
2439 2460 1.681793 TCTGACTATGGTAGAAGCCGC 59.318 52.381 0.00 0.00 0.00 6.53
2440 2461 4.386867 TTTCTGACTATGGTAGAAGCCG 57.613 45.455 0.00 0.00 32.59 5.52
2463 2484 8.563732 GCTAGAAAAGAGAGAAAAATGTGTCTT 58.436 33.333 0.00 0.00 0.00 3.01
2464 2485 7.936301 AGCTAGAAAAGAGAGAAAAATGTGTCT 59.064 33.333 0.00 0.00 0.00 3.41
2465 2486 8.014517 CAGCTAGAAAAGAGAGAAAAATGTGTC 58.985 37.037 0.00 0.00 0.00 3.67
2466 2487 7.716998 TCAGCTAGAAAAGAGAGAAAAATGTGT 59.283 33.333 0.00 0.00 0.00 3.72
2467 2488 8.092521 TCAGCTAGAAAAGAGAGAAAAATGTG 57.907 34.615 0.00 0.00 0.00 3.21
2468 2489 8.682936 TTCAGCTAGAAAAGAGAGAAAAATGT 57.317 30.769 0.00 0.00 32.05 2.71
2469 2490 7.750014 GCTTCAGCTAGAAAAGAGAGAAAAATG 59.250 37.037 0.00 0.00 35.40 2.32
2470 2491 7.446625 TGCTTCAGCTAGAAAAGAGAGAAAAAT 59.553 33.333 0.00 0.00 42.66 1.82
2471 2492 6.767902 TGCTTCAGCTAGAAAAGAGAGAAAAA 59.232 34.615 0.00 0.00 42.66 1.94
2472 2493 6.203723 GTGCTTCAGCTAGAAAAGAGAGAAAA 59.796 38.462 0.00 0.00 42.66 2.29
2473 2494 5.698545 GTGCTTCAGCTAGAAAAGAGAGAAA 59.301 40.000 0.00 0.00 42.66 2.52
2474 2495 5.221521 TGTGCTTCAGCTAGAAAAGAGAGAA 60.222 40.000 0.00 0.00 42.66 2.87
2475 2496 4.281941 TGTGCTTCAGCTAGAAAAGAGAGA 59.718 41.667 0.00 0.00 42.66 3.10
2476 2497 4.564041 TGTGCTTCAGCTAGAAAAGAGAG 58.436 43.478 0.00 0.00 42.66 3.20
2477 2498 4.281941 TCTGTGCTTCAGCTAGAAAAGAGA 59.718 41.667 0.00 0.00 43.32 3.10
2478 2499 4.388469 GTCTGTGCTTCAGCTAGAAAAGAG 59.612 45.833 0.00 0.00 43.32 2.85
2479 2500 4.039730 AGTCTGTGCTTCAGCTAGAAAAGA 59.960 41.667 0.00 0.00 43.32 2.52
2480 2501 4.314121 AGTCTGTGCTTCAGCTAGAAAAG 58.686 43.478 0.00 0.00 43.32 2.27
2481 2502 4.039730 AGAGTCTGTGCTTCAGCTAGAAAA 59.960 41.667 0.00 0.00 43.32 2.29
2482 2503 3.576118 AGAGTCTGTGCTTCAGCTAGAAA 59.424 43.478 0.00 0.00 43.32 2.52
2483 2504 3.161067 AGAGTCTGTGCTTCAGCTAGAA 58.839 45.455 0.00 0.00 43.32 2.10
2484 2505 2.752354 GAGAGTCTGTGCTTCAGCTAGA 59.248 50.000 0.00 1.71 43.32 2.43
2485 2506 2.477694 CGAGAGTCTGTGCTTCAGCTAG 60.478 54.545 0.00 0.00 43.32 3.42
2486 2507 1.470494 CGAGAGTCTGTGCTTCAGCTA 59.530 52.381 0.00 0.00 43.32 3.32
2487 2508 0.243365 CGAGAGTCTGTGCTTCAGCT 59.757 55.000 0.00 5.71 43.32 4.24
2488 2509 1.350706 GCGAGAGTCTGTGCTTCAGC 61.351 60.000 0.00 0.00 43.32 4.26
2489 2510 0.243365 AGCGAGAGTCTGTGCTTCAG 59.757 55.000 10.05 3.68 44.85 3.02
2490 2511 0.242286 GAGCGAGAGTCTGTGCTTCA 59.758 55.000 15.60 0.00 37.91 3.02
2491 2512 0.525761 AGAGCGAGAGTCTGTGCTTC 59.474 55.000 15.60 10.09 37.91 3.86
2492 2513 0.525761 GAGAGCGAGAGTCTGTGCTT 59.474 55.000 15.60 7.73 37.91 3.91
2493 2514 0.322456 AGAGAGCGAGAGTCTGTGCT 60.322 55.000 14.66 14.66 41.11 4.40
2494 2515 0.525761 AAGAGAGCGAGAGTCTGTGC 59.474 55.000 0.00 0.94 0.00 4.57
2495 2516 2.030363 ACAAAGAGAGCGAGAGTCTGTG 60.030 50.000 0.00 0.00 32.56 3.66
2496 2517 2.030363 CACAAAGAGAGCGAGAGTCTGT 60.030 50.000 0.00 0.00 0.00 3.41
2497 2518 2.227626 TCACAAAGAGAGCGAGAGTCTG 59.772 50.000 0.00 0.00 0.00 3.51
2498 2519 2.509569 TCACAAAGAGAGCGAGAGTCT 58.490 47.619 0.00 0.00 0.00 3.24
2499 2520 2.999507 TCACAAAGAGAGCGAGAGTC 57.000 50.000 0.00 0.00 0.00 3.36
2500 2521 3.735237 TTTCACAAAGAGAGCGAGAGT 57.265 42.857 0.00 0.00 0.00 3.24
2501 2522 3.616379 GGATTTCACAAAGAGAGCGAGAG 59.384 47.826 0.00 0.00 0.00 3.20
2502 2523 3.006859 TGGATTTCACAAAGAGAGCGAGA 59.993 43.478 0.00 0.00 0.00 4.04
2503 2524 3.329386 TGGATTTCACAAAGAGAGCGAG 58.671 45.455 0.00 0.00 0.00 5.03
2504 2525 3.401033 TGGATTTCACAAAGAGAGCGA 57.599 42.857 0.00 0.00 0.00 4.93
2505 2526 3.686241 TGATGGATTTCACAAAGAGAGCG 59.314 43.478 0.00 0.00 0.00 5.03
2506 2527 4.699257 AGTGATGGATTTCACAAAGAGAGC 59.301 41.667 7.28 0.00 46.81 4.09
2507 2528 6.814506 AAGTGATGGATTTCACAAAGAGAG 57.185 37.500 7.28 0.00 46.81 3.20
2508 2529 8.690203 TTAAAGTGATGGATTTCACAAAGAGA 57.310 30.769 7.28 0.00 46.81 3.10
2509 2530 9.918630 AATTAAAGTGATGGATTTCACAAAGAG 57.081 29.630 7.28 0.00 46.81 2.85
2543 2564 8.783833 AGAGATACGAATCATCCAAAATATGG 57.216 34.615 0.00 0.00 41.66 2.74
2544 2565 9.650539 AGAGAGATACGAATCATCCAAAATATG 57.349 33.333 0.00 0.00 34.28 1.78
2548 2569 9.884636 TTTAAGAGAGATACGAATCATCCAAAA 57.115 29.630 0.00 0.00 34.28 2.44
2549 2570 9.314321 GTTTAAGAGAGATACGAATCATCCAAA 57.686 33.333 0.00 0.00 34.28 3.28
2550 2571 8.474831 TGTTTAAGAGAGATACGAATCATCCAA 58.525 33.333 0.00 0.00 34.28 3.53
2551 2572 8.007405 TGTTTAAGAGAGATACGAATCATCCA 57.993 34.615 0.00 0.00 34.28 3.41
2552 2573 8.873215 TTGTTTAAGAGAGATACGAATCATCC 57.127 34.615 0.00 0.00 34.28 3.51
2596 2617 9.194972 TGGCACATGGAGTTCAAATATATAAAA 57.805 29.630 0.00 0.00 0.00 1.52
2597 2618 8.759481 TGGCACATGGAGTTCAAATATATAAA 57.241 30.769 0.00 0.00 0.00 1.40
2598 2619 8.759481 TTGGCACATGGAGTTCAAATATATAA 57.241 30.769 0.00 0.00 39.30 0.98
2599 2620 8.217111 TCTTGGCACATGGAGTTCAAATATATA 58.783 33.333 0.00 0.00 39.30 0.86
2600 2621 7.013655 GTCTTGGCACATGGAGTTCAAATATAT 59.986 37.037 0.00 0.00 39.30 0.86
2601 2622 6.318648 GTCTTGGCACATGGAGTTCAAATATA 59.681 38.462 0.00 0.00 39.30 0.86
2602 2623 5.126061 GTCTTGGCACATGGAGTTCAAATAT 59.874 40.000 0.00 0.00 39.30 1.28
2603 2624 4.458989 GTCTTGGCACATGGAGTTCAAATA 59.541 41.667 0.00 0.00 39.30 1.40
2604 2625 3.256631 GTCTTGGCACATGGAGTTCAAAT 59.743 43.478 0.00 0.00 39.30 2.32
2605 2626 2.622942 GTCTTGGCACATGGAGTTCAAA 59.377 45.455 0.00 0.00 39.30 2.69
2606 2627 2.229792 GTCTTGGCACATGGAGTTCAA 58.770 47.619 0.00 0.00 39.30 2.69
2607 2628 1.545428 GGTCTTGGCACATGGAGTTCA 60.545 52.381 0.00 0.00 39.30 3.18
2608 2629 1.168714 GGTCTTGGCACATGGAGTTC 58.831 55.000 0.00 0.00 39.30 3.01
2609 2630 0.606401 CGGTCTTGGCACATGGAGTT 60.606 55.000 0.00 0.00 39.30 3.01
2610 2631 1.003355 CGGTCTTGGCACATGGAGT 60.003 57.895 0.00 0.00 39.30 3.85
2611 2632 1.003355 ACGGTCTTGGCACATGGAG 60.003 57.895 0.00 0.00 39.30 3.86
2612 2633 1.003839 GACGGTCTTGGCACATGGA 60.004 57.895 0.00 0.00 39.30 3.41
2613 2634 1.300971 CTGACGGTCTTGGCACATGG 61.301 60.000 9.88 0.00 39.30 3.66
2614 2635 0.320683 TCTGACGGTCTTGGCACATG 60.321 55.000 9.88 0.00 39.30 3.21
2615 2636 0.396435 TTCTGACGGTCTTGGCACAT 59.604 50.000 9.88 0.00 39.30 3.21
2616 2637 0.396435 ATTCTGACGGTCTTGGCACA 59.604 50.000 9.88 0.00 0.00 4.57
2617 2638 2.380084 TATTCTGACGGTCTTGGCAC 57.620 50.000 9.88 0.00 0.00 5.01
2618 2639 2.565391 TCTTATTCTGACGGTCTTGGCA 59.435 45.455 9.88 0.00 0.00 4.92
2619 2640 3.247006 TCTTATTCTGACGGTCTTGGC 57.753 47.619 9.88 0.00 0.00 4.52
2620 2641 5.011090 TGATCTTATTCTGACGGTCTTGG 57.989 43.478 9.88 0.34 0.00 3.61
2621 2642 6.201806 GGATTGATCTTATTCTGACGGTCTTG 59.798 42.308 9.88 2.77 0.00 3.02
2622 2643 6.098982 AGGATTGATCTTATTCTGACGGTCTT 59.901 38.462 9.88 0.00 0.00 3.01
2623 2644 5.600484 AGGATTGATCTTATTCTGACGGTCT 59.400 40.000 9.88 0.00 0.00 3.85
2624 2645 5.848406 AGGATTGATCTTATTCTGACGGTC 58.152 41.667 0.00 0.00 0.00 4.79
2625 2646 5.878406 AGGATTGATCTTATTCTGACGGT 57.122 39.130 0.00 0.00 0.00 4.83
2642 2663 7.214467 ACGTGTTTCAAATGTATCAAGGATT 57.786 32.000 0.00 0.00 0.00 3.01
2643 2664 6.817765 ACGTGTTTCAAATGTATCAAGGAT 57.182 33.333 0.00 0.00 0.00 3.24
2644 2665 6.627395 AACGTGTTTCAAATGTATCAAGGA 57.373 33.333 0.00 0.00 0.00 3.36
2645 2666 8.789881 TTAAACGTGTTTCAAATGTATCAAGG 57.210 30.769 0.47 0.00 34.23 3.61
2652 2673 9.748100 GTCAAAAATTAAACGTGTTTCAAATGT 57.252 25.926 0.47 0.00 34.23 2.71
2653 2674 9.746711 TGTCAAAAATTAAACGTGTTTCAAATG 57.253 25.926 0.47 0.00 34.23 2.32
2657 2678 9.959775 GAAATGTCAAAAATTAAACGTGTTTCA 57.040 25.926 0.47 0.00 34.23 2.69
2658 2679 9.959775 TGAAATGTCAAAAATTAAACGTGTTTC 57.040 25.926 0.47 0.00 34.23 2.78
2659 2680 9.748100 GTGAAATGTCAAAAATTAAACGTGTTT 57.252 25.926 3.21 3.21 34.87 2.83
2660 2681 8.926710 TGTGAAATGTCAAAAATTAAACGTGTT 58.073 25.926 0.00 0.00 34.87 3.32
2661 2682 8.467402 TGTGAAATGTCAAAAATTAAACGTGT 57.533 26.923 0.00 0.00 34.87 4.49
2662 2683 9.913451 AATGTGAAATGTCAAAAATTAAACGTG 57.087 25.926 0.00 0.00 34.87 4.49
2671 2692 9.605955 CACGTATAGAATGTGAAATGTCAAAAA 57.394 29.630 0.00 0.00 46.40 1.94
2683 2704 7.129109 AGGTTTGTTTCACGTATAGAATGTG 57.871 36.000 0.00 0.00 45.08 3.21
2684 2705 9.444600 AATAGGTTTGTTTCACGTATAGAATGT 57.555 29.630 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.