Multiple sequence alignment - TraesCS6B01G105300

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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 TraesCS6B01G105300 chr6B 100.000 3264 0 0 1 3264 84850297 84847034 0 6028
1 TraesCS6B01G105300 chr6A 90.380 2422 139 48 1 2354 48170570 48168175 0 3096
2 TraesCS6B01G105300 chr6D 87.813 1797 147 33 590 2328 36582622 36580840 0 2039
3 TraesCS6B01G105300 chr2D 87.412 707 77 9 2567 3264 373983051 373983754 0 802
4 TraesCS6B01G105300 chr2D 87.752 694 75 8 2573 3258 587269067 587269758 0 802
5 TraesCS6B01G105300 chr2D 86.555 714 91 4 2556 3264 52585048 52585761 0 782
6 TraesCS6B01G105300 chr3A 86.975 714 84 8 2553 3258 128290782 128291494 0 795
7 TraesCS6B01G105300 chr3A 86.835 714 85 8 2553 3258 128289277 128289989 0 789
8 TraesCS6B01G105300 chr5D 86.846 707 85 7 2559 3258 458000556 458001261 0 784
9 TraesCS6B01G105300 chr1D 86.864 708 80 11 2557 3258 139138654 139139354 0 780
10 TraesCS6B01G105300 chr2B 86.536 713 84 10 2557 3258 131900391 131899680 0 774
11 TraesCS6B01G105300 chr1A 84.788 756 103 11 2510 3258 437234971 437235721 0 749


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 TraesCS6B01G105300 chr6B 84847034 84850297 3263 True 6028 6028 100.000 1 3264 1 chr6B.!!$R1 3263
1 TraesCS6B01G105300 chr6A 48168175 48170570 2395 True 3096 3096 90.380 1 2354 1 chr6A.!!$R1 2353
2 TraesCS6B01G105300 chr6D 36580840 36582622 1782 True 2039 2039 87.813 590 2328 1 chr6D.!!$R1 1738
3 TraesCS6B01G105300 chr2D 373983051 373983754 703 False 802 802 87.412 2567 3264 1 chr2D.!!$F2 697
4 TraesCS6B01G105300 chr2D 587269067 587269758 691 False 802 802 87.752 2573 3258 1 chr2D.!!$F3 685
5 TraesCS6B01G105300 chr2D 52585048 52585761 713 False 782 782 86.555 2556 3264 1 chr2D.!!$F1 708
6 TraesCS6B01G105300 chr3A 128289277 128291494 2217 False 792 795 86.905 2553 3258 2 chr3A.!!$F1 705
7 TraesCS6B01G105300 chr5D 458000556 458001261 705 False 784 784 86.846 2559 3258 1 chr5D.!!$F1 699
8 TraesCS6B01G105300 chr1D 139138654 139139354 700 False 780 780 86.864 2557 3258 1 chr1D.!!$F1 701
9 TraesCS6B01G105300 chr2B 131899680 131900391 711 True 774 774 86.536 2557 3258 1 chr2B.!!$R1 701
10 TraesCS6B01G105300 chr1A 437234971 437235721 750 False 749 749 84.788 2510 3258 1 chr1A.!!$F1 748

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
381 390 1.375908 TCGGCTTGAGACATGCACC 60.376 57.895 10.71 0.0 36.45 5.01 F
1039 1078 0.036952 AGCATCAACTGGTCACTCGG 60.037 55.000 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1448 0.387929 TGAAGACGAGCAGGAACGTT 59.612 50.0 0.00 0.0 42.74 3.99 R
2530 2620 0.038251 GCATCTGCGGATGGATACGA 60.038 55.0 31.65 0.0 46.77 3.43 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
24 25 4.519350 TGATATGTCCTACTCCTGCTTACG 59.481 45.833 0.00 0.00 0.00 3.18
61 62 5.506317 GGTGTCAACTTCAAGAAACCATCTG 60.506 44.000 0.00 0.00 41.04 2.90
76 85 9.347240 AGAAACCATCTGATGTTTGGATTATAG 57.653 33.333 15.95 0.00 36.88 1.31
200 209 3.390135 TGTCTCCGACACATGAGTTTTC 58.610 45.455 0.00 0.00 37.67 2.29
206 215 3.002862 CCGACACATGAGTTTTCGGAAAA 59.997 43.478 14.11 11.68 46.65 2.29
209 218 4.359706 ACACATGAGTTTTCGGAAAAAGC 58.640 39.130 16.83 12.16 35.10 3.51
248 257 4.227300 ACAATATTTAGGGCTGAGGTGACA 59.773 41.667 0.00 0.00 0.00 3.58
348 357 4.327680 GGATGGGTTCCATATGCTAAGTC 58.672 47.826 0.00 0.00 45.26 3.01
361 370 3.982516 TGCTAAGTCACTAGAGGGACAT 58.017 45.455 14.21 4.84 36.50 3.06
362 371 3.954904 TGCTAAGTCACTAGAGGGACATC 59.045 47.826 14.21 1.24 36.50 3.06
381 390 1.375908 TCGGCTTGAGACATGCACC 60.376 57.895 10.71 0.00 36.45 5.01
397 406 7.994911 AGACATGCACCTCATATTTCTCATTAA 59.005 33.333 0.00 0.00 33.19 1.40
398 407 8.162878 ACATGCACCTCATATTTCTCATTAAG 57.837 34.615 0.00 0.00 33.19 1.85
399 408 7.776969 ACATGCACCTCATATTTCTCATTAAGT 59.223 33.333 0.00 0.00 33.19 2.24
401 410 7.337938 TGCACCTCATATTTCTCATTAAGTGA 58.662 34.615 0.00 0.00 35.05 3.41
402 411 7.280876 TGCACCTCATATTTCTCATTAAGTGAC 59.719 37.037 0.00 0.00 32.22 3.67
403 412 7.497249 GCACCTCATATTTCTCATTAAGTGACT 59.503 37.037 0.00 0.00 32.22 3.41
422 431 8.511604 AGTGACTATAATGGAAGGAATTTGTG 57.488 34.615 0.00 0.00 0.00 3.33
428 437 9.793252 CTATAATGGAAGGAATTTGTGTCTTTG 57.207 33.333 0.00 0.00 0.00 2.77
470 479 9.495572 TTGAGTTGTGGTTTTCTTGTTAAAAAT 57.504 25.926 0.00 0.00 30.53 1.82
472 481 9.366216 GAGTTGTGGTTTTCTTGTTAAAAATCT 57.634 29.630 0.00 0.00 29.90 2.40
539 549 5.699097 TTGTGTAATTTCCTCTTTTCGGG 57.301 39.130 0.00 0.00 0.00 5.14
550 560 8.502105 TTTCCTCTTTTCGGGAAATCTTATAC 57.498 34.615 3.42 0.00 43.86 1.47
553 563 8.639761 TCCTCTTTTCGGGAAATCTTATACTAG 58.360 37.037 0.00 0.00 0.00 2.57
583 593 8.707938 AAATTTGCCTATGAAAATCTTACAGC 57.292 30.769 0.00 0.00 0.00 4.40
831 855 6.949352 ATTGTAGCAAGTATTCTGATTGGG 57.051 37.500 0.00 0.00 0.00 4.12
834 858 3.907221 AGCAAGTATTCTGATTGGGCAT 58.093 40.909 0.00 0.00 0.00 4.40
869 893 3.475932 TGGTTAGCCAGTGAGACCT 57.524 52.632 0.00 0.00 40.46 3.85
933 958 1.539388 CCAAAACATTGCAGGCTCGTA 59.461 47.619 0.00 0.00 0.00 3.43
979 1011 6.149973 GGGCTACATACACGACTACATATACA 59.850 42.308 0.00 0.00 0.00 2.29
1013 1045 1.543802 CGCTTCTCACCAGTTCTCTCT 59.456 52.381 0.00 0.00 0.00 3.10
1039 1078 0.036952 AGCATCAACTGGTCACTCGG 60.037 55.000 0.00 0.00 0.00 4.63
1085 1124 5.826601 TTGCTGCATCGGTGATTAAATTA 57.173 34.783 1.84 0.00 0.00 1.40
1162 1204 0.807496 GCTTTCTCCATGGACAGCAC 59.193 55.000 22.80 7.12 38.46 4.40
1226 1268 1.413767 CTTCGGTGAAGATCGTGCCG 61.414 60.000 12.71 12.71 41.71 5.69
1259 1301 3.444034 ACGACGAGAATGAGAAATCTCCA 59.556 43.478 0.00 0.00 42.20 3.86
1304 1346 2.416547 CGTGCATCTGGTTAAGAAGGTG 59.583 50.000 0.00 0.00 38.79 4.00
1305 1347 3.674997 GTGCATCTGGTTAAGAAGGTGA 58.325 45.455 0.00 0.00 38.79 4.02
1311 1353 4.703897 TCTGGTTAAGAAGGTGAGTGTTG 58.296 43.478 0.00 0.00 29.54 3.33
1324 1367 4.082463 GGTGAGTGTTGTTTCCTGTGAAAA 60.082 41.667 0.00 0.00 41.92 2.29
1330 1373 4.396478 TGTTGTTTCCTGTGAAAATCGTGA 59.604 37.500 0.00 0.00 41.92 4.35
1331 1374 4.545823 TGTTTCCTGTGAAAATCGTGAC 57.454 40.909 0.00 0.00 41.92 3.67
1346 1397 3.295973 TCGTGACCATGTATGAGATGGA 58.704 45.455 9.46 0.00 42.81 3.41
1351 1402 4.063689 GACCATGTATGAGATGGAGCTTG 58.936 47.826 9.46 0.00 42.81 4.01
1396 1448 0.322456 CAATGGCCGAGTTCTTGGGA 60.322 55.000 0.00 0.00 0.00 4.37
1447 1499 1.586422 CGGCCATCATGAACGAGATT 58.414 50.000 2.24 0.00 0.00 2.40
1531 1583 3.173240 GCGTCGCTCTTCCACGTC 61.173 66.667 10.68 0.00 35.91 4.34
1555 1607 2.847234 AGCCACCTGAACCCGTCA 60.847 61.111 0.00 0.00 34.17 4.35
1680 1738 4.603946 GATCTACCACCCGGCGGC 62.604 72.222 23.20 0.00 34.57 6.53
1736 1794 2.032681 GCACGTTGGAGGCCTTCT 59.967 61.111 13.68 0.00 0.00 2.85
1784 1842 2.279451 TCTTCGCCATCATCGCCG 60.279 61.111 0.00 0.00 0.00 6.46
1808 1866 1.404986 CCACCGATCCGAAAGCAGTAA 60.405 52.381 0.00 0.00 0.00 2.24
1817 1875 1.993370 CGAAAGCAGTAAGGAAGACCG 59.007 52.381 0.00 0.00 41.83 4.79
1840 1902 7.281324 ACCGGATTATATTATCTCTCAGTCTCG 59.719 40.741 9.46 0.00 0.00 4.04
1863 1933 2.881513 TCACTCACTCACTCACTGACTC 59.118 50.000 0.00 0.00 0.00 3.36
1865 1935 3.255395 CACTCACTCACTCACTGACTCAT 59.745 47.826 0.00 0.00 0.00 2.90
1895 1965 8.000780 ACTGCCAAATGATCTTTAAATAGGTC 57.999 34.615 0.00 0.00 0.00 3.85
1936 2006 1.748122 CTGGGGCAGCACTGATGAC 60.748 63.158 0.81 0.00 0.00 3.06
1972 2042 2.540515 CGCGTAAGTGGAATGATCAGT 58.459 47.619 0.09 0.00 46.11 3.41
1989 2059 4.537936 TCAGTCGATCAATGACTCTACG 57.462 45.455 0.00 0.00 44.60 3.51
1993 2063 4.036352 GTCGATCAATGACTCTACGGTTC 58.964 47.826 0.00 0.00 33.54 3.62
2001 2071 6.368791 TCAATGACTCTACGGTTCTTTTCATG 59.631 38.462 0.00 0.00 0.00 3.07
2002 2072 3.994392 TGACTCTACGGTTCTTTTCATGC 59.006 43.478 0.00 0.00 0.00 4.06
2057 2127 0.465705 GGGAATCGACAGGAGCATCA 59.534 55.000 0.00 0.00 36.25 3.07
2132 2202 2.666272 TCTGGGTTTACATGGTTGCA 57.334 45.000 0.00 0.00 0.00 4.08
2203 2275 2.964464 ACTGATGCATCTAGACCCTCAG 59.036 50.000 26.32 16.02 35.82 3.35
2206 2278 2.836636 TGCATCTAGACCCTCAGAGT 57.163 50.000 0.00 0.00 0.00 3.24
2212 2284 2.432874 TCTAGACCCTCAGAGTCTCGAG 59.567 54.545 5.93 5.93 43.48 4.04
2213 2285 0.393808 AGACCCTCAGAGTCTCGAGC 60.394 60.000 7.81 2.90 40.61 5.03
2219 2291 3.821055 AGAGTCTCGAGCCGCTGC 61.821 66.667 7.81 0.00 37.95 5.25
2238 2310 4.443394 GCTGCTGTAGAATTTTATGCATGC 59.557 41.667 11.82 11.82 0.00 4.06
2303 2393 4.104383 ACACTGTTCTTGGGATGACATT 57.896 40.909 0.00 0.00 0.00 2.71
2305 2395 4.895297 ACACTGTTCTTGGGATGACATTTT 59.105 37.500 0.00 0.00 0.00 1.82
2307 2397 6.549364 ACACTGTTCTTGGGATGACATTTTAA 59.451 34.615 0.00 0.00 0.00 1.52
2321 2411 8.630054 ATGACATTTTAACAAGCTTGTAGGTA 57.370 30.769 31.31 17.81 41.31 3.08
2328 2418 5.782893 AACAAGCTTGTAGGTATTGCAAA 57.217 34.783 31.31 0.00 41.31 3.68
2329 2419 5.782893 ACAAGCTTGTAGGTATTGCAAAA 57.217 34.783 30.25 0.00 40.16 2.44
2340 2430 9.237187 TGTAGGTATTGCAAAATCATGACTAAA 57.763 29.630 1.71 0.00 0.00 1.85
2342 2432 7.250569 AGGTATTGCAAAATCATGACTAAACG 58.749 34.615 1.71 0.00 0.00 3.60
2343 2433 6.472163 GGTATTGCAAAATCATGACTAAACGG 59.528 38.462 1.71 0.00 0.00 4.44
2354 2444 4.022464 TGACTAAACGGTGTTGCAAAAG 57.978 40.909 0.00 0.00 0.00 2.27
2355 2445 2.787129 GACTAAACGGTGTTGCAAAAGC 59.213 45.455 8.84 8.84 0.00 3.51
2356 2446 2.425668 ACTAAACGGTGTTGCAAAAGCT 59.574 40.909 16.41 1.01 0.00 3.74
2357 2447 1.921243 AAACGGTGTTGCAAAAGCTC 58.079 45.000 16.41 0.00 0.00 4.09
2358 2448 0.814457 AACGGTGTTGCAAAAGCTCA 59.186 45.000 16.41 0.00 0.00 4.26
2359 2449 1.032014 ACGGTGTTGCAAAAGCTCAT 58.968 45.000 16.41 0.00 0.00 2.90
2360 2450 1.269206 ACGGTGTTGCAAAAGCTCATG 60.269 47.619 16.41 3.82 0.00 3.07
2361 2451 1.001487 CGGTGTTGCAAAAGCTCATGA 60.001 47.619 16.41 0.00 0.00 3.07
2362 2452 2.669364 GGTGTTGCAAAAGCTCATGAG 58.331 47.619 18.84 18.84 0.00 2.90
2363 2453 2.608752 GGTGTTGCAAAAGCTCATGAGG 60.609 50.000 23.89 8.12 0.00 3.86
2364 2454 2.035066 GTGTTGCAAAAGCTCATGAGGT 59.965 45.455 21.55 21.55 41.53 3.85
2365 2455 2.034939 TGTTGCAAAAGCTCATGAGGTG 59.965 45.455 27.11 16.03 39.39 4.00
2366 2456 0.599558 TGCAAAAGCTCATGAGGTGC 59.400 50.000 27.11 24.28 39.39 5.01
2368 2458 1.135460 GCAAAAGCTCATGAGGTGCTC 60.135 52.381 27.11 13.20 45.11 4.26
2369 2459 1.471684 CAAAAGCTCATGAGGTGCTCC 59.528 52.381 27.11 7.87 45.11 4.70
2370 2460 0.694771 AAAGCTCATGAGGTGCTCCA 59.305 50.000 27.11 0.00 45.11 3.86
2371 2461 0.917533 AAGCTCATGAGGTGCTCCAT 59.082 50.000 27.11 8.41 45.11 3.41
2372 2462 0.469070 AGCTCATGAGGTGCTCCATC 59.531 55.000 25.97 4.92 42.40 3.51
2373 2463 0.534652 GCTCATGAGGTGCTCCATCC 60.535 60.000 23.89 0.00 35.89 3.51
2374 2464 1.129917 CTCATGAGGTGCTCCATCCT 58.870 55.000 15.38 0.00 36.70 3.24
2378 2468 1.145819 GAGGTGCTCCATCCTCTGC 59.854 63.158 7.70 0.00 44.68 4.26
2379 2469 1.614525 AGGTGCTCCATCCTCTGCA 60.615 57.895 7.70 0.00 35.89 4.41
2380 2470 4.215349 GTGCTCCATCCTCTGCAC 57.785 61.111 0.00 0.00 46.66 4.57
2381 2471 4.142045 TGCTCCATCCTCTGCACT 57.858 55.556 0.00 0.00 0.00 4.40
2382 2472 1.903294 TGCTCCATCCTCTGCACTC 59.097 57.895 0.00 0.00 0.00 3.51
2383 2473 0.616964 TGCTCCATCCTCTGCACTCT 60.617 55.000 0.00 0.00 0.00 3.24
2384 2474 0.540923 GCTCCATCCTCTGCACTCTT 59.459 55.000 0.00 0.00 0.00 2.85
2385 2475 1.473080 GCTCCATCCTCTGCACTCTTC 60.473 57.143 0.00 0.00 0.00 2.87
2386 2476 2.109774 CTCCATCCTCTGCACTCTTCT 58.890 52.381 0.00 0.00 0.00 2.85
2387 2477 3.295093 CTCCATCCTCTGCACTCTTCTA 58.705 50.000 0.00 0.00 0.00 2.10
2388 2478 3.703556 CTCCATCCTCTGCACTCTTCTAA 59.296 47.826 0.00 0.00 0.00 2.10
2389 2479 4.293494 TCCATCCTCTGCACTCTTCTAAT 58.707 43.478 0.00 0.00 0.00 1.73
2390 2480 5.458595 TCCATCCTCTGCACTCTTCTAATA 58.541 41.667 0.00 0.00 0.00 0.98
2391 2481 5.538053 TCCATCCTCTGCACTCTTCTAATAG 59.462 44.000 0.00 0.00 0.00 1.73
2392 2482 4.927978 TCCTCTGCACTCTTCTAATAGC 57.072 45.455 0.00 0.00 0.00 2.97
2393 2483 4.281657 TCCTCTGCACTCTTCTAATAGCA 58.718 43.478 0.00 0.00 0.00 3.49
2394 2484 4.711846 TCCTCTGCACTCTTCTAATAGCAA 59.288 41.667 0.00 0.00 0.00 3.91
2395 2485 5.187772 TCCTCTGCACTCTTCTAATAGCAAA 59.812 40.000 0.00 0.00 0.00 3.68
2396 2486 5.523188 CCTCTGCACTCTTCTAATAGCAAAG 59.477 44.000 0.00 0.00 0.00 2.77
2397 2487 5.423015 TCTGCACTCTTCTAATAGCAAAGG 58.577 41.667 0.00 0.00 0.00 3.11
2398 2488 4.517285 TGCACTCTTCTAATAGCAAAGGG 58.483 43.478 0.00 0.00 0.00 3.95
2399 2489 3.313803 GCACTCTTCTAATAGCAAAGGGC 59.686 47.826 0.00 0.00 45.30 5.19
2411 2501 3.850122 GCAAAGGGCTCGTTCTTAAAT 57.150 42.857 0.00 0.00 40.25 1.40
2412 2502 4.174411 GCAAAGGGCTCGTTCTTAAATT 57.826 40.909 0.00 0.00 40.25 1.82
2413 2503 5.305139 GCAAAGGGCTCGTTCTTAAATTA 57.695 39.130 0.00 0.00 40.25 1.40
2414 2504 5.705902 GCAAAGGGCTCGTTCTTAAATTAA 58.294 37.500 0.00 0.00 40.25 1.40
2415 2505 5.571741 GCAAAGGGCTCGTTCTTAAATTAAC 59.428 40.000 0.00 0.00 40.25 2.01
2416 2506 6.569801 GCAAAGGGCTCGTTCTTAAATTAACT 60.570 38.462 0.00 0.00 40.25 2.24
2417 2507 7.361457 GCAAAGGGCTCGTTCTTAAATTAACTA 60.361 37.037 0.00 0.00 40.25 2.24
2418 2508 8.674607 CAAAGGGCTCGTTCTTAAATTAACTAT 58.325 33.333 0.00 0.00 0.00 2.12
2419 2509 7.787725 AGGGCTCGTTCTTAAATTAACTATG 57.212 36.000 0.00 0.00 0.00 2.23
2420 2510 6.260271 AGGGCTCGTTCTTAAATTAACTATGC 59.740 38.462 0.00 0.00 0.00 3.14
2421 2511 6.427974 GGCTCGTTCTTAAATTAACTATGCC 58.572 40.000 0.00 0.00 0.00 4.40
2422 2512 6.037830 GGCTCGTTCTTAAATTAACTATGCCA 59.962 38.462 0.00 0.00 35.23 4.92
2423 2513 7.414762 GGCTCGTTCTTAAATTAACTATGCCAA 60.415 37.037 0.00 0.00 35.23 4.52
2424 2514 7.966204 GCTCGTTCTTAAATTAACTATGCCAAA 59.034 33.333 0.00 0.00 0.00 3.28
2425 2515 9.490663 CTCGTTCTTAAATTAACTATGCCAAAG 57.509 33.333 0.00 0.00 0.00 2.77
2426 2516 7.966204 TCGTTCTTAAATTAACTATGCCAAAGC 59.034 33.333 0.00 0.00 40.48 3.51
2427 2517 7.968405 CGTTCTTAAATTAACTATGCCAAAGCT 59.032 33.333 0.00 0.00 40.80 3.74
2428 2518 9.639601 GTTCTTAAATTAACTATGCCAAAGCTT 57.360 29.630 0.00 0.00 40.80 3.74
2432 2522 9.988815 TTAAATTAACTATGCCAAAGCTTTTGA 57.011 25.926 14.13 0.00 40.80 2.69
2439 2529 9.971922 AACTATGCCAAAGCTTTTGATAATATC 57.028 29.630 14.13 0.00 40.80 1.63
2440 2530 9.135189 ACTATGCCAAAGCTTTTGATAATATCA 57.865 29.630 14.13 0.00 40.80 2.15
2441 2531 9.970395 CTATGCCAAAGCTTTTGATAATATCAA 57.030 29.630 14.13 11.32 42.89 2.57
2443 2533 9.841295 ATGCCAAAGCTTTTGATAATATCAATT 57.159 25.926 15.52 5.35 43.50 2.32
2444 2534 9.669887 TGCCAAAGCTTTTGATAATATCAATTT 57.330 25.926 15.52 10.47 43.50 1.82
2462 2552 8.735692 ATCAATTTTGTTTGTTGATCAAAGGT 57.264 26.923 10.35 0.00 45.15 3.50
2463 2553 8.558973 TCAATTTTGTTTGTTGATCAAAGGTT 57.441 26.923 10.35 0.00 45.15 3.50
2464 2554 8.663911 TCAATTTTGTTTGTTGATCAAAGGTTC 58.336 29.630 10.35 0.00 45.15 3.62
2465 2555 8.667463 CAATTTTGTTTGTTGATCAAAGGTTCT 58.333 29.630 10.35 0.00 45.15 3.01
2466 2556 8.791327 ATTTTGTTTGTTGATCAAAGGTTCTT 57.209 26.923 10.35 0.00 45.15 2.52
2467 2557 9.883142 ATTTTGTTTGTTGATCAAAGGTTCTTA 57.117 25.926 10.35 0.00 45.15 2.10
2468 2558 9.712305 TTTTGTTTGTTGATCAAAGGTTCTTAA 57.288 25.926 10.35 0.00 45.15 1.85
2469 2559 9.712305 TTTGTTTGTTGATCAAAGGTTCTTAAA 57.288 25.926 10.35 2.60 45.15 1.52
2470 2560 9.712305 TTGTTTGTTGATCAAAGGTTCTTAAAA 57.288 25.926 10.35 0.00 45.15 1.52
2471 2561 9.364989 TGTTTGTTGATCAAAGGTTCTTAAAAG 57.635 29.630 10.35 0.00 45.15 2.27
2472 2562 9.366216 GTTTGTTGATCAAAGGTTCTTAAAAGT 57.634 29.630 10.35 0.00 45.15 2.66
2475 2565 9.621629 TGTTGATCAAAGGTTCTTAAAAGTAGA 57.378 29.630 10.35 0.00 0.00 2.59
2477 2567 8.848474 TGATCAAAGGTTCTTAAAAGTAGAGG 57.152 34.615 0.00 0.00 0.00 3.69
2478 2568 8.437575 TGATCAAAGGTTCTTAAAAGTAGAGGT 58.562 33.333 0.00 0.00 0.00 3.85
2479 2569 9.286170 GATCAAAGGTTCTTAAAAGTAGAGGTT 57.714 33.333 0.00 0.00 0.00 3.50
2480 2570 9.642343 ATCAAAGGTTCTTAAAAGTAGAGGTTT 57.358 29.630 0.00 0.00 0.00 3.27
2481 2571 9.470399 TCAAAGGTTCTTAAAAGTAGAGGTTTT 57.530 29.630 0.00 0.00 0.00 2.43
2484 2574 8.151141 AGGTTCTTAAAAGTAGAGGTTTTTCG 57.849 34.615 0.00 0.00 0.00 3.46
2485 2575 7.772292 AGGTTCTTAAAAGTAGAGGTTTTTCGT 59.228 33.333 0.00 0.00 0.00 3.85
2486 2576 9.045223 GGTTCTTAAAAGTAGAGGTTTTTCGTA 57.955 33.333 0.00 0.00 0.00 3.43
2488 2578 8.822652 TCTTAAAAGTAGAGGTTTTTCGTAGG 57.177 34.615 0.00 0.00 0.00 3.18
2489 2579 5.936686 AAAAGTAGAGGTTTTTCGTAGGC 57.063 39.130 0.00 0.00 0.00 3.93
2490 2580 4.612264 AAGTAGAGGTTTTTCGTAGGCA 57.388 40.909 0.00 0.00 0.00 4.75
2491 2581 4.612264 AGTAGAGGTTTTTCGTAGGCAA 57.388 40.909 0.00 0.00 0.00 4.52
2492 2582 4.566987 AGTAGAGGTTTTTCGTAGGCAAG 58.433 43.478 0.00 0.00 0.00 4.01
2493 2583 3.487120 AGAGGTTTTTCGTAGGCAAGT 57.513 42.857 0.00 0.00 0.00 3.16
2494 2584 3.139077 AGAGGTTTTTCGTAGGCAAGTG 58.861 45.455 0.00 0.00 0.00 3.16
2495 2585 2.225727 GAGGTTTTTCGTAGGCAAGTGG 59.774 50.000 0.00 0.00 0.00 4.00
2496 2586 1.335597 GGTTTTTCGTAGGCAAGTGGC 60.336 52.381 0.00 0.00 43.74 5.01
2509 2599 3.774066 GCAAGTGGCAAGCTTAATTAGG 58.226 45.455 0.00 0.00 43.97 2.69
2510 2600 3.429410 GCAAGTGGCAAGCTTAATTAGGG 60.429 47.826 0.00 0.00 43.97 3.53
2511 2601 2.379005 AGTGGCAAGCTTAATTAGGGC 58.621 47.619 0.00 0.00 0.00 5.19
2512 2602 2.099405 GTGGCAAGCTTAATTAGGGCA 58.901 47.619 0.00 0.84 0.00 5.36
2513 2603 2.695147 GTGGCAAGCTTAATTAGGGCAT 59.305 45.455 10.90 1.36 33.34 4.40
2514 2604 2.958355 TGGCAAGCTTAATTAGGGCATC 59.042 45.455 0.00 4.03 0.00 3.91
2515 2605 3.225940 GGCAAGCTTAATTAGGGCATCT 58.774 45.455 0.00 0.00 0.00 2.90
2518 2608 4.464008 CAAGCTTAATTAGGGCATCTCCA 58.536 43.478 0.00 0.00 36.21 3.86
2529 2619 2.833943 GGGCATCTCCACAAATTTCCTT 59.166 45.455 0.00 0.00 36.21 3.36
2530 2620 3.261643 GGGCATCTCCACAAATTTCCTTT 59.738 43.478 0.00 0.00 36.21 3.11
2531 2621 4.498241 GGCATCTCCACAAATTTCCTTTC 58.502 43.478 0.00 0.00 34.01 2.62
2533 2623 4.321230 GCATCTCCACAAATTTCCTTTCGT 60.321 41.667 0.00 0.00 0.00 3.85
2538 2628 5.317808 TCCACAAATTTCCTTTCGTATCCA 58.682 37.500 0.00 0.00 0.00 3.41
2542 2632 5.065988 ACAAATTTCCTTTCGTATCCATCCG 59.934 40.000 0.00 0.00 0.00 4.18
2544 2634 1.116308 TCCTTTCGTATCCATCCGCA 58.884 50.000 0.00 0.00 0.00 5.69
2547 2637 2.289072 CCTTTCGTATCCATCCGCAGAT 60.289 50.000 0.00 0.00 0.00 2.90
2604 2695 0.180171 CGGGAGCACACCATCCAATA 59.820 55.000 0.00 0.00 37.33 1.90
2628 2720 1.654105 GCCGCATATATCCGAACTTCG 59.346 52.381 4.07 4.07 40.07 3.79
2636 2732 7.010023 GCATATATCCGAACTTCGTCATTTTC 58.990 38.462 10.22 0.00 38.40 2.29
2792 4401 5.453057 GCTCAATCAGATCTTCCTTCAGCTA 60.453 44.000 0.00 0.00 0.00 3.32
2796 4405 4.604156 TCAGATCTTCCTTCAGCTACTCA 58.396 43.478 0.00 0.00 0.00 3.41
2826 4435 5.240403 TGGTCGATGTTGAATTTGTTGATGA 59.760 36.000 0.00 0.00 0.00 2.92
2979 4589 2.309755 ACAACATGTCATCACCTCCCAT 59.690 45.455 0.00 0.00 0.00 4.00
3005 4616 4.514401 GTCTCCGAATCCCATTGTTTAGT 58.486 43.478 0.00 0.00 0.00 2.24
3010 4621 4.574828 CCGAATCCCATTGTTTAGTAGGTG 59.425 45.833 0.00 0.00 0.00 4.00
3073 4687 4.138290 CCTCTCGACATCCTTTCTAGCTA 58.862 47.826 0.00 0.00 0.00 3.32
3098 4712 2.435372 TGTCTTTGGGCAAAGTGAGT 57.565 45.000 0.00 0.00 45.88 3.41
3110 4725 3.181487 GCAAAGTGAGTCTTTTTCTGGCA 60.181 43.478 0.00 0.00 42.95 4.92
3115 4730 4.336713 AGTGAGTCTTTTTCTGGCAAACTC 59.663 41.667 0.00 0.00 33.86 3.01
3148 4763 4.165180 TGATGCTAATAAAGGTAGCCCACA 59.835 41.667 1.26 0.00 42.79 4.17
3205 4823 7.362315 CCATGTTGTACTCATGTTCATTGACAT 60.362 37.037 21.03 0.00 40.43 3.06
3258 4877 0.601841 ACCTCGAAACAACGGCGATT 60.602 50.000 16.62 0.55 33.20 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.753452 TCTGTTCGTAAGCAGGAGTAGG 59.247 50.000 0.00 0.00 33.81 3.18
18 19 2.128035 CCGATGGATCTGTTCGTAAGC 58.872 52.381 10.16 0.00 37.18 3.09
24 25 2.672961 TGACACCGATGGATCTGTTC 57.327 50.000 0.00 0.00 0.00 3.18
61 62 8.658499 ACGTTAAGACCTATAATCCAAACATC 57.342 34.615 0.00 0.00 0.00 3.06
76 85 5.182380 TGGATTTTGAATGGACGTTAAGACC 59.818 40.000 0.00 0.00 35.19 3.85
127 136 8.736751 TTATATTCTTTGTTCGTTTGCCTTTC 57.263 30.769 0.00 0.00 0.00 2.62
200 209 3.940657 TTGTGCAATTTGCTTTTTCCG 57.059 38.095 21.19 0.00 45.31 4.30
206 215 6.864360 ATTGTGTATTTGTGCAATTTGCTT 57.136 29.167 21.19 5.11 45.31 3.91
248 257 8.429641 TGATTAGTTCTAGAGTTGTGGTTTTCT 58.570 33.333 0.00 0.00 0.00 2.52
348 357 0.671251 GCCGAGATGTCCCTCTAGTG 59.329 60.000 0.00 0.00 0.00 2.74
362 371 1.364626 GGTGCATGTCTCAAGCCGAG 61.365 60.000 0.00 0.00 43.80 4.63
397 406 8.109634 ACACAAATTCCTTCCATTATAGTCACT 58.890 33.333 0.00 0.00 0.00 3.41
398 407 8.281212 ACACAAATTCCTTCCATTATAGTCAC 57.719 34.615 0.00 0.00 0.00 3.67
399 408 8.328758 AGACACAAATTCCTTCCATTATAGTCA 58.671 33.333 0.00 0.00 0.00 3.41
401 410 9.533831 AAAGACACAAATTCCTTCCATTATAGT 57.466 29.630 0.00 0.00 0.00 2.12
402 411 9.793252 CAAAGACACAAATTCCTTCCATTATAG 57.207 33.333 0.00 0.00 0.00 1.31
403 412 8.748412 CCAAAGACACAAATTCCTTCCATTATA 58.252 33.333 0.00 0.00 0.00 0.98
404 413 7.235399 ACCAAAGACACAAATTCCTTCCATTAT 59.765 33.333 0.00 0.00 0.00 1.28
422 431 7.328737 TCAAGGACTAATAAGCTACCAAAGAC 58.671 38.462 0.00 0.00 0.00 3.01
428 437 6.535508 CACAACTCAAGGACTAATAAGCTACC 59.464 42.308 0.00 0.00 0.00 3.18
487 496 7.179269 ACAATATTAAGGGCTGAGGTAACAAA 58.821 34.615 0.00 0.00 41.41 2.83
558 568 8.313292 TGCTGTAAGATTTTCATAGGCAAATTT 58.687 29.630 0.00 0.00 34.07 1.82
559 569 7.839907 TGCTGTAAGATTTTCATAGGCAAATT 58.160 30.769 0.00 0.00 34.07 1.82
560 570 7.340232 TCTGCTGTAAGATTTTCATAGGCAAAT 59.660 33.333 0.00 0.00 34.07 2.32
561 571 6.658816 TCTGCTGTAAGATTTTCATAGGCAAA 59.341 34.615 0.00 0.00 34.07 3.68
562 572 6.179756 TCTGCTGTAAGATTTTCATAGGCAA 58.820 36.000 0.00 0.00 34.07 4.52
563 573 5.744171 TCTGCTGTAAGATTTTCATAGGCA 58.256 37.500 0.00 0.00 34.07 4.75
564 574 6.683974 TTCTGCTGTAAGATTTTCATAGGC 57.316 37.500 0.00 0.00 34.07 3.93
565 575 8.674263 AGATTCTGCTGTAAGATTTTCATAGG 57.326 34.615 0.00 0.00 34.07 2.57
569 579 9.725019 TCTTAAGATTCTGCTGTAAGATTTTCA 57.275 29.630 0.00 0.00 34.07 2.69
576 586 9.376075 TCTGAATTCTTAAGATTCTGCTGTAAG 57.624 33.333 19.44 11.76 0.00 2.34
580 590 8.772705 GGTATCTGAATTCTTAAGATTCTGCTG 58.227 37.037 19.44 8.11 32.92 4.41
813 837 3.370840 TGCCCAATCAGAATACTTGCT 57.629 42.857 0.00 0.00 0.00 3.91
815 839 5.840243 TCAATGCCCAATCAGAATACTTG 57.160 39.130 0.00 0.00 0.00 3.16
816 840 5.954150 AGTTCAATGCCCAATCAGAATACTT 59.046 36.000 0.00 0.00 0.00 2.24
820 844 6.608405 TGATTAGTTCAATGCCCAATCAGAAT 59.392 34.615 0.00 0.00 30.95 2.40
831 855 6.199937 ACCAGTCAATGATTAGTTCAATGC 57.800 37.500 0.00 0.00 38.03 3.56
834 858 6.374333 GGCTAACCAGTCAATGATTAGTTCAA 59.626 38.462 0.00 0.00 35.03 2.69
865 889 6.560253 TGTTCAAATTAAGAAGCTGAGGTC 57.440 37.500 0.00 0.00 0.00 3.85
867 891 5.860716 GCTTGTTCAAATTAAGAAGCTGAGG 59.139 40.000 13.04 0.00 46.63 3.86
979 1011 4.096682 GTGAGAAGCGTATAGTGGAGAAGT 59.903 45.833 0.00 0.00 0.00 3.01
1013 1045 2.229792 GACCAGTTGATGCTTGGTGAA 58.770 47.619 0.00 0.00 32.35 3.18
1061 1100 3.696281 TTAATCACCGATGCAGCAATG 57.304 42.857 1.53 0.00 0.00 2.82
1062 1101 4.924305 ATTTAATCACCGATGCAGCAAT 57.076 36.364 1.53 0.00 0.00 3.56
1064 1103 4.275689 CCTAATTTAATCACCGATGCAGCA 59.724 41.667 1.53 0.00 0.00 4.41
1085 1124 1.235696 GCTCTCCTCCATCCTCCCT 59.764 63.158 0.00 0.00 0.00 4.20
1116 1155 5.389935 GGTTGATGTTCAGAGAAATGTCGAC 60.390 44.000 9.11 9.11 0.00 4.20
1117 1156 4.690748 GGTTGATGTTCAGAGAAATGTCGA 59.309 41.667 0.00 0.00 0.00 4.20
1286 1328 3.686726 CACTCACCTTCTTAACCAGATGC 59.313 47.826 0.00 0.00 0.00 3.91
1304 1346 4.970003 CGATTTTCACAGGAAACAACACTC 59.030 41.667 0.00 0.00 42.48 3.51
1305 1347 4.398044 ACGATTTTCACAGGAAACAACACT 59.602 37.500 0.00 0.00 42.48 3.55
1311 1353 3.314080 TGGTCACGATTTTCACAGGAAAC 59.686 43.478 0.00 0.00 42.48 2.78
1324 1367 3.897505 TCCATCTCATACATGGTCACGAT 59.102 43.478 0.00 0.00 41.59 3.73
1330 1373 3.181447 CCAAGCTCCATCTCATACATGGT 60.181 47.826 0.00 0.00 41.59 3.55
1331 1374 3.409570 CCAAGCTCCATCTCATACATGG 58.590 50.000 0.00 0.00 42.16 3.66
1346 1397 2.226962 ACATCCAAATCAGCCAAGCT 57.773 45.000 0.00 0.00 40.77 3.74
1351 1402 4.022068 TGACAAGAAACATCCAAATCAGCC 60.022 41.667 0.00 0.00 0.00 4.85
1396 1448 0.387929 TGAAGACGAGCAGGAACGTT 59.612 50.000 0.00 0.00 42.74 3.99
1531 1583 3.003173 TTCAGGTGGCTCCCCGAG 61.003 66.667 1.14 0.00 36.75 4.63
1736 1794 2.427095 ACGTGATGATGAACTCGATGGA 59.573 45.455 0.00 0.00 0.00 3.41
1739 1797 4.110036 TGAACGTGATGATGAACTCGAT 57.890 40.909 0.00 0.00 0.00 3.59
1784 1842 2.125832 TTTCGGATCGGTGGCGAC 60.126 61.111 0.00 0.00 0.00 5.19
1798 1856 2.028385 TCCGGTCTTCCTTACTGCTTTC 60.028 50.000 0.00 0.00 0.00 2.62
1808 1866 8.116669 TGAGAGATAATATAATCCGGTCTTCCT 58.883 37.037 0.00 0.00 0.00 3.36
1817 1875 9.997482 GAACGAGACTGAGAGATAATATAATCC 57.003 37.037 0.00 0.00 0.00 3.01
1840 1902 3.067461 AGTCAGTGAGTGAGTGAGTGAAC 59.933 47.826 0.00 0.00 37.45 3.18
1863 1933 4.627611 AGATCATTTGGCAGTTCGAATG 57.372 40.909 0.00 2.16 38.98 2.67
1865 1935 6.567687 TTAAAGATCATTTGGCAGTTCGAA 57.432 33.333 0.00 0.00 0.00 3.71
1895 1965 0.392193 CCACTGCTACCAGCTCCTTG 60.392 60.000 0.00 0.00 42.97 3.61
1936 2006 2.987593 CGGCGATGAGAACGTTCG 59.012 61.111 21.87 12.24 0.00 3.95
1971 2041 3.694535 ACCGTAGAGTCATTGATCGAC 57.305 47.619 0.00 0.00 0.00 4.20
1972 2042 3.945921 AGAACCGTAGAGTCATTGATCGA 59.054 43.478 0.00 0.00 0.00 3.59
1980 2050 3.994392 GCATGAAAAGAACCGTAGAGTCA 59.006 43.478 0.00 0.00 0.00 3.41
1989 2059 2.415168 TCGTGATCGCATGAAAAGAACC 59.585 45.455 7.12 0.00 37.12 3.62
1993 2063 4.263139 TCAATCGTGATCGCATGAAAAG 57.737 40.909 7.12 0.00 42.90 2.27
2001 2071 6.021596 ACTAAACATTTTCAATCGTGATCGC 58.978 36.000 0.00 0.00 36.96 4.58
2002 2072 7.533900 ACAACTAAACATTTTCAATCGTGATCG 59.466 33.333 0.00 0.00 32.48 3.69
2057 2127 0.462047 GTGTCCTCGCCGGATTCATT 60.462 55.000 5.05 0.00 45.44 2.57
2093 2163 1.154150 CTTCGTGTACGTCCCCGTC 60.154 63.158 4.20 0.00 46.28 4.79
2108 2178 4.142381 GCAACCATGTAAACCCAGATCTTC 60.142 45.833 0.00 0.00 0.00 2.87
2199 2271 2.112198 AGCGGCTCGAGACTCTGAG 61.112 63.158 18.75 15.62 35.30 3.35
2212 2284 3.621794 CATAAAATTCTACAGCAGCGGC 58.378 45.455 0.00 0.00 41.61 6.53
2213 2285 3.065233 TGCATAAAATTCTACAGCAGCGG 59.935 43.478 0.00 0.00 0.00 5.52
2277 2367 5.163248 TGTCATCCCAAGAACAGTGTTCTAA 60.163 40.000 33.12 20.86 0.00 2.10
2278 2368 4.346709 TGTCATCCCAAGAACAGTGTTCTA 59.653 41.667 33.12 20.78 0.00 2.10
2279 2369 3.136443 TGTCATCCCAAGAACAGTGTTCT 59.864 43.478 28.97 28.97 0.00 3.01
2280 2370 3.476552 TGTCATCCCAAGAACAGTGTTC 58.523 45.455 25.51 25.51 0.00 3.18
2281 2371 3.576078 TGTCATCCCAAGAACAGTGTT 57.424 42.857 8.61 8.61 0.00 3.32
2303 2393 6.885952 TGCAATACCTACAAGCTTGTTAAA 57.114 33.333 35.20 18.00 42.35 1.52
2305 2395 6.885952 TTTGCAATACCTACAAGCTTGTTA 57.114 33.333 35.20 22.34 42.35 2.41
2307 2397 5.782893 TTTTGCAATACCTACAAGCTTGT 57.217 34.783 32.97 32.97 44.86 3.16
2321 2411 5.863397 CACCGTTTAGTCATGATTTTGCAAT 59.137 36.000 0.00 0.00 0.00 3.56
2328 2418 3.818210 TGCAACACCGTTTAGTCATGATT 59.182 39.130 0.00 0.00 0.00 2.57
2329 2419 3.407698 TGCAACACCGTTTAGTCATGAT 58.592 40.909 0.00 0.00 0.00 2.45
2354 2444 0.534652 GGATGGAGCACCTCATGAGC 60.535 60.000 17.76 7.28 37.04 4.26
2355 2445 1.129917 AGGATGGAGCACCTCATGAG 58.870 55.000 16.24 16.24 37.04 2.90
2356 2446 3.329497 AGGATGGAGCACCTCATGA 57.671 52.632 0.71 0.00 37.04 3.07
2361 2451 1.614525 TGCAGAGGATGGAGCACCT 60.615 57.895 0.71 0.00 39.41 4.00
2362 2452 2.993008 TGCAGAGGATGGAGCACC 59.007 61.111 0.00 0.00 31.05 5.01
2364 2454 0.616964 AGAGTGCAGAGGATGGAGCA 60.617 55.000 0.00 0.00 34.10 4.26
2365 2455 0.540923 AAGAGTGCAGAGGATGGAGC 59.459 55.000 0.00 0.00 0.00 4.70
2366 2456 2.109774 AGAAGAGTGCAGAGGATGGAG 58.890 52.381 0.00 0.00 0.00 3.86
2367 2457 2.244486 AGAAGAGTGCAGAGGATGGA 57.756 50.000 0.00 0.00 0.00 3.41
2368 2458 4.686191 ATTAGAAGAGTGCAGAGGATGG 57.314 45.455 0.00 0.00 0.00 3.51
2369 2459 5.221402 TGCTATTAGAAGAGTGCAGAGGATG 60.221 44.000 0.00 0.00 0.00 3.51
2370 2460 4.898265 TGCTATTAGAAGAGTGCAGAGGAT 59.102 41.667 0.00 0.00 0.00 3.24
2371 2461 4.281657 TGCTATTAGAAGAGTGCAGAGGA 58.718 43.478 0.00 0.00 0.00 3.71
2372 2462 4.662468 TGCTATTAGAAGAGTGCAGAGG 57.338 45.455 0.00 0.00 0.00 3.69
2373 2463 5.523188 CCTTTGCTATTAGAAGAGTGCAGAG 59.477 44.000 0.00 0.00 34.05 3.35
2374 2464 5.423015 CCTTTGCTATTAGAAGAGTGCAGA 58.577 41.667 0.00 0.00 0.00 4.26
2375 2465 4.574013 CCCTTTGCTATTAGAAGAGTGCAG 59.426 45.833 0.00 0.00 0.00 4.41
2376 2466 4.517285 CCCTTTGCTATTAGAAGAGTGCA 58.483 43.478 0.00 0.00 0.00 4.57
2377 2467 3.313803 GCCCTTTGCTATTAGAAGAGTGC 59.686 47.826 0.00 0.00 36.87 4.40
2391 2481 3.850122 ATTTAAGAACGAGCCCTTTGC 57.150 42.857 0.00 0.00 41.71 3.68
2392 2482 6.909909 AGTTAATTTAAGAACGAGCCCTTTG 58.090 36.000 0.00 0.00 0.00 2.77
2393 2483 8.674607 CATAGTTAATTTAAGAACGAGCCCTTT 58.325 33.333 0.00 0.00 0.00 3.11
2394 2484 7.201705 GCATAGTTAATTTAAGAACGAGCCCTT 60.202 37.037 0.00 0.00 0.00 3.95
2395 2485 6.260271 GCATAGTTAATTTAAGAACGAGCCCT 59.740 38.462 0.00 0.00 0.00 5.19
2396 2486 6.427974 GCATAGTTAATTTAAGAACGAGCCC 58.572 40.000 0.00 0.00 0.00 5.19
2397 2487 6.037830 TGGCATAGTTAATTTAAGAACGAGCC 59.962 38.462 15.30 15.30 39.69 4.70
2398 2488 7.011828 TGGCATAGTTAATTTAAGAACGAGC 57.988 36.000 0.00 0.00 0.00 5.03
2399 2489 9.490663 CTTTGGCATAGTTAATTTAAGAACGAG 57.509 33.333 0.00 0.00 0.00 4.18
2400 2490 7.966204 GCTTTGGCATAGTTAATTTAAGAACGA 59.034 33.333 6.81 0.00 38.54 3.85
2401 2491 7.968405 AGCTTTGGCATAGTTAATTTAAGAACG 59.032 33.333 6.81 0.00 41.70 3.95
2402 2492 9.639601 AAGCTTTGGCATAGTTAATTTAAGAAC 57.360 29.630 6.81 0.00 41.70 3.01
2406 2496 9.988815 TCAAAAGCTTTGGCATAGTTAATTTAA 57.011 25.926 13.54 0.00 41.70 1.52
2413 2503 9.971922 GATATTATCAAAAGCTTTGGCATAGTT 57.028 29.630 13.54 0.00 41.70 2.24
2414 2504 9.135189 TGATATTATCAAAAGCTTTGGCATAGT 57.865 29.630 13.54 8.58 37.34 2.12
2415 2505 9.970395 TTGATATTATCAAAAGCTTTGGCATAG 57.030 29.630 13.54 0.09 45.57 2.23
2436 2526 9.829507 ACCTTTGATCAACAAACAAAATTGATA 57.170 25.926 7.89 0.00 41.89 2.15
2437 2527 8.735692 ACCTTTGATCAACAAACAAAATTGAT 57.264 26.923 7.89 0.00 43.93 2.57
2438 2528 8.558973 AACCTTTGATCAACAAACAAAATTGA 57.441 26.923 7.89 0.00 42.57 2.57
2439 2529 8.667463 AGAACCTTTGATCAACAAACAAAATTG 58.333 29.630 7.89 0.00 42.57 2.32
2440 2530 8.791327 AGAACCTTTGATCAACAAACAAAATT 57.209 26.923 7.89 0.00 42.57 1.82
2441 2531 8.791327 AAGAACCTTTGATCAACAAACAAAAT 57.209 26.923 7.89 0.00 42.57 1.82
2442 2532 9.712305 TTAAGAACCTTTGATCAACAAACAAAA 57.288 25.926 7.89 0.00 42.57 2.44
2443 2533 9.712305 TTTAAGAACCTTTGATCAACAAACAAA 57.288 25.926 7.89 0.00 42.57 2.83
2444 2534 9.712305 TTTTAAGAACCTTTGATCAACAAACAA 57.288 25.926 7.89 0.00 42.57 2.83
2445 2535 9.364989 CTTTTAAGAACCTTTGATCAACAAACA 57.635 29.630 7.89 0.00 42.57 2.83
2446 2536 9.366216 ACTTTTAAGAACCTTTGATCAACAAAC 57.634 29.630 7.89 0.00 42.57 2.93
2449 2539 9.621629 TCTACTTTTAAGAACCTTTGATCAACA 57.378 29.630 7.89 0.00 0.00 3.33
2451 2541 9.284968 CCTCTACTTTTAAGAACCTTTGATCAA 57.715 33.333 3.38 3.38 0.00 2.57
2452 2542 8.437575 ACCTCTACTTTTAAGAACCTTTGATCA 58.562 33.333 0.00 0.00 0.00 2.92
2453 2543 8.850007 ACCTCTACTTTTAAGAACCTTTGATC 57.150 34.615 0.00 0.00 0.00 2.92
2454 2544 9.642343 AAACCTCTACTTTTAAGAACCTTTGAT 57.358 29.630 0.00 0.00 0.00 2.57
2455 2545 9.470399 AAAACCTCTACTTTTAAGAACCTTTGA 57.530 29.630 0.00 0.00 0.00 2.69
2458 2548 8.618677 CGAAAAACCTCTACTTTTAAGAACCTT 58.381 33.333 0.00 0.00 0.00 3.50
2459 2549 7.772292 ACGAAAAACCTCTACTTTTAAGAACCT 59.228 33.333 0.00 0.00 0.00 3.50
2460 2550 7.923888 ACGAAAAACCTCTACTTTTAAGAACC 58.076 34.615 0.00 0.00 0.00 3.62
2462 2552 9.264719 CCTACGAAAAACCTCTACTTTTAAGAA 57.735 33.333 0.00 0.00 0.00 2.52
2463 2553 7.386025 GCCTACGAAAAACCTCTACTTTTAAGA 59.614 37.037 0.00 0.00 0.00 2.10
2464 2554 7.172019 TGCCTACGAAAAACCTCTACTTTTAAG 59.828 37.037 0.00 0.00 0.00 1.85
2465 2555 6.991531 TGCCTACGAAAAACCTCTACTTTTAA 59.008 34.615 0.00 0.00 0.00 1.52
2466 2556 6.523840 TGCCTACGAAAAACCTCTACTTTTA 58.476 36.000 0.00 0.00 0.00 1.52
2467 2557 5.370679 TGCCTACGAAAAACCTCTACTTTT 58.629 37.500 0.00 0.00 0.00 2.27
2468 2558 4.964593 TGCCTACGAAAAACCTCTACTTT 58.035 39.130 0.00 0.00 0.00 2.66
2469 2559 4.612264 TGCCTACGAAAAACCTCTACTT 57.388 40.909 0.00 0.00 0.00 2.24
2470 2560 4.040095 ACTTGCCTACGAAAAACCTCTACT 59.960 41.667 0.00 0.00 0.00 2.57
2471 2561 4.151867 CACTTGCCTACGAAAAACCTCTAC 59.848 45.833 0.00 0.00 0.00 2.59
2472 2562 4.312443 CACTTGCCTACGAAAAACCTCTA 58.688 43.478 0.00 0.00 0.00 2.43
2473 2563 3.139077 CACTTGCCTACGAAAAACCTCT 58.861 45.455 0.00 0.00 0.00 3.69
2474 2564 2.225727 CCACTTGCCTACGAAAAACCTC 59.774 50.000 0.00 0.00 0.00 3.85
2475 2565 2.227194 CCACTTGCCTACGAAAAACCT 58.773 47.619 0.00 0.00 0.00 3.50
2476 2566 1.335597 GCCACTTGCCTACGAAAAACC 60.336 52.381 0.00 0.00 0.00 3.27
2477 2567 1.335496 TGCCACTTGCCTACGAAAAAC 59.665 47.619 0.00 0.00 40.16 2.43
2478 2568 1.681538 TGCCACTTGCCTACGAAAAA 58.318 45.000 0.00 0.00 40.16 1.94
2479 2569 1.606668 CTTGCCACTTGCCTACGAAAA 59.393 47.619 0.00 0.00 40.16 2.29
2480 2570 1.234821 CTTGCCACTTGCCTACGAAA 58.765 50.000 0.00 0.00 40.16 3.46
2481 2571 1.234615 GCTTGCCACTTGCCTACGAA 61.235 55.000 0.00 0.00 40.16 3.85
2482 2572 1.671054 GCTTGCCACTTGCCTACGA 60.671 57.895 0.00 0.00 40.16 3.43
2483 2573 1.237285 AAGCTTGCCACTTGCCTACG 61.237 55.000 0.00 0.00 40.16 3.51
2484 2574 1.821216 TAAGCTTGCCACTTGCCTAC 58.179 50.000 9.86 0.00 40.16 3.18
2485 2575 2.577606 TTAAGCTTGCCACTTGCCTA 57.422 45.000 9.86 0.00 40.16 3.93
2486 2576 1.928868 ATTAAGCTTGCCACTTGCCT 58.071 45.000 9.86 0.00 40.16 4.75
2487 2577 2.749280 AATTAAGCTTGCCACTTGCC 57.251 45.000 9.86 0.00 40.16 4.52
2488 2578 3.429410 CCCTAATTAAGCTTGCCACTTGC 60.429 47.826 9.86 0.00 41.77 4.01
2489 2579 3.429410 GCCCTAATTAAGCTTGCCACTTG 60.429 47.826 9.86 0.00 0.00 3.16
2490 2580 2.760650 GCCCTAATTAAGCTTGCCACTT 59.239 45.455 9.86 0.00 0.00 3.16
2491 2581 2.291540 TGCCCTAATTAAGCTTGCCACT 60.292 45.455 9.86 0.00 0.00 4.00
2492 2582 2.099405 TGCCCTAATTAAGCTTGCCAC 58.901 47.619 9.86 0.00 0.00 5.01
2493 2583 2.523325 TGCCCTAATTAAGCTTGCCA 57.477 45.000 9.86 0.00 0.00 4.92
2494 2584 3.225940 AGATGCCCTAATTAAGCTTGCC 58.774 45.455 9.86 0.00 0.00 4.52
2495 2585 3.254411 GGAGATGCCCTAATTAAGCTTGC 59.746 47.826 9.86 2.12 0.00 4.01
2496 2586 4.276926 GTGGAGATGCCCTAATTAAGCTTG 59.723 45.833 9.86 0.00 34.97 4.01
2497 2587 4.079787 TGTGGAGATGCCCTAATTAAGCTT 60.080 41.667 3.48 3.48 34.97 3.74
2498 2588 3.459598 TGTGGAGATGCCCTAATTAAGCT 59.540 43.478 8.24 0.00 34.97 3.74
2499 2589 3.820557 TGTGGAGATGCCCTAATTAAGC 58.179 45.455 1.09 1.09 34.97 3.09
2500 2590 6.966534 ATTTGTGGAGATGCCCTAATTAAG 57.033 37.500 0.00 0.00 34.97 1.85
2501 2591 7.147742 GGAAATTTGTGGAGATGCCCTAATTAA 60.148 37.037 0.00 0.00 34.97 1.40
2502 2592 6.323739 GGAAATTTGTGGAGATGCCCTAATTA 59.676 38.462 0.00 0.00 34.97 1.40
2503 2593 5.129320 GGAAATTTGTGGAGATGCCCTAATT 59.871 40.000 0.00 0.00 34.97 1.40
2504 2594 4.651045 GGAAATTTGTGGAGATGCCCTAAT 59.349 41.667 0.00 0.00 34.97 1.73
2505 2595 4.023291 GGAAATTTGTGGAGATGCCCTAA 58.977 43.478 0.00 0.00 34.97 2.69
2506 2596 3.269381 AGGAAATTTGTGGAGATGCCCTA 59.731 43.478 0.00 0.00 34.97 3.53
2507 2597 2.043526 AGGAAATTTGTGGAGATGCCCT 59.956 45.455 0.00 0.00 34.97 5.19
2508 2598 2.460669 AGGAAATTTGTGGAGATGCCC 58.539 47.619 0.00 0.00 34.97 5.36
2509 2599 4.498241 GAAAGGAAATTTGTGGAGATGCC 58.502 43.478 0.00 0.00 37.10 4.40
2510 2600 4.168760 CGAAAGGAAATTTGTGGAGATGC 58.831 43.478 0.00 0.00 0.00 3.91
2511 2601 5.376854 ACGAAAGGAAATTTGTGGAGATG 57.623 39.130 0.00 0.00 0.00 2.90
2512 2602 6.318900 GGATACGAAAGGAAATTTGTGGAGAT 59.681 38.462 0.00 0.00 0.00 2.75
2513 2603 5.646360 GGATACGAAAGGAAATTTGTGGAGA 59.354 40.000 0.00 0.00 0.00 3.71
2514 2604 5.414454 TGGATACGAAAGGAAATTTGTGGAG 59.586 40.000 0.00 0.00 42.51 3.86
2515 2605 5.317808 TGGATACGAAAGGAAATTTGTGGA 58.682 37.500 0.00 0.00 42.51 4.02
2518 2608 5.065988 CGGATGGATACGAAAGGAAATTTGT 59.934 40.000 0.00 0.00 35.77 2.83
2529 2619 1.605457 GCATCTGCGGATGGATACGAA 60.605 52.381 31.65 0.00 46.77 3.85
2530 2620 0.038251 GCATCTGCGGATGGATACGA 60.038 55.000 31.65 0.00 46.77 3.43
2531 2621 2.449548 GCATCTGCGGATGGATACG 58.550 57.895 31.65 10.36 46.77 3.06
2561 2651 3.936203 TGTCCACGGACTGGTGCC 61.936 66.667 16.88 0.00 44.80 5.01
2562 2652 2.665185 GTGTCCACGGACTGGTGC 60.665 66.667 16.88 0.00 44.80 5.01
2591 2682 2.483876 CGGCTACTATTGGATGGTGTG 58.516 52.381 0.00 0.00 0.00 3.82
2594 2685 1.128200 TGCGGCTACTATTGGATGGT 58.872 50.000 0.00 0.00 0.00 3.55
2604 2695 3.090037 AGTTCGGATATATGCGGCTACT 58.910 45.455 23.95 20.12 42.14 2.57
2628 2720 3.430895 TCGTGCGGACTTAAGAAAATGAC 59.569 43.478 10.09 0.00 0.00 3.06
2636 2732 5.490213 GTTATTTGATCGTGCGGACTTAAG 58.510 41.667 5.27 0.00 0.00 1.85
2719 4321 9.857656 AGACATGTCAGGATGTAATATTTGATT 57.142 29.630 27.02 0.00 36.67 2.57
2720 4322 9.857656 AAGACATGTCAGGATGTAATATTTGAT 57.142 29.630 27.02 0.00 36.67 2.57
2736 4342 4.069304 CGGTTAAAGGGAAAGACATGTCA 58.931 43.478 27.02 0.42 0.00 3.58
2737 4343 3.119955 GCGGTTAAAGGGAAAGACATGTC 60.120 47.826 18.47 18.47 0.00 3.06
2742 4348 1.171308 GGGCGGTTAAAGGGAAAGAC 58.829 55.000 0.00 0.00 0.00 3.01
2743 4349 0.772384 TGGGCGGTTAAAGGGAAAGA 59.228 50.000 0.00 0.00 0.00 2.52
2744 4350 1.847328 ATGGGCGGTTAAAGGGAAAG 58.153 50.000 0.00 0.00 0.00 2.62
2792 4401 3.006859 TCAACATCGACCAACTCATGAGT 59.993 43.478 22.89 22.89 44.94 3.41
2796 4405 5.241506 ACAAATTCAACATCGACCAACTCAT 59.758 36.000 0.00 0.00 0.00 2.90
2838 4447 2.442236 ATCCGGCCACATTTGAAGAT 57.558 45.000 2.24 0.00 0.00 2.40
2979 4589 3.112263 ACAATGGGATTCGGAGACCTTA 58.888 45.455 0.00 0.00 34.32 2.69
3005 4616 1.756430 TGCAGTTGTTTGTGCACCTA 58.244 45.000 15.69 0.00 44.70 3.08
3010 4621 1.060409 CCGTTTTGCAGTTGTTTGTGC 59.940 47.619 0.00 0.00 40.29 4.57
3098 4712 2.650322 ACCGAGTTTGCCAGAAAAAGA 58.350 42.857 0.00 0.00 0.00 2.52
3110 4725 4.744795 AGCATCATCTCTAACCGAGTTT 57.255 40.909 0.00 0.00 40.75 2.66
3115 4730 7.155328 ACCTTTATTAGCATCATCTCTAACCG 58.845 38.462 0.00 0.00 0.00 4.44
3127 4742 4.412199 TCTGTGGGCTACCTTTATTAGCAT 59.588 41.667 0.00 0.00 43.30 3.79
3132 4747 3.460825 TCCTCTGTGGGCTACCTTTATT 58.539 45.455 0.00 0.00 37.76 1.40
3134 4749 2.634639 TCCTCTGTGGGCTACCTTTA 57.365 50.000 0.00 0.00 37.76 1.85
3148 4763 4.141228 TCTGGTTGACGGTATCTATCCTCT 60.141 45.833 0.00 0.00 0.00 3.69
3205 4823 2.764269 AGCTCCTCCTTGCCACTATAA 58.236 47.619 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.