Multiple sequence alignment - TraesCS1B01G019300

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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 TraesCS1B01G019300 chr1B 100.000 2849 0 0 1 2849 9080292 9083140 0.000000e+00 5262
1 TraesCS1B01G019300 chr1B 93.796 274 14 3 2401 2672 321700278 321700006 2.640000e-110 409
2 TraesCS1B01G019300 chr1D 91.128 2446 127 29 3 2403 6767702 6765302 0.000000e+00 3232
3 TraesCS1B01G019300 chr1A 92.617 1490 87 10 3 1491 8240394 8238927 0.000000e+00 2121
4 TraesCS1B01G019300 chr1A 86.108 943 66 32 1500 2404 8238969 8238054 0.000000e+00 955
5 TraesCS1B01G019300 chr1A 94.118 68 4 0 2696 2763 8238067 8238000 1.400000e-18 104
6 TraesCS1B01G019300 chr1A 95.652 46 2 0 2762 2807 8237885 8237840 1.090000e-09 75
7 TraesCS1B01G019300 chr5B 93.197 294 19 1 2401 2693 660842802 660842509 5.640000e-117 431
8 TraesCS1B01G019300 chr3D 89.597 298 27 3 2401 2696 124386784 124387079 2.680000e-100 375
9 TraesCS1B01G019300 chr3D 88.294 299 31 3 2401 2697 516957418 516957122 3.490000e-94 355
10 TraesCS1B01G019300 chr3D 87.025 316 33 7 2386 2696 379054677 379054989 1.620000e-92 350
11 TraesCS1B01G019300 chr2A 88.926 298 29 3 2401 2696 297234174 297234469 5.800000e-97 364
12 TraesCS1B01G019300 chr3A 88.629 299 29 4 2401 2696 14767184 14767480 2.700000e-95 359
13 TraesCS1B01G019300 chr4D 88.552 297 29 4 2401 2696 480466855 480467147 3.490000e-94 355
14 TraesCS1B01G019300 chr7D 86.420 324 30 11 2387 2706 575501717 575502030 2.720000e-90 342


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 TraesCS1B01G019300 chr1B 9080292 9083140 2848 False 5262.00 5262 100.00000 1 2849 1 chr1B.!!$F1 2848
1 TraesCS1B01G019300 chr1D 6765302 6767702 2400 True 3232.00 3232 91.12800 3 2403 1 chr1D.!!$R1 2400
2 TraesCS1B01G019300 chr1A 8237840 8240394 2554 True 813.75 2121 92.12375 3 2807 4 chr1A.!!$R1 2804

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
71 72 1.676746 CATCCATGGGTGAGAAGCAG 58.323 55.0 21.24 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 1919 0.035725 TTGGAGAGTGCATCTGCCTG 60.036 55.0 12.59 0.0 45.39 4.85 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
71 72 1.676746 CATCCATGGGTGAGAAGCAG 58.323 55.000 21.24 0.00 0.00 4.24
138 139 9.838339 CTTCATACCACTTGTCTATCCTTATTT 57.162 33.333 0.00 0.00 0.00 1.40
177 178 7.816031 TGGCACTTATTTGTACTACTTACAGTC 59.184 37.037 0.00 0.00 41.86 3.51
210 211 1.833630 TCATCCGATCTGCTTTGTCCT 59.166 47.619 0.00 0.00 0.00 3.85
216 217 3.806521 CCGATCTGCTTTGTCCTATTCAG 59.193 47.826 0.00 0.00 0.00 3.02
231 236 7.771361 TGTCCTATTCAGTGTTTTAACTGTCAA 59.229 33.333 4.41 0.00 46.33 3.18
232 237 8.617809 GTCCTATTCAGTGTTTTAACTGTCAAA 58.382 33.333 4.41 0.00 46.33 2.69
233 238 8.836413 TCCTATTCAGTGTTTTAACTGTCAAAG 58.164 33.333 4.41 0.04 46.33 2.77
343 348 4.628074 TGTTTCTTGAAGAAGAGGTACGG 58.372 43.478 7.76 0.00 39.44 4.02
371 376 5.559148 ATTGTGTCTCTCCATTATCTCCC 57.441 43.478 0.00 0.00 0.00 4.30
406 411 5.645497 ACTTCTGGAGTTCTATTGTTCATGC 59.355 40.000 0.00 0.00 33.92 4.06
422 427 4.944962 TCATGCACAAAAGTCCGATTAG 57.055 40.909 0.00 0.00 0.00 1.73
466 471 6.416161 GTCTTTGAAAGAATCTGCTTGTGAAC 59.584 38.462 9.51 0.00 39.67 3.18
478 483 4.746729 TGCTTGTGAACATGCCAATATTC 58.253 39.130 16.07 0.00 43.75 1.75
569 574 3.909258 GACGGCTTCGCTCGTGGAA 62.909 63.158 7.00 0.00 36.12 3.53
692 697 8.197988 ACCGCACTATGATTACTTTAAAAGAG 57.802 34.615 0.00 0.00 0.00 2.85
749 754 3.576078 TGTGGTCTTCTTGGTGTGATT 57.424 42.857 0.00 0.00 0.00 2.57
769 774 9.549509 TGTGATTTTATATTTGTTTAGACACGC 57.450 29.630 0.00 0.00 34.98 5.34
778 783 1.993370 GTTTAGACACGCGAGATGCTT 59.007 47.619 15.93 0.00 43.27 3.91
801 806 6.609237 TTATTTTATAGCTGTGCTGCTGAG 57.391 37.500 12.75 0.00 43.87 3.35
825 830 4.548991 CAGAGATGCTGTTTTCATAGCC 57.451 45.455 0.00 0.00 39.85 3.93
833 848 3.614870 GCTGTTTTCATAGCCCTTTGTGG 60.615 47.826 0.00 0.00 33.89 4.17
883 898 3.949586 TCCTCATCATATGGCCACAAA 57.050 42.857 8.16 0.00 0.00 2.83
907 922 4.201950 GCCTCACACCACAAATAATGCTAG 60.202 45.833 0.00 0.00 0.00 3.42
932 947 9.125026 AGAACTCATATTTCTTTGTTTCTGTGT 57.875 29.630 0.00 0.00 28.36 3.72
935 950 8.778358 ACTCATATTTCTTTGTTTCTGTGTCTC 58.222 33.333 0.00 0.00 0.00 3.36
1034 1050 0.888619 GGGCTGTAAACTTGGAAGGC 59.111 55.000 0.00 0.00 0.00 4.35
1077 1093 4.816984 GCAGCCATGGAGCCTGCT 62.817 66.667 26.59 10.19 35.43 4.24
1108 1124 2.444706 TCTCCCTGAGGGCATCCG 60.445 66.667 14.20 0.00 43.94 4.18
1228 1246 7.014711 TGGTATGAGTATCTCCTCACAGAATTC 59.985 40.741 0.00 0.00 43.86 2.17
1417 1435 2.960170 GCTGCAAGGCAAGACCAG 59.040 61.111 0.00 0.00 43.14 4.00
1425 1443 1.376553 GGCAAGACCAGTCTCTGCC 60.377 63.158 24.79 24.79 46.17 4.85
1469 1487 9.561069 TCTTATCTTCTGAAGGCCATTTATTAC 57.439 33.333 16.83 0.00 0.00 1.89
1559 1577 5.552870 TTCTTAATACTGATGAGGGGAGC 57.447 43.478 0.00 0.00 0.00 4.70
1573 1591 2.436173 AGGGGAGCTAACTGTCTAATGC 59.564 50.000 0.00 0.00 0.00 3.56
1638 1659 6.333416 TCTTCGAGAGATGGAAGTATGTTTG 58.667 40.000 1.27 0.00 40.36 2.93
1702 1731 5.715429 ACTACGTGTAGTCGAAGTATCAG 57.285 43.478 6.85 0.00 42.30 2.90
1705 1734 6.813649 ACTACGTGTAGTCGAAGTATCAGTTA 59.186 38.462 6.85 0.00 42.30 2.24
1720 1749 9.823647 AAGTATCAGTTATTACTCCAGTGATTG 57.176 33.333 0.00 0.00 30.26 2.67
1755 1788 4.848357 ACTGCTGGTATTATGGGATATGC 58.152 43.478 0.00 0.00 0.00 3.14
1854 1887 6.322201 AGCAGAGAGGAGAAAGATAGAAGAAG 59.678 42.308 0.00 0.00 0.00 2.85
1885 1920 2.441348 CCATCCATGGCAGCTGCA 60.441 61.111 37.63 24.48 41.75 4.41
1886 1921 2.490148 CCATCCATGGCAGCTGCAG 61.490 63.158 37.63 25.83 41.75 4.41
1887 1922 2.123854 ATCCATGGCAGCTGCAGG 60.124 61.111 37.63 32.35 44.36 4.85
1890 1925 3.826754 CATGGCAGCTGCAGGCAG 61.827 66.667 37.63 19.27 45.09 4.85
1980 2015 4.526970 AGTATCAACCAGAATCGCCAAAT 58.473 39.130 0.00 0.00 0.00 2.32
2069 2104 5.302568 AGCAGAATGTTGTGAGGAAATCAAA 59.697 36.000 0.00 0.00 37.97 2.69
2092 2127 1.463444 GGTTTCTGCGCGTATTGACTT 59.537 47.619 8.43 0.00 0.00 3.01
2094 2129 0.442310 TTCTGCGCGTATTGACTTGC 59.558 50.000 8.43 0.00 0.00 4.01
2113 2148 4.182693 TGCTTGGATGCTTTTGAATCTG 57.817 40.909 0.00 0.00 34.81 2.90
2410 2471 8.980481 ATGTATCCACACTAAATTAAAGGGAG 57.020 34.615 0.00 0.00 37.54 4.30
2411 2472 7.343357 TGTATCCACACTAAATTAAAGGGAGG 58.657 38.462 1.37 1.37 30.07 4.30
2412 2473 5.853572 TCCACACTAAATTAAAGGGAGGT 57.146 39.130 6.41 0.00 30.83 3.85
2413 2474 5.566469 TCCACACTAAATTAAAGGGAGGTG 58.434 41.667 6.41 0.00 30.83 4.00
2414 2475 5.311121 TCCACACTAAATTAAAGGGAGGTGA 59.689 40.000 6.41 0.00 30.83 4.02
2415 2476 6.011981 TCCACACTAAATTAAAGGGAGGTGAT 60.012 38.462 6.41 0.00 30.83 3.06
2416 2477 7.183112 TCCACACTAAATTAAAGGGAGGTGATA 59.817 37.037 6.41 0.00 30.83 2.15
2417 2478 7.998964 CCACACTAAATTAAAGGGAGGTGATAT 59.001 37.037 0.00 0.00 0.00 1.63
2418 2479 9.408648 CACACTAAATTAAAGGGAGGTGATATT 57.591 33.333 0.00 0.00 0.00 1.28
2419 2480 9.628500 ACACTAAATTAAAGGGAGGTGATATTC 57.372 33.333 0.00 0.00 0.00 1.75
2420 2481 9.853177 CACTAAATTAAAGGGAGGTGATATTCT 57.147 33.333 0.00 0.00 0.00 2.40
2423 2484 8.539117 AAATTAAAGGGAGGTGATATTCTTGG 57.461 34.615 0.00 0.00 0.00 3.61
2424 2485 6.652205 TTAAAGGGAGGTGATATTCTTGGT 57.348 37.500 0.00 0.00 0.00 3.67
2425 2486 5.536497 AAAGGGAGGTGATATTCTTGGTT 57.464 39.130 0.00 0.00 0.00 3.67
2426 2487 5.536497 AAGGGAGGTGATATTCTTGGTTT 57.464 39.130 0.00 0.00 0.00 3.27
2427 2488 5.117406 AGGGAGGTGATATTCTTGGTTTC 57.883 43.478 0.00 0.00 0.00 2.78
2428 2489 3.877508 GGGAGGTGATATTCTTGGTTTCG 59.122 47.826 0.00 0.00 0.00 3.46
2429 2490 4.514401 GGAGGTGATATTCTTGGTTTCGT 58.486 43.478 0.00 0.00 0.00 3.85
2430 2491 4.571176 GGAGGTGATATTCTTGGTTTCGTC 59.429 45.833 0.00 0.00 0.00 4.20
2431 2492 4.514401 AGGTGATATTCTTGGTTTCGTCC 58.486 43.478 0.00 0.00 0.00 4.79
2432 2493 3.626217 GGTGATATTCTTGGTTTCGTCCC 59.374 47.826 0.00 0.00 0.00 4.46
2433 2494 3.308866 GTGATATTCTTGGTTTCGTCCCG 59.691 47.826 0.00 0.00 0.00 5.14
2434 2495 3.055675 TGATATTCTTGGTTTCGTCCCGT 60.056 43.478 0.00 0.00 0.00 5.28
2435 2496 2.265589 ATTCTTGGTTTCGTCCCGTT 57.734 45.000 0.00 0.00 0.00 4.44
2436 2497 2.041251 TTCTTGGTTTCGTCCCGTTT 57.959 45.000 0.00 0.00 0.00 3.60
2437 2498 1.585297 TCTTGGTTTCGTCCCGTTTC 58.415 50.000 0.00 0.00 0.00 2.78
2438 2499 0.233848 CTTGGTTTCGTCCCGTTTCG 59.766 55.000 0.00 0.00 0.00 3.46
2439 2500 0.461693 TTGGTTTCGTCCCGTTTCGT 60.462 50.000 0.00 0.00 0.00 3.85
2440 2501 0.461693 TGGTTTCGTCCCGTTTCGTT 60.462 50.000 0.00 0.00 0.00 3.85
2441 2502 0.657312 GGTTTCGTCCCGTTTCGTTT 59.343 50.000 0.00 0.00 0.00 3.60
2442 2503 1.595246 GGTTTCGTCCCGTTTCGTTTG 60.595 52.381 0.00 0.00 0.00 2.93
2443 2504 0.656785 TTTCGTCCCGTTTCGTTTGG 59.343 50.000 0.00 0.00 0.00 3.28
2444 2505 0.461693 TTCGTCCCGTTTCGTTTGGT 60.462 50.000 0.00 0.00 0.00 3.67
2445 2506 0.875474 TCGTCCCGTTTCGTTTGGTC 60.875 55.000 0.00 0.00 0.00 4.02
2446 2507 1.834458 CGTCCCGTTTCGTTTGGTCC 61.834 60.000 0.00 0.00 0.00 4.46
2447 2508 0.814812 GTCCCGTTTCGTTTGGTCCA 60.815 55.000 0.00 0.00 0.00 4.02
2448 2509 0.107312 TCCCGTTTCGTTTGGTCCAA 60.107 50.000 0.00 0.00 0.00 3.53
2449 2510 0.955905 CCCGTTTCGTTTGGTCCAAT 59.044 50.000 4.80 0.00 0.00 3.16
2450 2511 1.338655 CCCGTTTCGTTTGGTCCAATT 59.661 47.619 4.80 0.00 0.00 2.32
2451 2512 2.606065 CCCGTTTCGTTTGGTCCAATTC 60.606 50.000 4.80 1.37 0.00 2.17
2452 2513 2.033550 CCGTTTCGTTTGGTCCAATTCA 59.966 45.455 4.80 0.00 0.00 2.57
2453 2514 3.489398 CCGTTTCGTTTGGTCCAATTCAA 60.489 43.478 4.80 0.00 0.00 2.69
2454 2515 4.295051 CGTTTCGTTTGGTCCAATTCAAT 58.705 39.130 4.80 0.00 0.00 2.57
2455 2516 4.742659 CGTTTCGTTTGGTCCAATTCAATT 59.257 37.500 4.80 0.00 0.00 2.32
2456 2517 5.915758 CGTTTCGTTTGGTCCAATTCAATTA 59.084 36.000 4.80 0.00 0.00 1.40
2457 2518 6.418226 CGTTTCGTTTGGTCCAATTCAATTAA 59.582 34.615 4.80 0.00 0.00 1.40
2458 2519 7.115663 CGTTTCGTTTGGTCCAATTCAATTAAT 59.884 33.333 4.80 0.00 0.00 1.40
2459 2520 8.769891 GTTTCGTTTGGTCCAATTCAATTAATT 58.230 29.630 4.80 0.00 38.36 1.40
2460 2521 8.894768 TTCGTTTGGTCCAATTCAATTAATTT 57.105 26.923 4.80 0.00 35.54 1.82
2461 2522 8.527567 TCGTTTGGTCCAATTCAATTAATTTC 57.472 30.769 4.80 0.00 35.54 2.17
2462 2523 8.144478 TCGTTTGGTCCAATTCAATTAATTTCA 58.856 29.630 4.80 0.00 35.54 2.69
2463 2524 8.220434 CGTTTGGTCCAATTCAATTAATTTCAC 58.780 33.333 4.80 0.00 35.54 3.18
2464 2525 7.881643 TTGGTCCAATTCAATTAATTTCACG 57.118 32.000 0.00 0.00 35.54 4.35
2465 2526 6.987386 TGGTCCAATTCAATTAATTTCACGT 58.013 32.000 0.00 0.00 35.54 4.49
2466 2527 8.112016 TGGTCCAATTCAATTAATTTCACGTA 57.888 30.769 0.00 0.00 35.54 3.57
2467 2528 8.240682 TGGTCCAATTCAATTAATTTCACGTAG 58.759 33.333 0.00 0.00 35.54 3.51
2468 2529 7.700656 GGTCCAATTCAATTAATTTCACGTAGG 59.299 37.037 0.00 0.00 35.54 3.18
2469 2530 7.220108 GTCCAATTCAATTAATTTCACGTAGGC 59.780 37.037 0.00 0.00 35.54 3.93
2470 2531 7.122055 TCCAATTCAATTAATTTCACGTAGGCT 59.878 33.333 0.00 0.00 35.54 4.58
2471 2532 8.402472 CCAATTCAATTAATTTCACGTAGGCTA 58.598 33.333 0.00 0.00 35.54 3.93
2472 2533 9.950680 CAATTCAATTAATTTCACGTAGGCTAT 57.049 29.630 0.00 0.00 35.54 2.97
2475 2536 9.781834 TTCAATTAATTTCACGTAGGCTATTTG 57.218 29.630 0.00 0.00 0.00 2.32
2476 2537 8.402472 TCAATTAATTTCACGTAGGCTATTTGG 58.598 33.333 0.00 0.00 0.00 3.28
2477 2538 7.875327 ATTAATTTCACGTAGGCTATTTGGT 57.125 32.000 0.00 0.00 0.00 3.67
2478 2539 7.690952 TTAATTTCACGTAGGCTATTTGGTT 57.309 32.000 0.00 0.00 0.00 3.67
2479 2540 6.584185 AATTTCACGTAGGCTATTTGGTTT 57.416 33.333 0.00 0.00 0.00 3.27
2480 2541 5.616488 TTTCACGTAGGCTATTTGGTTTC 57.384 39.130 0.00 0.00 0.00 2.78
2481 2542 3.255725 TCACGTAGGCTATTTGGTTTCG 58.744 45.455 0.00 0.00 0.00 3.46
2482 2543 2.997986 CACGTAGGCTATTTGGTTTCGT 59.002 45.455 0.00 0.00 0.00 3.85
2483 2544 3.434299 CACGTAGGCTATTTGGTTTCGTT 59.566 43.478 0.00 0.00 0.00 3.85
2484 2545 4.626604 CACGTAGGCTATTTGGTTTCGTTA 59.373 41.667 0.00 0.00 0.00 3.18
2485 2546 4.627035 ACGTAGGCTATTTGGTTTCGTTAC 59.373 41.667 0.00 0.00 0.00 2.50
2486 2547 4.866486 CGTAGGCTATTTGGTTTCGTTACT 59.134 41.667 0.00 0.00 0.00 2.24
2487 2548 5.349543 CGTAGGCTATTTGGTTTCGTTACTT 59.650 40.000 0.00 0.00 0.00 2.24
2488 2549 5.622770 AGGCTATTTGGTTTCGTTACTTG 57.377 39.130 0.00 0.00 0.00 3.16
2489 2550 4.082949 AGGCTATTTGGTTTCGTTACTTGC 60.083 41.667 0.00 0.00 0.00 4.01
2490 2551 4.163552 GCTATTTGGTTTCGTTACTTGCC 58.836 43.478 0.00 0.00 0.00 4.52
2491 2552 4.320641 GCTATTTGGTTTCGTTACTTGCCA 60.321 41.667 0.00 0.00 0.00 4.92
2492 2553 3.423996 TTTGGTTTCGTTACTTGCCAC 57.576 42.857 0.00 0.00 0.00 5.01
2493 2554 1.310904 TGGTTTCGTTACTTGCCACC 58.689 50.000 0.00 0.00 0.00 4.61
2494 2555 0.594602 GGTTTCGTTACTTGCCACCC 59.405 55.000 0.00 0.00 0.00 4.61
2495 2556 0.236449 GTTTCGTTACTTGCCACCCG 59.764 55.000 0.00 0.00 0.00 5.28
2496 2557 0.179051 TTTCGTTACTTGCCACCCGT 60.179 50.000 0.00 0.00 0.00 5.28
2497 2558 0.179051 TTCGTTACTTGCCACCCGTT 60.179 50.000 0.00 0.00 0.00 4.44
2498 2559 0.179051 TCGTTACTTGCCACCCGTTT 60.179 50.000 0.00 0.00 0.00 3.60
2499 2560 0.664224 CGTTACTTGCCACCCGTTTT 59.336 50.000 0.00 0.00 0.00 2.43
2500 2561 1.598430 CGTTACTTGCCACCCGTTTTG 60.598 52.381 0.00 0.00 0.00 2.44
2501 2562 1.033574 TTACTTGCCACCCGTTTTGG 58.966 50.000 0.00 0.00 37.17 3.28
2506 2567 2.840102 CCACCCGTTTTGGCCCAA 60.840 61.111 0.00 0.00 35.87 4.12
2507 2568 2.419620 CACCCGTTTTGGCCCAAC 59.580 61.111 0.00 2.02 35.87 3.77
2508 2569 2.042843 ACCCGTTTTGGCCCAACA 60.043 55.556 13.80 0.00 35.87 3.33
2509 2570 2.131067 ACCCGTTTTGGCCCAACAG 61.131 57.895 13.80 7.70 35.87 3.16
2510 2571 1.830408 CCCGTTTTGGCCCAACAGA 60.830 57.895 13.80 0.00 35.87 3.41
2511 2572 1.659794 CCGTTTTGGCCCAACAGAG 59.340 57.895 13.80 0.00 0.00 3.35
2512 2573 1.659794 CGTTTTGGCCCAACAGAGG 59.340 57.895 13.80 0.00 0.00 3.69
2513 2574 0.821711 CGTTTTGGCCCAACAGAGGA 60.822 55.000 13.80 0.00 0.00 3.71
2514 2575 1.408969 GTTTTGGCCCAACAGAGGAA 58.591 50.000 0.00 0.00 0.00 3.36
2515 2576 1.341209 GTTTTGGCCCAACAGAGGAAG 59.659 52.381 0.00 0.00 0.00 3.46
2516 2577 0.827507 TTTGGCCCAACAGAGGAAGC 60.828 55.000 0.00 0.00 0.00 3.86
2517 2578 2.361737 GGCCCAACAGAGGAAGCC 60.362 66.667 0.00 0.00 0.00 4.35
2518 2579 2.361737 GCCCAACAGAGGAAGCCC 60.362 66.667 0.00 0.00 0.00 5.19
2519 2580 3.170362 CCCAACAGAGGAAGCCCA 58.830 61.111 0.00 0.00 33.88 5.36
2520 2581 1.303643 CCCAACAGAGGAAGCCCAC 60.304 63.158 0.00 0.00 33.88 4.61
2521 2582 1.303643 CCAACAGAGGAAGCCCACC 60.304 63.158 0.00 0.00 33.88 4.61
2522 2583 1.763770 CAACAGAGGAAGCCCACCT 59.236 57.895 0.00 0.00 40.80 4.00
2523 2584 0.607489 CAACAGAGGAAGCCCACCTG 60.607 60.000 0.00 0.00 39.62 4.00
2524 2585 0.768221 AACAGAGGAAGCCCACCTGA 60.768 55.000 0.00 0.00 38.18 3.86
2525 2586 1.298014 CAGAGGAAGCCCACCTGAC 59.702 63.158 0.00 0.00 37.49 3.51
2526 2587 2.266055 GAGGAAGCCCACCTGACG 59.734 66.667 0.00 0.00 37.93 4.35
2527 2588 3.316573 GAGGAAGCCCACCTGACGG 62.317 68.421 0.00 0.00 37.93 4.79
2535 2596 4.969196 CACCTGACGGCGCACTGT 62.969 66.667 10.83 3.86 38.42 3.55
2536 2597 4.969196 ACCTGACGGCGCACTGTG 62.969 66.667 10.83 2.76 34.75 3.66
2545 2606 4.673298 CGCACTGTGGCCCACGTA 62.673 66.667 9.78 0.00 37.14 3.57
2546 2607 3.047877 GCACTGTGGCCCACGTAC 61.048 66.667 9.78 1.51 37.14 3.67
2547 2608 2.736995 CACTGTGGCCCACGTACG 60.737 66.667 15.01 15.01 37.14 3.67
2548 2609 3.998672 ACTGTGGCCCACGTACGG 61.999 66.667 21.06 8.46 37.14 4.02
2549 2610 3.687102 CTGTGGCCCACGTACGGA 61.687 66.667 21.06 0.00 37.14 4.69
2550 2611 3.642778 CTGTGGCCCACGTACGGAG 62.643 68.421 21.06 11.52 37.14 4.63
2551 2612 3.376078 GTGGCCCACGTACGGAGA 61.376 66.667 21.06 0.00 0.00 3.71
2552 2613 3.066190 TGGCCCACGTACGGAGAG 61.066 66.667 21.06 6.36 0.00 3.20
2553 2614 2.753043 GGCCCACGTACGGAGAGA 60.753 66.667 21.06 0.00 0.00 3.10
2554 2615 2.125961 GGCCCACGTACGGAGAGAT 61.126 63.158 21.06 0.00 0.00 2.75
2555 2616 0.820891 GGCCCACGTACGGAGAGATA 60.821 60.000 21.06 0.00 0.00 1.98
2556 2617 0.592148 GCCCACGTACGGAGAGATAG 59.408 60.000 21.06 0.37 0.00 2.08
2557 2618 0.592148 CCCACGTACGGAGAGATAGC 59.408 60.000 21.06 0.00 0.00 2.97
2558 2619 1.306148 CCACGTACGGAGAGATAGCA 58.694 55.000 21.06 0.00 0.00 3.49
2559 2620 1.674441 CCACGTACGGAGAGATAGCAA 59.326 52.381 21.06 0.00 0.00 3.91
2560 2621 2.098607 CCACGTACGGAGAGATAGCAAA 59.901 50.000 21.06 0.00 0.00 3.68
2561 2622 3.428452 CCACGTACGGAGAGATAGCAAAA 60.428 47.826 21.06 0.00 0.00 2.44
2562 2623 4.171005 CACGTACGGAGAGATAGCAAAAA 58.829 43.478 21.06 0.00 0.00 1.94
2563 2624 4.804139 CACGTACGGAGAGATAGCAAAAAT 59.196 41.667 21.06 0.00 0.00 1.82
2564 2625 5.291128 CACGTACGGAGAGATAGCAAAAATT 59.709 40.000 21.06 0.00 0.00 1.82
2565 2626 6.474427 CACGTACGGAGAGATAGCAAAAATTA 59.526 38.462 21.06 0.00 0.00 1.40
2566 2627 7.009815 CACGTACGGAGAGATAGCAAAAATTAA 59.990 37.037 21.06 0.00 0.00 1.40
2567 2628 7.546667 ACGTACGGAGAGATAGCAAAAATTAAA 59.453 33.333 21.06 0.00 0.00 1.52
2568 2629 8.548721 CGTACGGAGAGATAGCAAAAATTAAAT 58.451 33.333 7.57 0.00 0.00 1.40
2571 2632 9.573133 ACGGAGAGATAGCAAAAATTAAATTTG 57.427 29.630 0.00 10.98 40.04 2.32
2590 2651 3.614399 CCGATGGCAGGGTTAGATC 57.386 57.895 0.00 0.00 0.00 2.75
2591 2652 1.051812 CCGATGGCAGGGTTAGATCT 58.948 55.000 0.00 0.00 0.00 2.75
2592 2653 1.001406 CCGATGGCAGGGTTAGATCTC 59.999 57.143 0.00 0.00 0.00 2.75
2593 2654 1.688735 CGATGGCAGGGTTAGATCTCA 59.311 52.381 0.00 0.00 0.00 3.27
2594 2655 2.301296 CGATGGCAGGGTTAGATCTCAT 59.699 50.000 0.00 0.00 0.00 2.90
2595 2656 3.511540 CGATGGCAGGGTTAGATCTCATA 59.488 47.826 0.00 0.00 0.00 2.15
2596 2657 4.021104 CGATGGCAGGGTTAGATCTCATAA 60.021 45.833 0.00 0.00 0.00 1.90
2597 2658 4.689612 TGGCAGGGTTAGATCTCATAAC 57.310 45.455 0.00 0.00 33.29 1.89
2604 2665 5.367945 GGTTAGATCTCATAACCCACCAA 57.632 43.478 13.06 0.00 44.28 3.67
2605 2666 5.123936 GGTTAGATCTCATAACCCACCAAC 58.876 45.833 13.06 2.17 44.28 3.77
2606 2667 3.933861 AGATCTCATAACCCACCAACC 57.066 47.619 0.00 0.00 0.00 3.77
2607 2668 2.170607 AGATCTCATAACCCACCAACCG 59.829 50.000 0.00 0.00 0.00 4.44
2608 2669 0.616371 TCTCATAACCCACCAACCGG 59.384 55.000 0.00 0.00 38.77 5.28
2609 2670 1.001887 TCATAACCCACCAACCGGC 60.002 57.895 0.00 0.00 34.57 6.13
2610 2671 2.049767 CATAACCCACCAACCGGCC 61.050 63.158 0.00 0.00 34.57 6.13
2611 2672 2.540021 ATAACCCACCAACCGGCCA 61.540 57.895 0.00 0.00 34.57 5.36
2612 2673 1.869824 ATAACCCACCAACCGGCCAT 61.870 55.000 0.00 0.00 34.57 4.40
2613 2674 2.773007 TAACCCACCAACCGGCCATG 62.773 60.000 0.00 0.00 34.57 3.66
2616 2677 4.054825 CACCAACCGGCCATGCAC 62.055 66.667 0.00 0.00 34.57 4.57
2622 2683 4.418401 CCGGCCATGCACGGTTTG 62.418 66.667 15.64 0.00 44.85 2.93
2623 2684 3.669344 CGGCCATGCACGGTTTGT 61.669 61.111 2.24 0.00 0.00 2.83
2624 2685 2.258286 GGCCATGCACGGTTTGTC 59.742 61.111 0.00 0.00 0.00 3.18
2625 2686 2.258286 GCCATGCACGGTTTGTCC 59.742 61.111 0.00 0.00 0.00 4.02
2626 2687 2.560119 GCCATGCACGGTTTGTCCA 61.560 57.895 0.00 0.00 35.57 4.02
2627 2688 2.037053 CCATGCACGGTTTGTCCAA 58.963 52.632 0.00 0.00 35.57 3.53
2628 2689 0.318614 CCATGCACGGTTTGTCCAAC 60.319 55.000 0.00 0.00 35.57 3.77
2629 2690 0.667993 CATGCACGGTTTGTCCAACT 59.332 50.000 0.00 0.00 35.46 3.16
2630 2691 0.667993 ATGCACGGTTTGTCCAACTG 59.332 50.000 0.00 0.00 46.19 3.16
2631 2692 0.393132 TGCACGGTTTGTCCAACTGA 60.393 50.000 2.74 0.00 43.78 3.41
2632 2693 0.028902 GCACGGTTTGTCCAACTGAC 59.971 55.000 2.74 0.00 43.78 3.51
2633 2694 0.661020 CACGGTTTGTCCAACTGACC 59.339 55.000 2.74 0.00 43.78 4.02
2634 2695 0.464916 ACGGTTTGTCCAACTGACCC 60.465 55.000 2.74 0.00 43.78 4.46
2635 2696 0.464735 CGGTTTGTCCAACTGACCCA 60.465 55.000 0.00 0.00 43.78 4.51
2636 2697 1.318576 GGTTTGTCCAACTGACCCAG 58.681 55.000 0.00 0.00 43.78 4.45
2637 2698 0.668535 GTTTGTCCAACTGACCCAGC 59.331 55.000 0.00 0.00 43.78 4.85
2638 2699 0.550914 TTTGTCCAACTGACCCAGCT 59.449 50.000 0.00 0.00 43.78 4.24
2639 2700 1.429930 TTGTCCAACTGACCCAGCTA 58.570 50.000 0.00 0.00 43.78 3.32
2640 2701 0.976641 TGTCCAACTGACCCAGCTAG 59.023 55.000 0.00 0.00 43.78 3.42
2641 2702 1.267121 GTCCAACTGACCCAGCTAGA 58.733 55.000 0.00 0.00 38.09 2.43
2642 2703 1.205893 GTCCAACTGACCCAGCTAGAG 59.794 57.143 0.00 0.00 38.09 2.43
2643 2704 1.077169 TCCAACTGACCCAGCTAGAGA 59.923 52.381 0.00 0.00 34.37 3.10
2644 2705 2.114616 CCAACTGACCCAGCTAGAGAT 58.885 52.381 0.00 0.00 34.37 2.75
2645 2706 3.052869 TCCAACTGACCCAGCTAGAGATA 60.053 47.826 0.00 0.00 34.37 1.98
2646 2707 3.900601 CCAACTGACCCAGCTAGAGATAT 59.099 47.826 0.00 0.00 34.37 1.63
2647 2708 5.080337 CCAACTGACCCAGCTAGAGATATA 58.920 45.833 0.00 0.00 34.37 0.86
2648 2709 5.540337 CCAACTGACCCAGCTAGAGATATAA 59.460 44.000 0.00 0.00 34.37 0.98
2649 2710 6.295011 CCAACTGACCCAGCTAGAGATATAAG 60.295 46.154 0.00 0.00 34.37 1.73
2650 2711 5.959512 ACTGACCCAGCTAGAGATATAAGT 58.040 41.667 0.00 0.00 34.37 2.24
2651 2712 5.772672 ACTGACCCAGCTAGAGATATAAGTG 59.227 44.000 0.00 0.00 34.37 3.16
2652 2713 5.080337 TGACCCAGCTAGAGATATAAGTGG 58.920 45.833 0.00 0.00 0.00 4.00
2653 2714 5.081032 GACCCAGCTAGAGATATAAGTGGT 58.919 45.833 0.00 0.00 0.00 4.16
2654 2715 5.468658 ACCCAGCTAGAGATATAAGTGGTT 58.531 41.667 0.00 0.00 0.00 3.67
2655 2716 5.905913 ACCCAGCTAGAGATATAAGTGGTTT 59.094 40.000 0.00 0.00 0.00 3.27
2656 2717 6.387220 ACCCAGCTAGAGATATAAGTGGTTTT 59.613 38.462 0.00 0.00 0.00 2.43
2657 2718 7.092399 ACCCAGCTAGAGATATAAGTGGTTTTT 60.092 37.037 0.00 0.00 0.00 1.94
2674 2735 3.209091 TTTTTCTCCCCCGTTGCAA 57.791 47.368 0.00 0.00 0.00 4.08
2675 2736 0.747852 TTTTTCTCCCCCGTTGCAAC 59.252 50.000 19.89 19.89 0.00 4.17
2688 2749 4.279043 GCAACGCACGGGCCTTTT 62.279 61.111 2.82 0.00 36.38 2.27
2689 2750 2.415426 CAACGCACGGGCCTTTTT 59.585 55.556 2.82 0.00 36.38 1.94
2690 2751 1.948635 CAACGCACGGGCCTTTTTG 60.949 57.895 2.82 0.00 36.38 2.44
2691 2752 3.783478 AACGCACGGGCCTTTTTGC 62.783 57.895 2.82 5.50 36.38 3.68
2692 2753 3.977244 CGCACGGGCCTTTTTGCT 61.977 61.111 2.82 0.00 36.38 3.91
2693 2754 2.622011 CGCACGGGCCTTTTTGCTA 61.622 57.895 2.82 0.00 36.38 3.49
2694 2755 1.212751 GCACGGGCCTTTTTGCTAG 59.787 57.895 0.00 0.00 32.00 3.42
2695 2756 1.524008 GCACGGGCCTTTTTGCTAGT 61.524 55.000 0.00 0.00 32.00 2.57
2696 2757 0.521735 CACGGGCCTTTTTGCTAGTC 59.478 55.000 0.84 0.00 0.00 2.59
2697 2758 0.608308 ACGGGCCTTTTTGCTAGTCC 60.608 55.000 0.84 0.00 0.00 3.85
2698 2759 0.608035 CGGGCCTTTTTGCTAGTCCA 60.608 55.000 0.84 0.00 0.00 4.02
2699 2760 0.888619 GGGCCTTTTTGCTAGTCCAC 59.111 55.000 0.84 0.00 0.00 4.02
2700 2761 1.616159 GGCCTTTTTGCTAGTCCACA 58.384 50.000 0.00 0.00 0.00 4.17
2750 2811 6.040842 AGCCAATGGAATCGCAAAATATTAGT 59.959 34.615 2.05 0.00 0.00 2.24
2800 2977 0.889186 TCGCTCAAGTTTCTTGCCCC 60.889 55.000 4.82 0.00 0.00 5.80
2801 2978 1.581447 GCTCAAGTTTCTTGCCCCG 59.419 57.895 4.82 0.00 0.00 5.73
2807 2984 2.749839 TTTCTTGCCCCGGATGCG 60.750 61.111 0.73 0.00 0.00 4.73
2808 2985 3.261039 TTTCTTGCCCCGGATGCGA 62.261 57.895 8.71 4.08 0.00 5.10
2809 2986 2.756321 TTTCTTGCCCCGGATGCGAA 62.756 55.000 8.71 2.58 0.00 4.70
2810 2987 2.749839 CTTGCCCCGGATGCGAAA 60.750 61.111 8.71 0.00 0.00 3.46
2811 2988 2.282532 TTGCCCCGGATGCGAAAA 60.283 55.556 8.71 0.00 0.00 2.29
2812 2989 2.542211 CTTGCCCCGGATGCGAAAAC 62.542 60.000 8.71 0.00 0.00 2.43
2813 2990 4.174129 GCCCCGGATGCGAAAACG 62.174 66.667 8.71 0.00 0.00 3.60
2814 2991 2.435234 CCCCGGATGCGAAAACGA 60.435 61.111 8.71 0.00 0.00 3.85
2815 2992 2.036006 CCCCGGATGCGAAAACGAA 61.036 57.895 8.71 0.00 0.00 3.85
2816 2993 1.579084 CCCCGGATGCGAAAACGAAA 61.579 55.000 8.71 0.00 0.00 3.46
2817 2994 0.453782 CCCGGATGCGAAAACGAAAC 60.454 55.000 8.71 0.00 0.00 2.78
2818 2995 0.236187 CCGGATGCGAAAACGAAACA 59.764 50.000 8.71 0.00 0.00 2.83
2819 2996 1.135803 CCGGATGCGAAAACGAAACAT 60.136 47.619 8.71 0.00 0.00 2.71
2820 2997 2.094575 CCGGATGCGAAAACGAAACATA 59.905 45.455 8.71 0.00 0.00 2.29
2821 2998 3.242608 CCGGATGCGAAAACGAAACATAT 60.243 43.478 8.71 0.00 0.00 1.78
2822 2999 4.025563 CCGGATGCGAAAACGAAACATATA 60.026 41.667 8.71 0.00 0.00 0.86
2823 3000 5.333798 CCGGATGCGAAAACGAAACATATAT 60.334 40.000 8.71 0.00 0.00 0.86
2824 3001 6.128769 CCGGATGCGAAAACGAAACATATATA 60.129 38.462 8.71 0.00 0.00 0.86
2825 3002 7.412563 CCGGATGCGAAAACGAAACATATATAT 60.413 37.037 8.71 0.00 0.00 0.86
2826 3003 8.588789 CGGATGCGAAAACGAAACATATATATA 58.411 33.333 0.00 0.00 0.00 0.86
2848 3025 7.976414 ATATTTGGATCCCTGATCAACAAAA 57.024 32.000 9.90 0.00 40.50 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.009473 TGCAGGATAGAAAAGTTCCAGCT 59.991 43.478 7.04 0.00 41.24 4.24
1 2 3.347216 TGCAGGATAGAAAAGTTCCAGC 58.653 45.455 0.00 0.00 41.09 4.85
2 3 4.201990 GCATGCAGGATAGAAAAGTTCCAG 60.202 45.833 14.21 0.00 31.65 3.86
3 4 3.696051 GCATGCAGGATAGAAAAGTTCCA 59.304 43.478 14.21 0.00 31.65 3.53
5 6 4.918037 CTGCATGCAGGATAGAAAAGTTC 58.082 43.478 35.39 0.00 40.17 3.01
6 7 4.978083 CTGCATGCAGGATAGAAAAGTT 57.022 40.909 35.39 0.00 40.17 2.66
71 72 2.036346 AGGCAGTTTCTTTGTCAATGGC 59.964 45.455 1.06 1.06 0.00 4.40
138 139 1.140312 AGTGCCAGAGGGAGACAAAA 58.860 50.000 0.00 0.00 35.59 2.44
143 144 2.912956 ACAAATAAGTGCCAGAGGGAGA 59.087 45.455 0.00 0.00 35.59 3.71
177 178 3.084070 TCGGATGAACGATCTGTCATG 57.916 47.619 11.51 0.00 38.47 3.07
243 248 4.079970 TCCAACCTACACACACACAAAAA 58.920 39.130 0.00 0.00 0.00 1.94
244 249 3.687125 TCCAACCTACACACACACAAAA 58.313 40.909 0.00 0.00 0.00 2.44
245 250 3.351794 TCCAACCTACACACACACAAA 57.648 42.857 0.00 0.00 0.00 2.83
246 251 3.351794 TTCCAACCTACACACACACAA 57.648 42.857 0.00 0.00 0.00 3.33
247 252 3.275143 CTTTCCAACCTACACACACACA 58.725 45.455 0.00 0.00 0.00 3.72
248 253 2.032924 GCTTTCCAACCTACACACACAC 59.967 50.000 0.00 0.00 0.00 3.82
249 254 2.092646 AGCTTTCCAACCTACACACACA 60.093 45.455 0.00 0.00 0.00 3.72
250 255 2.290641 CAGCTTTCCAACCTACACACAC 59.709 50.000 0.00 0.00 0.00 3.82
251 256 2.171659 TCAGCTTTCCAACCTACACACA 59.828 45.455 0.00 0.00 0.00 3.72
252 257 2.846193 TCAGCTTTCCAACCTACACAC 58.154 47.619 0.00 0.00 0.00 3.82
343 348 9.311916 GAGATAATGGAGAGACACAATATATGC 57.688 37.037 0.00 0.00 0.00 3.14
371 376 2.158755 ACTCCAGAAGTTCAACTGTGGG 60.159 50.000 16.11 10.80 35.11 4.61
406 411 8.557029 AGTACTTTTTCTAATCGGACTTTTGTG 58.443 33.333 0.00 0.00 0.00 3.33
422 427 7.540745 TCAAAGACAACAAAGCAGTACTTTTTC 59.459 33.333 0.00 0.00 46.73 2.29
437 442 6.127647 ACAAGCAGATTCTTTCAAAGACAACA 60.128 34.615 0.00 0.00 37.23 3.33
504 509 3.658757 GCATCCCTGCTAAAACACAAA 57.341 42.857 0.00 0.00 45.32 2.83
569 574 1.207791 CTCCTGTGCCTATCCCAAGT 58.792 55.000 0.00 0.00 0.00 3.16
749 754 7.815398 TCTCGCGTGTCTAAACAAATATAAA 57.185 32.000 5.77 0.00 37.08 1.40
769 774 6.794158 GCACAGCTATAAAATAAAGCATCTCG 59.206 38.462 0.00 0.00 38.75 4.04
778 783 6.348498 TCTCAGCAGCACAGCTATAAAATAA 58.652 36.000 0.00 0.00 44.54 1.40
825 830 1.001641 CTCTCTGCCCCCACAAAGG 60.002 63.158 0.00 0.00 37.03 3.11
833 848 1.064832 AGCTGATTTTCTCTCTGCCCC 60.065 52.381 0.00 0.00 38.06 5.80
883 898 2.493278 GCATTATTTGTGGTGTGAGGCT 59.507 45.455 0.00 0.00 0.00 4.58
907 922 9.387123 GACACAGAAACAAAGAAATATGAGTTC 57.613 33.333 0.00 0.00 0.00 3.01
932 947 1.542547 GCGACTGGGAAACTTTGGAGA 60.543 52.381 0.00 0.00 0.00 3.71
935 950 0.593128 CAGCGACTGGGAAACTTTGG 59.407 55.000 0.00 0.00 0.00 3.28
1007 1022 2.684881 CAAGTTTACAGCCCTATGCAGG 59.315 50.000 0.00 0.00 44.83 4.85
1034 1050 1.235281 TGCTGCTGCTTGCTCAGAAG 61.235 55.000 17.00 5.40 41.69 2.85
1121 1137 1.372251 CGACACGAGAAGCAGCTGT 60.372 57.895 16.64 0.00 0.00 4.40
1228 1246 3.822735 TGCCAAGAAGATGAAGAAACTGG 59.177 43.478 0.00 0.00 0.00 4.00
1425 1443 3.055209 AGATATGTATGGCAGCAGCAG 57.945 47.619 2.65 0.00 44.61 4.24
1491 1509 7.500559 ACAAATGGCCTTCAGAAGATAACTATC 59.499 37.037 12.14 0.00 0.00 2.08
1495 1513 5.904362 ACAAATGGCCTTCAGAAGATAAC 57.096 39.130 12.14 0.00 0.00 1.89
1546 1564 2.102252 GACAGTTAGCTCCCCTCATCAG 59.898 54.545 0.00 0.00 0.00 2.90
1573 1591 1.751927 GCCAGTCCCCTGCATCAAG 60.752 63.158 0.00 0.00 37.38 3.02
1676 1705 4.917887 ACTTCGACTACACGTAGTACTG 57.082 45.455 9.78 4.10 45.63 2.74
1678 1707 6.254589 ACTGATACTTCGACTACACGTAGTAC 59.745 42.308 9.78 3.91 45.63 2.73
1681 1710 5.715429 ACTGATACTTCGACTACACGTAG 57.285 43.478 2.63 2.63 39.04 3.51
1720 1749 2.949644 ACCAGCAGTTTAGTCACAAACC 59.050 45.455 0.00 0.00 38.86 3.27
1755 1788 1.294659 GGCAGTCGAAGCACCTGAAG 61.295 60.000 12.48 0.00 0.00 3.02
1854 1887 2.799017 TGGATGGATGGATGCTTATGC 58.201 47.619 0.00 0.00 40.20 3.14
1883 1918 1.818785 GGAGAGTGCATCTGCCTGC 60.819 63.158 0.00 0.00 40.36 4.85
1884 1919 0.035725 TTGGAGAGTGCATCTGCCTG 60.036 55.000 12.59 0.00 45.39 4.85
1885 1920 0.917533 ATTGGAGAGTGCATCTGCCT 59.082 50.000 12.59 0.00 45.39 4.75
1886 1921 1.022735 CATTGGAGAGTGCATCTGCC 58.977 55.000 12.59 9.65 45.39 4.85
1887 1922 1.669779 GACATTGGAGAGTGCATCTGC 59.330 52.381 9.60 9.60 46.13 4.26
1888 1923 2.981898 TGACATTGGAGAGTGCATCTG 58.018 47.619 0.00 0.00 38.84 2.90
1889 1924 3.928005 ATGACATTGGAGAGTGCATCT 57.072 42.857 0.00 0.00 42.61 2.90
1890 1925 6.630444 AAATATGACATTGGAGAGTGCATC 57.370 37.500 0.00 0.00 0.00 3.91
2006 2041 6.103222 GGTTCTCAAACCGATTATGTGTAC 57.897 41.667 0.00 0.00 45.33 2.90
2069 2104 0.796312 CAATACGCGCAGAAACCAGT 59.204 50.000 5.73 0.00 0.00 4.00
2092 2127 3.575256 ACAGATTCAAAAGCATCCAAGCA 59.425 39.130 0.00 0.00 36.85 3.91
2094 2129 5.747197 GCATACAGATTCAAAAGCATCCAAG 59.253 40.000 0.00 0.00 0.00 3.61
2318 2379 9.434420 CAGATGAACTTAATGGGCAAAATTTTA 57.566 29.630 2.44 0.00 0.00 1.52
2322 2383 6.664816 TCTCAGATGAACTTAATGGGCAAAAT 59.335 34.615 0.00 0.00 0.00 1.82
2366 2427 9.174166 GGATACATAAACTTGTTACCACTTGAT 57.826 33.333 0.00 0.00 0.00 2.57
2403 2464 5.536497 AACCAAGAATATCACCTCCCTTT 57.464 39.130 0.00 0.00 0.00 3.11
2404 2465 5.510430 GAAACCAAGAATATCACCTCCCTT 58.490 41.667 0.00 0.00 0.00 3.95
2405 2466 4.384208 CGAAACCAAGAATATCACCTCCCT 60.384 45.833 0.00 0.00 0.00 4.20
2406 2467 3.877508 CGAAACCAAGAATATCACCTCCC 59.122 47.826 0.00 0.00 0.00 4.30
2407 2468 4.514401 ACGAAACCAAGAATATCACCTCC 58.486 43.478 0.00 0.00 0.00 4.30
2408 2469 4.571176 GGACGAAACCAAGAATATCACCTC 59.429 45.833 0.00 0.00 0.00 3.85
2409 2470 4.514401 GGACGAAACCAAGAATATCACCT 58.486 43.478 0.00 0.00 0.00 4.00
2410 2471 3.626217 GGGACGAAACCAAGAATATCACC 59.374 47.826 0.00 0.00 0.00 4.02
2411 2472 4.877323 GGGACGAAACCAAGAATATCAC 57.123 45.455 0.00 0.00 0.00 3.06
2428 2489 0.814812 TGGACCAAACGAAACGGGAC 60.815 55.000 0.00 0.00 0.00 4.46
2429 2490 0.107312 TTGGACCAAACGAAACGGGA 60.107 50.000 3.84 0.00 0.00 5.14
2430 2491 0.955905 ATTGGACCAAACGAAACGGG 59.044 50.000 11.82 0.00 0.00 5.28
2431 2492 2.033550 TGAATTGGACCAAACGAAACGG 59.966 45.455 11.82 0.00 0.00 4.44
2432 2493 3.341857 TGAATTGGACCAAACGAAACG 57.658 42.857 11.82 0.00 0.00 3.60
2433 2494 7.701809 TTAATTGAATTGGACCAAACGAAAC 57.298 32.000 11.82 0.52 0.00 2.78
2434 2495 8.894768 AATTAATTGAATTGGACCAAACGAAA 57.105 26.923 11.82 4.37 36.35 3.46
2435 2496 8.894768 AAATTAATTGAATTGGACCAAACGAA 57.105 26.923 11.82 4.41 37.82 3.85
2436 2497 8.144478 TGAAATTAATTGAATTGGACCAAACGA 58.856 29.630 11.82 8.88 37.82 3.85
2437 2498 8.220434 GTGAAATTAATTGAATTGGACCAAACG 58.780 33.333 11.82 0.00 37.82 3.60
2438 2499 8.220434 CGTGAAATTAATTGAATTGGACCAAAC 58.780 33.333 11.82 9.22 37.82 2.93
2439 2500 7.928706 ACGTGAAATTAATTGAATTGGACCAAA 59.071 29.630 11.82 0.00 37.82 3.28
2440 2501 7.437748 ACGTGAAATTAATTGAATTGGACCAA 58.562 30.769 9.92 9.92 37.82 3.67
2441 2502 6.987386 ACGTGAAATTAATTGAATTGGACCA 58.013 32.000 0.39 0.00 37.82 4.02
2442 2503 7.700656 CCTACGTGAAATTAATTGAATTGGACC 59.299 37.037 0.39 0.00 37.82 4.46
2443 2504 7.220108 GCCTACGTGAAATTAATTGAATTGGAC 59.780 37.037 0.39 0.00 37.82 4.02
2444 2505 7.122055 AGCCTACGTGAAATTAATTGAATTGGA 59.878 33.333 0.39 0.00 37.82 3.53
2445 2506 7.257722 AGCCTACGTGAAATTAATTGAATTGG 58.742 34.615 0.39 0.90 37.82 3.16
2446 2507 9.950680 ATAGCCTACGTGAAATTAATTGAATTG 57.049 29.630 0.39 0.00 37.82 2.32
2449 2510 9.781834 CAAATAGCCTACGTGAAATTAATTGAA 57.218 29.630 0.39 0.00 0.00 2.69
2450 2511 8.402472 CCAAATAGCCTACGTGAAATTAATTGA 58.598 33.333 0.39 0.00 0.00 2.57
2451 2512 8.188139 ACCAAATAGCCTACGTGAAATTAATTG 58.812 33.333 0.39 0.00 0.00 2.32
2452 2513 8.288689 ACCAAATAGCCTACGTGAAATTAATT 57.711 30.769 0.00 0.00 0.00 1.40
2453 2514 7.875327 ACCAAATAGCCTACGTGAAATTAAT 57.125 32.000 0.00 0.00 0.00 1.40
2454 2515 7.690952 AACCAAATAGCCTACGTGAAATTAA 57.309 32.000 0.00 0.00 0.00 1.40
2455 2516 7.413219 CGAAACCAAATAGCCTACGTGAAATTA 60.413 37.037 0.00 0.00 0.00 1.40
2456 2517 6.584185 AAACCAAATAGCCTACGTGAAATT 57.416 33.333 0.00 0.00 0.00 1.82
2457 2518 5.163794 CGAAACCAAATAGCCTACGTGAAAT 60.164 40.000 0.00 0.00 0.00 2.17
2458 2519 4.152759 CGAAACCAAATAGCCTACGTGAAA 59.847 41.667 0.00 0.00 0.00 2.69
2459 2520 3.680937 CGAAACCAAATAGCCTACGTGAA 59.319 43.478 0.00 0.00 0.00 3.18
2460 2521 3.255725 CGAAACCAAATAGCCTACGTGA 58.744 45.455 0.00 0.00 0.00 4.35
2461 2522 2.997986 ACGAAACCAAATAGCCTACGTG 59.002 45.455 0.00 0.00 0.00 4.49
2462 2523 3.323751 ACGAAACCAAATAGCCTACGT 57.676 42.857 0.00 0.00 0.00 3.57
2463 2524 4.866486 AGTAACGAAACCAAATAGCCTACG 59.134 41.667 0.00 0.00 0.00 3.51
2464 2525 6.540205 CAAGTAACGAAACCAAATAGCCTAC 58.460 40.000 0.00 0.00 0.00 3.18
2465 2526 5.122711 GCAAGTAACGAAACCAAATAGCCTA 59.877 40.000 0.00 0.00 0.00 3.93
2466 2527 4.082949 GCAAGTAACGAAACCAAATAGCCT 60.083 41.667 0.00 0.00 0.00 4.58
2467 2528 4.163552 GCAAGTAACGAAACCAAATAGCC 58.836 43.478 0.00 0.00 0.00 3.93
2468 2529 4.163552 GGCAAGTAACGAAACCAAATAGC 58.836 43.478 0.00 0.00 0.00 2.97
2469 2530 5.151389 GTGGCAAGTAACGAAACCAAATAG 58.849 41.667 0.00 0.00 0.00 1.73
2470 2531 4.023021 GGTGGCAAGTAACGAAACCAAATA 60.023 41.667 0.00 0.00 0.00 1.40
2471 2532 3.243602 GGTGGCAAGTAACGAAACCAAAT 60.244 43.478 0.00 0.00 0.00 2.32
2472 2533 2.099427 GGTGGCAAGTAACGAAACCAAA 59.901 45.455 0.00 0.00 0.00 3.28
2473 2534 1.677052 GGTGGCAAGTAACGAAACCAA 59.323 47.619 0.00 0.00 0.00 3.67
2474 2535 1.310904 GGTGGCAAGTAACGAAACCA 58.689 50.000 0.00 0.00 0.00 3.67
2475 2536 0.594602 GGGTGGCAAGTAACGAAACC 59.405 55.000 0.00 0.00 0.00 3.27
2476 2537 0.236449 CGGGTGGCAAGTAACGAAAC 59.764 55.000 0.00 0.00 0.00 2.78
2477 2538 0.179051 ACGGGTGGCAAGTAACGAAA 60.179 50.000 0.00 0.00 0.00 3.46
2478 2539 0.179051 AACGGGTGGCAAGTAACGAA 60.179 50.000 0.00 0.00 0.00 3.85
2479 2540 0.179051 AAACGGGTGGCAAGTAACGA 60.179 50.000 0.00 0.00 0.00 3.85
2480 2541 0.664224 AAAACGGGTGGCAAGTAACG 59.336 50.000 0.00 0.00 0.00 3.18
2481 2542 1.269361 CCAAAACGGGTGGCAAGTAAC 60.269 52.381 0.00 0.00 0.00 2.50
2482 2543 1.033574 CCAAAACGGGTGGCAAGTAA 58.966 50.000 0.00 0.00 0.00 2.24
2483 2544 2.721945 CCAAAACGGGTGGCAAGTA 58.278 52.632 0.00 0.00 0.00 2.24
2484 2545 3.532501 CCAAAACGGGTGGCAAGT 58.467 55.556 0.00 0.00 0.00 3.16
2489 2550 2.840102 TTGGGCCAAAACGGGTGG 60.840 61.111 18.51 0.00 39.33 4.61
2490 2551 2.362329 CTGTTGGGCCAAAACGGGTG 62.362 60.000 22.82 0.00 34.06 4.61
2491 2552 2.042843 TGTTGGGCCAAAACGGGT 60.043 55.556 22.82 0.00 34.06 5.28
2492 2553 1.805428 CTCTGTTGGGCCAAAACGGG 61.805 60.000 22.82 8.38 35.11 5.28
2493 2554 1.659794 CTCTGTTGGGCCAAAACGG 59.340 57.895 22.82 15.81 35.60 4.44
2494 2555 0.821711 TCCTCTGTTGGGCCAAAACG 60.822 55.000 22.82 12.22 0.00 3.60
2495 2556 1.341209 CTTCCTCTGTTGGGCCAAAAC 59.659 52.381 22.82 11.39 0.00 2.43
2496 2557 1.703411 CTTCCTCTGTTGGGCCAAAA 58.297 50.000 22.82 15.90 0.00 2.44
2497 2558 0.827507 GCTTCCTCTGTTGGGCCAAA 60.828 55.000 22.82 10.57 0.00 3.28
2498 2559 1.228552 GCTTCCTCTGTTGGGCCAA 60.229 57.895 16.66 16.66 0.00 4.52
2499 2560 2.436109 GCTTCCTCTGTTGGGCCA 59.564 61.111 0.00 0.00 0.00 5.36
2500 2561 2.361737 GGCTTCCTCTGTTGGGCC 60.362 66.667 0.00 0.00 0.00 5.80
2501 2562 2.361737 GGGCTTCCTCTGTTGGGC 60.362 66.667 0.00 0.00 0.00 5.36
2502 2563 1.303643 GTGGGCTTCCTCTGTTGGG 60.304 63.158 0.00 0.00 0.00 4.12
2503 2564 1.303643 GGTGGGCTTCCTCTGTTGG 60.304 63.158 0.00 0.00 0.00 3.77
2504 2565 0.607489 CAGGTGGGCTTCCTCTGTTG 60.607 60.000 0.00 0.00 32.37 3.33
2505 2566 0.768221 TCAGGTGGGCTTCCTCTGTT 60.768 55.000 0.00 0.00 35.57 3.16
2506 2567 1.152030 TCAGGTGGGCTTCCTCTGT 60.152 57.895 0.00 0.00 35.57 3.41
2507 2568 1.298014 GTCAGGTGGGCTTCCTCTG 59.702 63.158 0.00 0.00 35.47 3.35
2508 2569 2.286523 CGTCAGGTGGGCTTCCTCT 61.287 63.158 0.00 0.00 32.37 3.69
2509 2570 2.266055 CGTCAGGTGGGCTTCCTC 59.734 66.667 0.00 0.00 32.37 3.71
2510 2571 3.322466 CCGTCAGGTGGGCTTCCT 61.322 66.667 0.00 0.00 35.45 3.36
2519 2580 4.969196 CACAGTGCGCCGTCAGGT 62.969 66.667 4.18 0.00 40.50 4.00
2528 2589 4.673298 TACGTGGGCCACAGTGCG 62.673 66.667 34.11 22.86 33.40 5.34
2529 2590 3.047877 GTACGTGGGCCACAGTGC 61.048 66.667 34.11 28.43 33.40 4.40
2530 2591 2.736995 CGTACGTGGGCCACAGTG 60.737 66.667 34.11 21.24 33.40 3.66
2531 2592 3.998672 CCGTACGTGGGCCACAGT 61.999 66.667 34.11 30.57 33.40 3.55
2532 2593 3.642778 CTCCGTACGTGGGCCACAG 62.643 68.421 34.11 27.14 33.40 3.66
2533 2594 3.687102 CTCCGTACGTGGGCCACA 61.687 66.667 34.11 15.16 33.40 4.17
2534 2595 3.352338 CTCTCCGTACGTGGGCCAC 62.352 68.421 26.95 26.95 0.00 5.01
2535 2596 2.849096 ATCTCTCCGTACGTGGGCCA 62.849 60.000 15.21 0.00 0.00 5.36
2536 2597 0.820891 TATCTCTCCGTACGTGGGCC 60.821 60.000 15.21 0.00 0.00 5.80
2537 2598 0.592148 CTATCTCTCCGTACGTGGGC 59.408 60.000 15.21 0.00 0.00 5.36
2538 2599 0.592148 GCTATCTCTCCGTACGTGGG 59.408 60.000 15.21 6.78 0.00 4.61
2539 2600 1.306148 TGCTATCTCTCCGTACGTGG 58.694 55.000 15.21 6.45 0.00 4.94
2540 2601 3.416119 TTTGCTATCTCTCCGTACGTG 57.584 47.619 15.21 6.84 0.00 4.49
2541 2602 4.445452 TTTTTGCTATCTCTCCGTACGT 57.555 40.909 15.21 0.00 0.00 3.57
2542 2603 5.968387 AATTTTTGCTATCTCTCCGTACG 57.032 39.130 8.69 8.69 0.00 3.67
2545 2606 9.573133 CAAATTTAATTTTTGCTATCTCTCCGT 57.427 29.630 0.00 0.00 0.00 4.69
2572 2633 1.001406 GAGATCTAACCCTGCCATCGG 59.999 57.143 0.00 0.00 0.00 4.18
2573 2634 1.688735 TGAGATCTAACCCTGCCATCG 59.311 52.381 0.00 0.00 0.00 3.84
2574 2635 5.241662 GTTATGAGATCTAACCCTGCCATC 58.758 45.833 0.00 0.00 0.00 3.51
2575 2636 4.042187 GGTTATGAGATCTAACCCTGCCAT 59.958 45.833 13.06 4.93 41.45 4.40
2576 2637 3.391296 GGTTATGAGATCTAACCCTGCCA 59.609 47.826 13.06 0.00 41.45 4.92
2577 2638 4.009370 GGTTATGAGATCTAACCCTGCC 57.991 50.000 13.06 0.00 41.45 4.85
2582 2643 5.123936 GTTGGTGGGTTATGAGATCTAACC 58.876 45.833 15.04 15.04 44.89 2.85
2583 2644 5.123936 GGTTGGTGGGTTATGAGATCTAAC 58.876 45.833 0.00 0.00 0.00 2.34
2584 2645 4.141801 CGGTTGGTGGGTTATGAGATCTAA 60.142 45.833 0.00 0.00 0.00 2.10
2585 2646 3.386726 CGGTTGGTGGGTTATGAGATCTA 59.613 47.826 0.00 0.00 0.00 1.98
2586 2647 2.170607 CGGTTGGTGGGTTATGAGATCT 59.829 50.000 0.00 0.00 0.00 2.75
2587 2648 2.561569 CGGTTGGTGGGTTATGAGATC 58.438 52.381 0.00 0.00 0.00 2.75
2588 2649 1.211949 CCGGTTGGTGGGTTATGAGAT 59.788 52.381 0.00 0.00 0.00 2.75
2589 2650 0.616371 CCGGTTGGTGGGTTATGAGA 59.384 55.000 0.00 0.00 0.00 3.27
2590 2651 1.029947 GCCGGTTGGTGGGTTATGAG 61.030 60.000 1.90 0.00 37.67 2.90
2591 2652 1.001887 GCCGGTTGGTGGGTTATGA 60.002 57.895 1.90 0.00 37.67 2.15
2592 2653 2.049767 GGCCGGTTGGTGGGTTATG 61.050 63.158 1.90 0.00 37.67 1.90
2593 2654 1.869824 ATGGCCGGTTGGTGGGTTAT 61.870 55.000 1.90 0.00 37.67 1.89
2594 2655 2.540021 ATGGCCGGTTGGTGGGTTA 61.540 57.895 1.90 0.00 37.67 2.85
2595 2656 3.909651 ATGGCCGGTTGGTGGGTT 61.910 61.111 1.90 0.00 37.67 4.11
2596 2657 4.676951 CATGGCCGGTTGGTGGGT 62.677 66.667 1.90 0.00 37.67 4.51
2599 2660 4.054825 GTGCATGGCCGGTTGGTG 62.055 66.667 1.90 0.00 37.67 4.17
2605 2666 4.418401 CAAACCGTGCATGGCCGG 62.418 66.667 25.30 18.12 43.93 6.13
2606 2667 3.609214 GACAAACCGTGCATGGCCG 62.609 63.158 25.30 15.28 0.00 6.13
2607 2668 2.258286 GACAAACCGTGCATGGCC 59.742 61.111 25.30 0.00 0.00 5.36
2608 2669 2.081425 TTGGACAAACCGTGCATGGC 62.081 55.000 25.30 7.92 46.32 4.40
2609 2670 0.318614 GTTGGACAAACCGTGCATGG 60.319 55.000 23.83 23.83 46.32 3.66
2610 2671 0.667993 AGTTGGACAAACCGTGCATG 59.332 50.000 0.00 0.00 46.32 4.06
2611 2672 0.667993 CAGTTGGACAAACCGTGCAT 59.332 50.000 0.00 0.00 46.32 3.96
2612 2673 0.393132 TCAGTTGGACAAACCGTGCA 60.393 50.000 0.00 0.00 45.30 4.57
2613 2674 0.028902 GTCAGTTGGACAAACCGTGC 59.971 55.000 0.00 0.00 46.19 5.34
2622 2683 1.205893 CTCTAGCTGGGTCAGTTGGAC 59.794 57.143 0.00 0.00 46.20 4.02
2623 2684 1.077169 TCTCTAGCTGGGTCAGTTGGA 59.923 52.381 0.00 0.00 32.34 3.53
2624 2685 1.561643 TCTCTAGCTGGGTCAGTTGG 58.438 55.000 0.00 0.00 33.43 3.77
2625 2686 6.266558 ACTTATATCTCTAGCTGGGTCAGTTG 59.733 42.308 0.00 0.00 33.43 3.16
2626 2687 6.266558 CACTTATATCTCTAGCTGGGTCAGTT 59.733 42.308 0.00 0.00 33.43 3.16
2627 2688 5.772672 CACTTATATCTCTAGCTGGGTCAGT 59.227 44.000 0.00 0.00 33.43 3.41
2628 2689 5.184864 CCACTTATATCTCTAGCTGGGTCAG 59.815 48.000 0.00 0.00 34.12 3.51
2629 2690 5.080337 CCACTTATATCTCTAGCTGGGTCA 58.920 45.833 0.00 0.00 0.00 4.02
2630 2691 5.081032 ACCACTTATATCTCTAGCTGGGTC 58.919 45.833 0.00 0.00 0.00 4.46
2631 2692 5.081315 ACCACTTATATCTCTAGCTGGGT 57.919 43.478 0.00 0.00 0.00 4.51
2632 2693 6.426646 AAACCACTTATATCTCTAGCTGGG 57.573 41.667 0.00 0.00 0.00 4.45
2656 2717 0.747852 GTTGCAACGGGGGAGAAAAA 59.252 50.000 14.90 0.00 0.00 1.94
2657 2718 2.421220 GTTGCAACGGGGGAGAAAA 58.579 52.632 14.90 0.00 0.00 2.29
2658 2719 4.167597 GTTGCAACGGGGGAGAAA 57.832 55.556 14.90 0.00 0.00 2.52
2671 2732 3.783478 AAAAAGGCCCGTGCGTTGC 62.783 57.895 0.00 0.00 44.30 4.17
2672 2733 1.948635 CAAAAAGGCCCGTGCGTTG 60.949 57.895 0.00 0.00 44.30 4.10
2673 2734 2.415426 CAAAAAGGCCCGTGCGTT 59.585 55.556 0.00 0.00 46.85 4.84
2674 2735 4.279043 GCAAAAAGGCCCGTGCGT 62.279 61.111 0.00 0.00 38.85 5.24
2675 2736 2.527547 CTAGCAAAAAGGCCCGTGCG 62.528 60.000 0.00 0.00 41.90 5.34
2676 2737 1.212751 CTAGCAAAAAGGCCCGTGC 59.787 57.895 0.00 4.01 37.26 5.34
2677 2738 0.521735 GACTAGCAAAAAGGCCCGTG 59.478 55.000 0.00 0.00 0.00 4.94
2678 2739 0.608308 GGACTAGCAAAAAGGCCCGT 60.608 55.000 0.00 0.00 35.96 5.28
2679 2740 0.608035 TGGACTAGCAAAAAGGCCCG 60.608 55.000 0.00 0.00 42.01 6.13
2680 2741 0.888619 GTGGACTAGCAAAAAGGCCC 59.111 55.000 0.00 0.00 42.01 5.80
2681 2742 1.269723 GTGTGGACTAGCAAAAAGGCC 59.730 52.381 0.00 0.00 43.12 5.19
2682 2743 2.230660 AGTGTGGACTAGCAAAAAGGC 58.769 47.619 0.00 0.00 0.00 4.35
2683 2744 6.575162 ATTTAGTGTGGACTAGCAAAAAGG 57.425 37.500 0.00 0.00 36.03 3.11
2685 2746 9.906660 CAATAATTTAGTGTGGACTAGCAAAAA 57.093 29.630 0.00 0.00 36.03 1.94
2686 2747 9.290988 TCAATAATTTAGTGTGGACTAGCAAAA 57.709 29.630 4.01 0.00 36.03 2.44
2687 2748 8.856153 TCAATAATTTAGTGTGGACTAGCAAA 57.144 30.769 4.01 0.00 36.03 3.68
2731 2792 8.669946 TGTATGACTAATATTTTGCGATTCCA 57.330 30.769 0.00 0.00 0.00 3.53
2759 2820 6.697019 GCGACCATCTTTTGCAAATACATATT 59.303 34.615 13.65 0.00 0.00 1.28
2800 2977 2.241259 ATGTTTCGTTTTCGCATCCG 57.759 45.000 0.00 0.00 43.73 4.18
2822 2999 9.659135 TTTTGTTGATCAGGGATCCAAATATAT 57.341 29.630 15.23 0.00 38.20 0.86
2824 3001 7.976414 TTTTGTTGATCAGGGATCCAAATAT 57.024 32.000 15.23 0.68 38.20 1.28


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

AutoCloner maintained by Alex Coulton.