Multiple sequence alignment - TraesCS5B01G067000

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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 TraesCS5B01G067000 chr5B 100.000 3213 0 0 1 3213 75031855 75035067 0.000000e+00 5934.0
1 TraesCS5B01G067000 chr5D 96.060 2386 75 5 1 2372 69112529 69114909 0.000000e+00 3868.0
2 TraesCS5B01G067000 chr5D 89.032 620 61 7 2460 3076 69114940 69115555 0.000000e+00 761.0
3 TraesCS5B01G067000 chr5D 74.755 408 87 12 1749 2143 379342619 379342215 5.510000e-38 169.0
4 TraesCS5B01G067000 chr5A 95.625 2400 73 12 1 2372 59719189 59721584 0.000000e+00 3821.0
5 TraesCS5B01G067000 chr5A 89.125 377 36 2 2842 3213 59766846 59767222 6.280000e-127 464.0
6 TraesCS5B01G067000 chr6D 89.535 86 6 3 2379 2463 24612239 24612322 4.380000e-19 106.0
7 TraesCS5B01G067000 chr6D 90.667 75 6 1 2390 2463 25007062 25006988 7.340000e-17 99.0
8 TraesCS5B01G067000 chr1D 87.952 83 10 0 2381 2463 433924078 433923996 7.340000e-17 99.0
9 TraesCS5B01G067000 chr1D 89.231 65 6 1 2400 2463 203758182 203758118 2.660000e-11 80.5
10 TraesCS5B01G067000 chr1D 95.745 47 2 0 2417 2463 462104087 462104041 3.440000e-10 76.8
11 TraesCS5B01G067000 chr2B 84.884 86 12 1 2379 2463 191754896 191754811 5.710000e-13 86.1
12 TraesCS5B01G067000 chr6A 84.524 84 11 2 2381 2463 23240164 23240246 7.390000e-12 82.4
13 TraesCS5B01G067000 chr4D 96.078 51 1 1 2414 2463 482938231 482938281 7.390000e-12 82.4
14 TraesCS5B01G067000 chr1B 82.759 87 12 3 2379 2463 298072300 298072385 1.240000e-09 75.0


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 TraesCS5B01G067000 chr5B 75031855 75035067 3212 False 5934.0 5934 100.000 1 3213 1 chr5B.!!$F1 3212
1 TraesCS5B01G067000 chr5D 69112529 69115555 3026 False 2314.5 3868 92.546 1 3076 2 chr5D.!!$F1 3075
2 TraesCS5B01G067000 chr5A 59719189 59721584 2395 False 3821.0 3821 95.625 1 2372 1 chr5A.!!$F1 2371

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
701 723 0.541063 TAGACGGGGCACTCTGTCAA 60.541 55.0 11.93 0.0 43.52 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2692 2726 0.179073 CTAGACCCGCCTGTCAATGG 60.179 60.0 3.4 0.0 37.73 3.16 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
213 217 2.171448 AGTGCCCATAGACAAGATGGTC 59.829 50.000 1.25 0.00 42.11 4.02
665 687 2.852449 TGTTGAAATGGCCACGTTAGA 58.148 42.857 8.16 0.00 0.00 2.10
669 691 2.084546 GAAATGGCCACGTTAGAAGCT 58.915 47.619 8.16 0.00 0.00 3.74
678 700 1.276421 ACGTTAGAAGCTGCATGGTCT 59.724 47.619 1.02 1.49 0.00 3.85
701 723 0.541063 TAGACGGGGCACTCTGTCAA 60.541 55.000 11.93 0.00 43.52 3.18
738 760 7.632721 TCCTTATGTCAAGTAAACGACAAAAC 58.367 34.615 0.00 0.00 44.78 2.43
856 882 6.308015 TCTATACCTGCAACAACATTAGGT 57.692 37.500 0.00 0.00 43.69 3.08
1138 1164 6.928492 GCCTCTAGATAAACTGAAAGATGAGG 59.072 42.308 0.00 0.00 39.15 3.86
1194 1220 4.406648 TGAGGTCAGCAACGATGATTAT 57.593 40.909 0.00 0.00 28.52 1.28
1252 1284 2.270352 ATTCACCACGGAACACATGT 57.730 45.000 0.00 0.00 0.00 3.21
1477 1509 0.249657 GCCCTGGAATACGCAGAGAG 60.250 60.000 0.00 0.00 0.00 3.20
1564 1596 7.777440 TGATGTGCTCAATATTACCACCAAATA 59.223 33.333 0.00 0.00 0.00 1.40
1616 1648 9.330063 GTGGTGATCTATTCATCATGTTTTCTA 57.670 33.333 0.00 0.00 46.89 2.10
1688 1720 5.819901 AGTTCAACAGAGGAGTTCAAGAAAG 59.180 40.000 0.00 0.00 0.00 2.62
1870 1902 8.249638 CCATATCAGAGGTACATATGTTCAGAG 58.750 40.741 14.77 0.94 31.18 3.35
1879 1911 6.095440 GGTACATATGTTCAGAGCACCAAATT 59.905 38.462 14.77 0.00 0.00 1.82
1889 1921 7.230849 TCAGAGCACCAAATTGACATAAAAT 57.769 32.000 0.00 0.00 0.00 1.82
2131 2164 2.576406 GCAGATAGCGTCGAGTCATAC 58.424 52.381 0.00 0.00 0.00 2.39
2199 2232 3.491276 CCGTATTTCTACCGTATGCCACA 60.491 47.826 0.00 0.00 0.00 4.17
2238 2271 5.596361 TGGACATTGTTGTTCACCTATTGTT 59.404 36.000 0.00 0.00 36.39 2.83
2312 2345 9.250986 CATTTCGTAAAACAGAAATAAGACTCG 57.749 33.333 3.53 0.00 42.96 4.18
2364 2397 9.342308 TCTATGTTTGAGATATCCAATTTCCAC 57.658 33.333 0.00 0.20 0.00 4.02
2372 2405 3.558608 ATCCAATTTCCACCCCTCAAA 57.441 42.857 0.00 0.00 0.00 2.69
2374 2407 2.448961 TCCAATTTCCACCCCTCAAAGA 59.551 45.455 0.00 0.00 0.00 2.52
2375 2408 3.077391 TCCAATTTCCACCCCTCAAAGAT 59.923 43.478 0.00 0.00 0.00 2.40
2376 2409 3.840078 CCAATTTCCACCCCTCAAAGATT 59.160 43.478 0.00 0.00 0.00 2.40
2377 2410 4.322953 CCAATTTCCACCCCTCAAAGATTG 60.323 45.833 0.00 0.00 0.00 2.67
2379 2412 3.893753 TTCCACCCCTCAAAGATTGAA 57.106 42.857 0.00 0.00 39.58 2.69
2381 2414 4.191804 TCCACCCCTCAAAGATTGAAAA 57.808 40.909 0.00 0.00 39.58 2.29
2382 2415 4.750941 TCCACCCCTCAAAGATTGAAAAT 58.249 39.130 0.00 0.00 39.58 1.82
2383 2416 5.154418 TCCACCCCTCAAAGATTGAAAATT 58.846 37.500 0.00 0.00 39.58 1.82
2384 2417 6.318913 TCCACCCCTCAAAGATTGAAAATTA 58.681 36.000 0.00 0.00 39.58 1.40
2385 2418 6.437162 TCCACCCCTCAAAGATTGAAAATTAG 59.563 38.462 0.00 0.00 39.58 1.73
2386 2419 6.211384 CCACCCCTCAAAGATTGAAAATTAGT 59.789 38.462 0.00 0.00 39.58 2.24
2387 2420 7.092716 CACCCCTCAAAGATTGAAAATTAGTG 58.907 38.462 0.00 0.00 39.58 2.74
2388 2421 6.211384 ACCCCTCAAAGATTGAAAATTAGTGG 59.789 38.462 0.00 0.00 39.58 4.00
2389 2422 6.211384 CCCCTCAAAGATTGAAAATTAGTGGT 59.789 38.462 0.00 0.00 39.58 4.16
2390 2423 7.256296 CCCCTCAAAGATTGAAAATTAGTGGTT 60.256 37.037 0.00 0.00 39.58 3.67
2398 2431 7.931407 AGATTGAAAATTAGTGGTTTTTGTCCC 59.069 33.333 0.00 0.00 0.00 4.46
2399 2432 6.546428 TGAAAATTAGTGGTTTTTGTCCCA 57.454 33.333 0.00 0.00 0.00 4.37
2400 2433 6.947464 TGAAAATTAGTGGTTTTTGTCCCAA 58.053 32.000 0.00 0.00 31.17 4.12
2401 2434 7.394816 TGAAAATTAGTGGTTTTTGTCCCAAA 58.605 30.769 0.00 0.00 31.17 3.28
2402 2435 8.049721 TGAAAATTAGTGGTTTTTGTCCCAAAT 58.950 29.630 0.00 0.00 31.17 2.32
2403 2436 8.815565 AAAATTAGTGGTTTTTGTCCCAAATT 57.184 26.923 0.00 0.00 31.17 1.82
2405 2438 7.800155 ATTAGTGGTTTTTGTCCCAAATTTG 57.200 32.000 11.40 11.40 31.17 2.32
2406 2439 5.172687 AGTGGTTTTTGTCCCAAATTTGT 57.827 34.783 16.73 0.00 31.17 2.83
2407 2440 6.301169 AGTGGTTTTTGTCCCAAATTTGTA 57.699 33.333 16.73 2.09 31.17 2.41
2408 2441 6.712276 AGTGGTTTTTGTCCCAAATTTGTAA 58.288 32.000 16.73 1.76 31.17 2.41
2409 2442 7.168905 AGTGGTTTTTGTCCCAAATTTGTAAA 58.831 30.769 16.73 9.46 31.17 2.01
2410 2443 7.119992 AGTGGTTTTTGTCCCAAATTTGTAAAC 59.880 33.333 16.73 14.14 31.17 2.01
2411 2444 7.119992 GTGGTTTTTGTCCCAAATTTGTAAACT 59.880 33.333 16.73 0.00 31.17 2.66
2412 2445 7.119846 TGGTTTTTGTCCCAAATTTGTAAACTG 59.880 33.333 16.73 0.55 0.00 3.16
2413 2446 7.414651 GGTTTTTGTCCCAAATTTGTAAACTGG 60.415 37.037 16.73 9.57 0.00 4.00
2414 2447 5.941555 TTGTCCCAAATTTGTAAACTGGT 57.058 34.783 16.73 0.00 0.00 4.00
2415 2448 5.269505 TGTCCCAAATTTGTAAACTGGTG 57.730 39.130 16.73 0.00 0.00 4.17
2416 2449 4.712337 TGTCCCAAATTTGTAAACTGGTGT 59.288 37.500 16.73 0.00 0.00 4.16
2417 2450 5.187967 TGTCCCAAATTTGTAAACTGGTGTT 59.812 36.000 16.73 0.00 38.16 3.32
2418 2451 6.110033 GTCCCAAATTTGTAAACTGGTGTTT 58.890 36.000 16.73 0.00 46.74 2.83
2419 2452 6.256975 GTCCCAAATTTGTAAACTGGTGTTTC 59.743 38.462 16.73 0.00 44.35 2.78
2420 2453 6.155393 TCCCAAATTTGTAAACTGGTGTTTCT 59.845 34.615 16.73 0.00 44.35 2.52
2421 2454 6.257630 CCCAAATTTGTAAACTGGTGTTTCTG 59.742 38.462 16.73 0.00 44.35 3.02
2422 2455 6.238076 CCAAATTTGTAAACTGGTGTTTCTGC 60.238 38.462 16.73 0.00 44.35 4.26
2423 2456 5.590530 ATTTGTAAACTGGTGTTTCTGCA 57.409 34.783 0.00 0.00 44.35 4.41
2424 2457 5.392767 TTTGTAAACTGGTGTTTCTGCAA 57.607 34.783 0.00 1.29 44.35 4.08
2425 2458 5.392767 TTGTAAACTGGTGTTTCTGCAAA 57.607 34.783 0.00 0.00 44.35 3.68
2426 2459 4.739195 TGTAAACTGGTGTTTCTGCAAAC 58.261 39.130 0.00 0.00 44.35 2.93
2427 2460 2.959507 AACTGGTGTTTCTGCAAACC 57.040 45.000 0.00 0.00 41.25 3.27
2428 2461 2.143876 ACTGGTGTTTCTGCAAACCT 57.856 45.000 0.00 0.00 41.25 3.50
2429 2462 3.290948 ACTGGTGTTTCTGCAAACCTA 57.709 42.857 0.00 0.00 41.25 3.08
2430 2463 3.214328 ACTGGTGTTTCTGCAAACCTAG 58.786 45.455 0.00 1.59 41.25 3.02
2431 2464 2.554032 CTGGTGTTTCTGCAAACCTAGG 59.446 50.000 7.41 7.41 41.25 3.02
2432 2465 1.269723 GGTGTTTCTGCAAACCTAGGC 59.730 52.381 9.30 0.00 41.25 3.93
2433 2466 2.230660 GTGTTTCTGCAAACCTAGGCT 58.769 47.619 9.30 0.00 41.25 4.58
2434 2467 2.623416 GTGTTTCTGCAAACCTAGGCTT 59.377 45.455 9.30 0.00 41.25 4.35
2435 2468 2.884639 TGTTTCTGCAAACCTAGGCTTC 59.115 45.455 9.30 0.00 41.25 3.86
2436 2469 2.884639 GTTTCTGCAAACCTAGGCTTCA 59.115 45.455 9.30 3.05 36.62 3.02
2437 2470 2.949177 TCTGCAAACCTAGGCTTCAA 57.051 45.000 9.30 0.00 0.00 2.69
2438 2471 3.439857 TCTGCAAACCTAGGCTTCAAT 57.560 42.857 9.30 0.00 0.00 2.57
2439 2472 3.084039 TCTGCAAACCTAGGCTTCAATG 58.916 45.455 9.30 0.23 0.00 2.82
2440 2473 2.821969 CTGCAAACCTAGGCTTCAATGT 59.178 45.455 9.30 0.00 0.00 2.71
2441 2474 2.557924 TGCAAACCTAGGCTTCAATGTG 59.442 45.455 9.30 0.00 0.00 3.21
2442 2475 2.094545 GCAAACCTAGGCTTCAATGTGG 60.095 50.000 9.30 0.00 0.00 4.17
2443 2476 3.157087 CAAACCTAGGCTTCAATGTGGT 58.843 45.455 9.30 0.00 0.00 4.16
2444 2477 2.496899 ACCTAGGCTTCAATGTGGTG 57.503 50.000 9.30 0.00 0.00 4.17
2445 2478 1.004745 ACCTAGGCTTCAATGTGGTGG 59.995 52.381 9.30 0.00 0.00 4.61
2446 2479 1.004745 CCTAGGCTTCAATGTGGTGGT 59.995 52.381 0.00 0.00 0.00 4.16
2447 2480 2.555227 CCTAGGCTTCAATGTGGTGGTT 60.555 50.000 0.00 0.00 0.00 3.67
2448 2481 2.086610 AGGCTTCAATGTGGTGGTTT 57.913 45.000 0.00 0.00 0.00 3.27
2449 2482 2.397597 AGGCTTCAATGTGGTGGTTTT 58.602 42.857 0.00 0.00 0.00 2.43
2450 2483 2.365293 AGGCTTCAATGTGGTGGTTTTC 59.635 45.455 0.00 0.00 0.00 2.29
2451 2484 2.365293 GGCTTCAATGTGGTGGTTTTCT 59.635 45.455 0.00 0.00 0.00 2.52
2452 2485 3.181466 GGCTTCAATGTGGTGGTTTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
2453 2486 4.051237 GCTTCAATGTGGTGGTTTTCTTC 58.949 43.478 0.00 0.00 0.00 2.87
2454 2487 4.441356 GCTTCAATGTGGTGGTTTTCTTCA 60.441 41.667 0.00 0.00 0.00 3.02
2455 2488 5.659463 CTTCAATGTGGTGGTTTTCTTCAA 58.341 37.500 0.00 0.00 0.00 2.69
2456 2489 5.867903 TCAATGTGGTGGTTTTCTTCAAT 57.132 34.783 0.00 0.00 0.00 2.57
2457 2490 6.232581 TCAATGTGGTGGTTTTCTTCAATT 57.767 33.333 0.00 0.00 0.00 2.32
2458 2491 6.279882 TCAATGTGGTGGTTTTCTTCAATTC 58.720 36.000 0.00 0.00 0.00 2.17
2459 2492 5.867903 ATGTGGTGGTTTTCTTCAATTCA 57.132 34.783 0.00 0.00 0.00 2.57
2460 2493 5.004922 TGTGGTGGTTTTCTTCAATTCAC 57.995 39.130 0.00 0.00 0.00 3.18
2461 2494 4.709397 TGTGGTGGTTTTCTTCAATTCACT 59.291 37.500 0.00 0.00 0.00 3.41
2462 2495 5.163561 TGTGGTGGTTTTCTTCAATTCACTC 60.164 40.000 0.00 0.00 0.00 3.51
2463 2496 4.952957 TGGTGGTTTTCTTCAATTCACTCA 59.047 37.500 0.00 0.00 0.00 3.41
2469 2502 8.310382 TGGTTTTCTTCAATTCACTCAAGAAAA 58.690 29.630 12.27 12.27 45.75 2.29
2492 2525 5.747342 ACCAGTTACTACACAACCTCAAAA 58.253 37.500 0.00 0.00 0.00 2.44
2493 2526 6.181908 ACCAGTTACTACACAACCTCAAAAA 58.818 36.000 0.00 0.00 0.00 1.94
2501 2534 8.062065 ACTACACAACCTCAAAAATCTCAAAA 57.938 30.769 0.00 0.00 0.00 2.44
2502 2535 8.527810 ACTACACAACCTCAAAAATCTCAAAAA 58.472 29.630 0.00 0.00 0.00 1.94
2503 2536 7.595311 ACACAACCTCAAAAATCTCAAAAAC 57.405 32.000 0.00 0.00 0.00 2.43
2523 2556 1.452470 TTTAATTCCCGCCTCGCCC 60.452 57.895 0.00 0.00 0.00 6.13
2540 2573 2.930682 CGCCCTAGTAGAAACTGCTTTC 59.069 50.000 0.00 0.00 36.36 2.62
2580 2613 2.230508 TGACTGAGTTACCACGTCATCC 59.769 50.000 0.00 0.00 30.41 3.51
2615 2649 3.790177 CCGCAGCGGGTAACTAAC 58.210 61.111 27.32 0.00 44.15 2.34
2616 2650 1.079681 CCGCAGCGGGTAACTAACA 60.080 57.895 27.32 0.00 44.15 2.41
2617 2651 0.461339 CCGCAGCGGGTAACTAACAT 60.461 55.000 27.32 0.00 44.15 2.71
2626 2660 3.272581 GGGTAACTAACATGCGCCTTTA 58.727 45.455 4.18 0.00 0.00 1.85
2646 2680 3.303351 AAAATCTATCCACCCAGGCTG 57.697 47.619 7.75 7.75 37.29 4.85
2662 2696 1.408702 GGCTGTCACAAACAACACCAT 59.591 47.619 0.00 0.00 37.45 3.55
2664 2698 2.098934 GCTGTCACAAACAACACCATCA 59.901 45.455 0.00 0.00 37.45 3.07
2686 2720 2.360350 CAGTGGTGCCGCTTCCAT 60.360 61.111 0.90 0.14 36.09 3.41
2692 2726 2.896854 TGCCGCTTCCATGATCGC 60.897 61.111 0.00 0.00 0.00 4.58
2695 2729 1.598962 CCGCTTCCATGATCGCCAT 60.599 57.895 0.00 0.00 35.44 4.40
2701 2735 1.957668 TCCATGATCGCCATTGACAG 58.042 50.000 0.00 0.00 31.94 3.51
2745 2780 3.276091 CACACACGCCGCTCCAAA 61.276 61.111 0.00 0.00 0.00 3.28
2760 2795 0.173255 CCAAATCACCCGCATTGTCC 59.827 55.000 0.00 0.00 0.00 4.02
2773 2808 4.966787 TGTCCCGCCTTTGGTGCC 62.967 66.667 0.00 0.00 0.00 5.01
2775 2810 3.897122 TCCCGCCTTTGGTGCCTT 61.897 61.111 0.00 0.00 0.00 4.35
2781 2816 1.611491 CGCCTTTGGTGCCTTTTCTTA 59.389 47.619 0.00 0.00 0.00 2.10
2790 2825 3.325870 GTGCCTTTTCTTATTGCCCAAC 58.674 45.455 0.00 0.00 0.00 3.77
2801 2836 2.113986 GCCCAACACTGGTGCTCT 59.886 61.111 0.17 0.00 41.72 4.09
2803 2838 0.955919 GCCCAACACTGGTGCTCTAC 60.956 60.000 0.17 0.00 41.72 2.59
2817 2852 1.555075 GCTCTACCAACCTCCATGTCA 59.445 52.381 0.00 0.00 0.00 3.58
2830 2865 3.023119 TCCATGTCAATATTGTGTGCCC 58.977 45.455 14.97 0.00 0.00 5.36
2860 2895 1.186267 CCTACGCCCCTCCTACCATC 61.186 65.000 0.00 0.00 0.00 3.51
2863 2898 3.942439 GCCCCTCCTACCATCGGC 61.942 72.222 0.00 0.00 0.00 5.54
2864 2899 3.616721 CCCCTCCTACCATCGGCG 61.617 72.222 0.00 0.00 0.00 6.46
2874 2909 0.385751 ACCATCGGCGTCTCTACATG 59.614 55.000 6.85 0.66 0.00 3.21
2881 2916 2.555199 GGCGTCTCTACATGCTTGATT 58.445 47.619 6.60 0.00 0.00 2.57
2897 2932 5.055812 GCTTGATTTTTGTTGATGTTCCCA 58.944 37.500 0.00 0.00 0.00 4.37
2904 2939 4.582701 TTGTTGATGTTCCCATGTTGTC 57.417 40.909 0.00 0.00 0.00 3.18
2920 2955 6.017605 CCATGTTGTCTGCCACTTCTAATATC 60.018 42.308 0.00 0.00 0.00 1.63
2931 2966 5.336055 CCACTTCTAATATCCCACTCTAGCG 60.336 48.000 0.00 0.00 0.00 4.26
2958 2993 0.179000 GACACTGATCCCGCCTCATT 59.821 55.000 0.00 0.00 0.00 2.57
2974 3009 1.854939 TCATTTCATCCCTCAGCCCAT 59.145 47.619 0.00 0.00 0.00 4.00
3005 3040 2.364842 GGCTGCTCCTCCCTCTCA 60.365 66.667 0.00 0.00 0.00 3.27
3011 3046 1.700368 CTCCTCCCTCTCACCCTGA 59.300 63.158 0.00 0.00 0.00 3.86
3014 3049 0.031716 CCTCCCTCTCACCCTGATGA 60.032 60.000 0.00 0.00 0.00 2.92
3037 3072 2.741145 CTACCTGCCTACCACTTCTCT 58.259 52.381 0.00 0.00 0.00 3.10
3047 3082 0.445436 CCACTTCTCTCGCATTGTGC 59.555 55.000 0.00 0.00 40.69 4.57
3048 3083 1.150827 CACTTCTCTCGCATTGTGCA 58.849 50.000 2.63 0.00 45.36 4.57
3053 3088 0.450583 CTCTCGCATTGTGCATTGCT 59.549 50.000 10.49 0.00 45.36 3.91
3056 3091 0.096802 TCGCATTGTGCATTGCTACG 59.903 50.000 10.49 4.95 45.36 3.51
3066 3101 1.473257 GCATTGCTACGACTCCATGGA 60.473 52.381 15.27 15.27 0.00 3.41
3067 3102 2.205074 CATTGCTACGACTCCATGGAC 58.795 52.381 11.44 0.50 0.00 4.02
3071 3106 1.092348 CTACGACTCCATGGACGTCA 58.908 55.000 27.83 16.00 39.59 4.35
3072 3107 1.676529 CTACGACTCCATGGACGTCAT 59.323 52.381 27.83 20.64 39.59 3.06
3078 3113 2.705220 CATGGACGTCATGCTGCG 59.295 61.111 18.91 0.00 45.58 5.18
3079 3114 2.102438 CATGGACGTCATGCTGCGT 61.102 57.895 18.91 8.98 45.58 5.24
3080 3115 1.375908 ATGGACGTCATGCTGCGTT 60.376 52.632 18.91 0.00 41.70 4.84
3081 3116 1.638388 ATGGACGTCATGCTGCGTTG 61.638 55.000 18.91 0.00 41.70 4.10
3082 3117 2.317609 GGACGTCATGCTGCGTTGT 61.318 57.895 18.91 0.00 41.70 3.32
3083 3118 1.154599 GACGTCATGCTGCGTTGTG 60.155 57.895 11.55 0.00 41.70 3.33
3084 3119 2.500369 CGTCATGCTGCGTTGTGC 60.500 61.111 0.00 0.00 46.70 4.57
3085 3120 2.126734 GTCATGCTGCGTTGTGCC 60.127 61.111 0.00 0.00 45.60 5.01
3086 3121 3.725459 TCATGCTGCGTTGTGCCG 61.725 61.111 0.00 0.00 45.60 5.69
3094 3129 3.725459 CGTTGTGCCGCTGATGCA 61.725 61.111 0.00 0.00 39.64 3.96
3099 3134 3.057548 TGCCGCTGATGCACCTTG 61.058 61.111 0.00 0.00 39.64 3.61
3100 3135 3.818787 GCCGCTGATGCACCTTGG 61.819 66.667 0.00 0.00 39.64 3.61
3101 3136 3.818787 CCGCTGATGCACCTTGGC 61.819 66.667 0.00 0.00 39.64 4.52
3102 3137 2.749044 CGCTGATGCACCTTGGCT 60.749 61.111 0.00 0.00 39.64 4.75
3103 3138 2.882876 GCTGATGCACCTTGGCTG 59.117 61.111 0.00 0.00 39.41 4.85
3104 3139 2.882876 CTGATGCACCTTGGCTGC 59.117 61.111 0.00 0.00 35.03 5.25
3105 3140 1.677966 CTGATGCACCTTGGCTGCT 60.678 57.895 0.00 2.78 35.53 4.24
3106 3141 1.654954 CTGATGCACCTTGGCTGCTC 61.655 60.000 0.00 9.37 35.53 4.26
3107 3142 2.362120 ATGCACCTTGGCTGCTCC 60.362 61.111 0.00 0.00 35.53 4.70
3121 3156 2.743928 CTCCGCACCCTGCACTTC 60.744 66.667 0.00 0.00 45.36 3.01
3122 3157 3.535629 CTCCGCACCCTGCACTTCA 62.536 63.158 0.00 0.00 45.36 3.02
3123 3158 3.357079 CCGCACCCTGCACTTCAC 61.357 66.667 0.00 0.00 45.36 3.18
3124 3159 3.716006 CGCACCCTGCACTTCACG 61.716 66.667 0.00 0.00 45.36 4.35
3125 3160 4.030452 GCACCCTGCACTTCACGC 62.030 66.667 0.00 0.00 44.26 5.34
3126 3161 3.357079 CACCCTGCACTTCACGCC 61.357 66.667 0.00 0.00 0.00 5.68
3127 3162 4.643387 ACCCTGCACTTCACGCCC 62.643 66.667 0.00 0.00 0.00 6.13
3129 3164 4.988598 CCTGCACTTCACGCCCGT 62.989 66.667 0.00 0.00 0.00 5.28
3130 3165 3.716006 CTGCACTTCACGCCCGTG 61.716 66.667 14.17 14.17 46.64 4.94
3140 3175 4.680237 CGCCCGTGAGAGCCACAA 62.680 66.667 0.00 0.00 45.98 3.33
3141 3176 2.045926 GCCCGTGAGAGCCACAAT 60.046 61.111 0.00 0.00 45.98 2.71
3142 3177 2.109126 GCCCGTGAGAGCCACAATC 61.109 63.158 0.00 0.00 45.98 2.67
3143 3178 1.296392 CCCGTGAGAGCCACAATCA 59.704 57.895 0.00 0.00 45.98 2.57
3144 3179 1.021390 CCCGTGAGAGCCACAATCAC 61.021 60.000 0.00 0.00 45.98 3.06
3145 3180 1.021390 CCGTGAGAGCCACAATCACC 61.021 60.000 0.00 0.00 45.98 4.02
3146 3181 0.320683 CGTGAGAGCCACAATCACCA 60.321 55.000 0.00 0.00 45.98 4.17
3147 3182 1.160137 GTGAGAGCCACAATCACCAC 58.840 55.000 0.00 0.00 45.03 4.16
3148 3183 1.059098 TGAGAGCCACAATCACCACT 58.941 50.000 0.00 0.00 0.00 4.00
3149 3184 1.002430 TGAGAGCCACAATCACCACTC 59.998 52.381 0.00 0.00 0.00 3.51
3150 3185 0.326264 AGAGCCACAATCACCACTCC 59.674 55.000 0.00 0.00 0.00 3.85
3151 3186 0.326264 GAGCCACAATCACCACTCCT 59.674 55.000 0.00 0.00 0.00 3.69
3152 3187 1.555075 GAGCCACAATCACCACTCCTA 59.445 52.381 0.00 0.00 0.00 2.94
3153 3188 1.279271 AGCCACAATCACCACTCCTAC 59.721 52.381 0.00 0.00 0.00 3.18
3154 3189 2.007049 GCCACAATCACCACTCCTACG 61.007 57.143 0.00 0.00 0.00 3.51
3155 3190 1.548719 CCACAATCACCACTCCTACGA 59.451 52.381 0.00 0.00 0.00 3.43
3156 3191 2.417379 CCACAATCACCACTCCTACGAG 60.417 54.545 0.00 0.00 42.32 4.18
3157 3192 2.492088 CACAATCACCACTCCTACGAGA 59.508 50.000 0.00 0.00 38.52 4.04
3158 3193 2.755655 ACAATCACCACTCCTACGAGAG 59.244 50.000 0.00 0.00 38.52 3.20
3163 3198 3.906718 ACTCCTACGAGAGTGCCG 58.093 61.111 6.70 0.00 45.41 5.69
3164 3199 1.298993 ACTCCTACGAGAGTGCCGA 59.701 57.895 6.70 0.00 45.41 5.54
3165 3200 1.025647 ACTCCTACGAGAGTGCCGAC 61.026 60.000 6.70 0.00 45.41 4.79
3166 3201 3.391778 ACTCCTACGAGAGTGCCGACT 62.392 57.143 6.70 0.00 45.41 4.18
3167 3202 4.057168 ACTCCTACGAGAGTGCCGACTA 62.057 54.545 6.70 0.00 45.41 2.59
3168 3203 5.318604 ACTCCTACGAGAGTGCCGACTAT 62.319 52.174 6.70 0.00 45.41 2.12
3169 3204 6.012977 ACTCCTACGAGAGTGCCGACTATA 62.013 50.000 6.70 0.00 45.41 1.31
3170 3205 7.256415 ACTCCTACGAGAGTGCCGACTATAT 62.256 48.000 6.70 0.00 45.41 0.86
3171 3206 8.643385 ACTCCTACGAGAGTGCCGACTATATT 62.643 46.154 6.70 0.00 45.41 1.28
3172 3207 3.900388 ACGAGAGTGCCGACTATATTC 57.100 47.619 0.00 0.00 46.97 1.75
3173 3208 3.478509 ACGAGAGTGCCGACTATATTCT 58.521 45.455 0.00 0.00 46.97 2.40
3174 3209 3.499157 ACGAGAGTGCCGACTATATTCTC 59.501 47.826 0.00 0.00 46.97 2.87
3175 3210 3.498777 CGAGAGTGCCGACTATATTCTCA 59.501 47.826 0.00 0.00 30.16 3.27
3176 3211 4.155099 CGAGAGTGCCGACTATATTCTCAT 59.845 45.833 0.00 0.00 30.16 2.90
3177 3212 5.384063 AGAGTGCCGACTATATTCTCATG 57.616 43.478 0.00 0.00 30.16 3.07
3178 3213 4.219507 AGAGTGCCGACTATATTCTCATGG 59.780 45.833 0.00 0.00 30.16 3.66
3179 3214 4.152647 AGTGCCGACTATATTCTCATGGA 58.847 43.478 0.00 0.00 0.00 3.41
3180 3215 4.021894 AGTGCCGACTATATTCTCATGGAC 60.022 45.833 0.00 0.00 0.00 4.02
3181 3216 3.895041 TGCCGACTATATTCTCATGGACA 59.105 43.478 0.00 0.00 0.00 4.02
3182 3217 4.238514 GCCGACTATATTCTCATGGACAC 58.761 47.826 0.00 0.00 0.00 3.67
3183 3218 4.810790 CCGACTATATTCTCATGGACACC 58.189 47.826 0.00 0.00 0.00 4.16
3184 3219 4.322049 CCGACTATATTCTCATGGACACCC 60.322 50.000 0.00 0.00 0.00 4.61
3185 3220 4.322049 CGACTATATTCTCATGGACACCCC 60.322 50.000 0.00 0.00 0.00 4.95
3186 3221 3.910627 ACTATATTCTCATGGACACCCCC 59.089 47.826 0.00 0.00 0.00 5.40
3187 3222 2.278657 TATTCTCATGGACACCCCCA 57.721 50.000 0.00 0.00 41.05 4.96
3188 3223 0.625849 ATTCTCATGGACACCCCCAC 59.374 55.000 0.00 0.00 39.34 4.61
3189 3224 0.770166 TTCTCATGGACACCCCCACA 60.770 55.000 0.00 0.00 39.34 4.17
3190 3225 0.770166 TCTCATGGACACCCCCACAA 60.770 55.000 0.00 0.00 39.34 3.33
3191 3226 0.112218 CTCATGGACACCCCCACAAA 59.888 55.000 0.00 0.00 39.34 2.83
3192 3227 0.558220 TCATGGACACCCCCACAAAA 59.442 50.000 0.00 0.00 39.34 2.44
3193 3228 1.062886 TCATGGACACCCCCACAAAAA 60.063 47.619 0.00 0.00 39.34 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 217 4.621068 TTCATTGCTTGCCTCTTTATCG 57.379 40.909 0.00 0.00 0.00 2.92
651 673 1.453155 CAGCTTCTAACGTGGCCATT 58.547 50.000 9.72 1.83 0.00 3.16
665 687 3.077359 GTCTAACAAGACCATGCAGCTT 58.923 45.455 0.00 0.00 32.97 3.74
669 691 1.338674 CCCGTCTAACAAGACCATGCA 60.339 52.381 0.00 0.00 35.52 3.96
678 700 0.320374 CAGAGTGCCCCGTCTAACAA 59.680 55.000 0.00 0.00 0.00 2.83
738 760 7.769272 ATTTTTACCCATAATTTGTGCATCG 57.231 32.000 0.00 0.00 0.00 3.84
783 809 3.055094 CCCTACCTGTGTAGTGCTGAAAT 60.055 47.826 0.00 0.00 42.49 2.17
784 810 2.301870 CCCTACCTGTGTAGTGCTGAAA 59.698 50.000 0.00 0.00 42.49 2.69
785 811 1.899814 CCCTACCTGTGTAGTGCTGAA 59.100 52.381 0.00 0.00 42.49 3.02
856 882 8.160765 TCCTAAGAAAATGTTGTTATGACCAGA 58.839 33.333 0.00 0.00 0.00 3.86
917 943 8.989653 AGAAAGAGTGAGCTTGTAATACTTAC 57.010 34.615 0.00 0.00 36.67 2.34
970 996 6.321181 TCTTTCTGCACAATTCAAACTTAGGT 59.679 34.615 0.00 0.00 0.00 3.08
1138 1164 3.406764 ACTCTTTGTCTGACCAGCAATC 58.593 45.455 5.17 0.00 0.00 2.67
1194 1220 7.283127 GGAGACTTGGTGCATGAATATCTTAAA 59.717 37.037 0.00 0.00 0.00 1.52
1371 1403 0.745468 CTAGTACCTCTCAACGGCCC 59.255 60.000 0.00 0.00 0.00 5.80
1564 1596 6.435292 AACCTTTTATGATATAGCGGAGGT 57.565 37.500 0.00 0.00 44.89 3.85
1616 1648 8.884124 TGGGATAAATGAGAAGAGAAATGTTT 57.116 30.769 0.00 0.00 0.00 2.83
1889 1921 5.951148 TGCTCTTCATCAAATCCACCAAATA 59.049 36.000 0.00 0.00 0.00 1.40
2131 2164 5.333645 CGCATTAAGGATTCCTGATTTCTCG 60.334 44.000 5.84 1.35 32.13 4.04
2238 2271 3.799574 GCAAATGCAGAAACCATGACACA 60.800 43.478 0.00 0.00 41.59 3.72
2286 2319 9.250986 CGAGTCTTATTTCTGTTTTACGAAATG 57.749 33.333 14.16 5.12 39.45 2.32
2312 2345 6.598753 AACATATACACATGGTTAACTCGC 57.401 37.500 5.42 0.00 0.00 5.03
2364 2397 6.211384 ACCACTAATTTTCAATCTTTGAGGGG 59.789 38.462 0.00 0.00 41.38 4.79
2372 2405 7.931407 GGGACAAAAACCACTAATTTTCAATCT 59.069 33.333 0.00 0.00 0.00 2.40
2374 2407 7.569240 TGGGACAAAAACCACTAATTTTCAAT 58.431 30.769 0.00 0.00 31.92 2.57
2375 2408 6.947464 TGGGACAAAAACCACTAATTTTCAA 58.053 32.000 0.00 0.00 31.92 2.69
2376 2409 6.546428 TGGGACAAAAACCACTAATTTTCA 57.454 33.333 0.00 0.00 31.92 2.69
2393 2426 4.712337 ACACCAGTTTACAAATTTGGGACA 59.288 37.500 21.74 0.49 32.82 4.02
2394 2427 5.270893 ACACCAGTTTACAAATTTGGGAC 57.729 39.130 21.74 15.57 32.82 4.46
2395 2428 5.941555 AACACCAGTTTACAAATTTGGGA 57.058 34.783 21.74 7.02 33.11 4.37
2408 2441 2.456577 AGGTTTGCAGAAACACCAGTT 58.543 42.857 3.80 0.00 42.95 3.16
2409 2442 2.143876 AGGTTTGCAGAAACACCAGT 57.856 45.000 3.80 0.00 42.95 4.00
2410 2443 2.554032 CCTAGGTTTGCAGAAACACCAG 59.446 50.000 0.00 0.00 42.95 4.00
2411 2444 2.582052 CCTAGGTTTGCAGAAACACCA 58.418 47.619 0.00 0.00 42.95 4.17
2412 2445 1.269723 GCCTAGGTTTGCAGAAACACC 59.730 52.381 11.31 0.00 42.95 4.16
2413 2446 2.230660 AGCCTAGGTTTGCAGAAACAC 58.769 47.619 11.31 0.00 42.95 3.32
2414 2447 2.656947 AGCCTAGGTTTGCAGAAACA 57.343 45.000 11.31 0.00 42.95 2.83
2415 2448 2.884639 TGAAGCCTAGGTTTGCAGAAAC 59.115 45.455 16.48 0.00 40.79 2.78
2416 2449 3.222173 TGAAGCCTAGGTTTGCAGAAA 57.778 42.857 16.48 0.00 0.00 2.52
2417 2450 2.949177 TGAAGCCTAGGTTTGCAGAA 57.051 45.000 16.48 0.00 0.00 3.02
2418 2451 2.949177 TTGAAGCCTAGGTTTGCAGA 57.051 45.000 16.48 0.00 0.00 4.26
2419 2452 2.821969 ACATTGAAGCCTAGGTTTGCAG 59.178 45.455 16.48 5.50 0.00 4.41
2420 2453 2.557924 CACATTGAAGCCTAGGTTTGCA 59.442 45.455 16.48 10.46 0.00 4.08
2421 2454 2.094545 CCACATTGAAGCCTAGGTTTGC 60.095 50.000 16.48 8.04 0.00 3.68
2422 2455 3.057315 CACCACATTGAAGCCTAGGTTTG 60.057 47.826 16.48 4.50 0.00 2.93
2423 2456 3.157087 CACCACATTGAAGCCTAGGTTT 58.843 45.455 11.11 11.11 0.00 3.27
2424 2457 2.555227 CCACCACATTGAAGCCTAGGTT 60.555 50.000 11.31 0.00 0.00 3.50
2425 2458 1.004745 CCACCACATTGAAGCCTAGGT 59.995 52.381 11.31 0.00 0.00 3.08
2426 2459 1.004745 ACCACCACATTGAAGCCTAGG 59.995 52.381 3.67 3.67 0.00 3.02
2427 2460 2.496899 ACCACCACATTGAAGCCTAG 57.503 50.000 0.00 0.00 0.00 3.02
2428 2461 2.969821 AACCACCACATTGAAGCCTA 57.030 45.000 0.00 0.00 0.00 3.93
2429 2462 2.086610 AAACCACCACATTGAAGCCT 57.913 45.000 0.00 0.00 0.00 4.58
2430 2463 2.365293 AGAAAACCACCACATTGAAGCC 59.635 45.455 0.00 0.00 0.00 4.35
2431 2464 3.733443 AGAAAACCACCACATTGAAGC 57.267 42.857 0.00 0.00 0.00 3.86
2432 2465 5.261209 TGAAGAAAACCACCACATTGAAG 57.739 39.130 0.00 0.00 0.00 3.02
2433 2466 5.667539 TTGAAGAAAACCACCACATTGAA 57.332 34.783 0.00 0.00 0.00 2.69
2434 2467 5.867903 ATTGAAGAAAACCACCACATTGA 57.132 34.783 0.00 0.00 0.00 2.57
2435 2468 6.018832 GTGAATTGAAGAAAACCACCACATTG 60.019 38.462 0.00 0.00 0.00 2.82
2436 2469 6.048509 GTGAATTGAAGAAAACCACCACATT 58.951 36.000 0.00 0.00 0.00 2.71
2437 2470 5.363580 AGTGAATTGAAGAAAACCACCACAT 59.636 36.000 0.00 0.00 0.00 3.21
2438 2471 4.709397 AGTGAATTGAAGAAAACCACCACA 59.291 37.500 0.00 0.00 0.00 4.17
2439 2472 5.163561 TGAGTGAATTGAAGAAAACCACCAC 60.164 40.000 0.00 0.00 0.00 4.16
2440 2473 4.952957 TGAGTGAATTGAAGAAAACCACCA 59.047 37.500 0.00 0.00 0.00 4.17
2441 2474 5.514274 TGAGTGAATTGAAGAAAACCACC 57.486 39.130 0.00 0.00 0.00 4.61
2442 2475 6.795399 TCTTGAGTGAATTGAAGAAAACCAC 58.205 36.000 0.00 0.00 0.00 4.16
2443 2476 7.403312 TTCTTGAGTGAATTGAAGAAAACCA 57.597 32.000 0.00 0.00 32.75 3.67
2444 2477 8.702163 TTTTCTTGAGTGAATTGAAGAAAACC 57.298 30.769 12.27 0.00 43.99 3.27
2446 2479 8.310382 TGGTTTTCTTGAGTGAATTGAAGAAAA 58.690 29.630 12.27 12.27 45.43 2.29
2447 2480 7.835822 TGGTTTTCTTGAGTGAATTGAAGAAA 58.164 30.769 0.00 0.00 40.78 2.52
2448 2481 7.122650 ACTGGTTTTCTTGAGTGAATTGAAGAA 59.877 33.333 0.00 0.00 33.62 2.52
2449 2482 6.603201 ACTGGTTTTCTTGAGTGAATTGAAGA 59.397 34.615 0.00 0.00 0.00 2.87
2450 2483 6.799512 ACTGGTTTTCTTGAGTGAATTGAAG 58.200 36.000 0.00 0.00 0.00 3.02
2451 2484 6.773976 ACTGGTTTTCTTGAGTGAATTGAA 57.226 33.333 0.00 0.00 0.00 2.69
2452 2485 6.773976 AACTGGTTTTCTTGAGTGAATTGA 57.226 33.333 0.00 0.00 0.00 2.57
2453 2486 7.707104 AGTAACTGGTTTTCTTGAGTGAATTG 58.293 34.615 0.00 0.00 0.00 2.32
2454 2487 7.881775 AGTAACTGGTTTTCTTGAGTGAATT 57.118 32.000 0.00 0.00 0.00 2.17
2455 2488 7.990886 TGTAGTAACTGGTTTTCTTGAGTGAAT 59.009 33.333 0.00 0.00 0.00 2.57
2456 2489 7.279313 GTGTAGTAACTGGTTTTCTTGAGTGAA 59.721 37.037 0.00 0.00 0.00 3.18
2457 2490 6.759827 GTGTAGTAACTGGTTTTCTTGAGTGA 59.240 38.462 0.00 0.00 0.00 3.41
2458 2491 6.537301 TGTGTAGTAACTGGTTTTCTTGAGTG 59.463 38.462 0.00 0.00 0.00 3.51
2459 2492 6.646267 TGTGTAGTAACTGGTTTTCTTGAGT 58.354 36.000 0.00 0.00 0.00 3.41
2460 2493 7.407337 GTTGTGTAGTAACTGGTTTTCTTGAG 58.593 38.462 0.00 0.00 0.00 3.02
2461 2494 6.316890 GGTTGTGTAGTAACTGGTTTTCTTGA 59.683 38.462 0.00 0.00 0.00 3.02
2462 2495 6.317893 AGGTTGTGTAGTAACTGGTTTTCTTG 59.682 38.462 0.00 0.00 0.00 3.02
2463 2496 6.420638 AGGTTGTGTAGTAACTGGTTTTCTT 58.579 36.000 0.00 0.00 0.00 2.52
2469 2502 5.362105 TTTGAGGTTGTGTAGTAACTGGT 57.638 39.130 0.00 0.00 0.00 4.00
2492 2525 5.631929 GCGGGAATTAAACGTTTTTGAGATT 59.368 36.000 20.19 11.40 0.00 2.40
2493 2526 5.158494 GCGGGAATTAAACGTTTTTGAGAT 58.842 37.500 20.19 3.61 0.00 2.75
2501 2534 1.081094 CGAGGCGGGAATTAAACGTT 58.919 50.000 0.00 0.00 0.00 3.99
2502 2535 1.363885 GCGAGGCGGGAATTAAACGT 61.364 55.000 0.00 0.00 0.00 3.99
2503 2536 1.350665 GCGAGGCGGGAATTAAACG 59.649 57.895 0.00 0.00 0.00 3.60
2540 2573 6.929049 TCAGTCAAAACCTCTAATATATGCGG 59.071 38.462 0.00 0.00 0.00 5.69
2547 2580 8.092687 GTGGTAACTCAGTCAAAACCTCTAATA 58.907 37.037 0.00 0.00 37.61 0.98
2548 2581 6.935208 GTGGTAACTCAGTCAAAACCTCTAAT 59.065 38.462 0.00 0.00 37.61 1.73
2599 2632 0.650512 CATGTTAGTTACCCGCTGCG 59.349 55.000 16.34 16.34 0.00 5.18
2601 2634 0.650512 CGCATGTTAGTTACCCGCTG 59.349 55.000 0.00 0.00 0.00 5.18
2602 2635 1.087771 GCGCATGTTAGTTACCCGCT 61.088 55.000 0.30 0.00 35.91 5.52
2603 2636 1.350665 GCGCATGTTAGTTACCCGC 59.649 57.895 0.30 0.00 33.10 6.13
2604 2637 0.461339 AGGCGCATGTTAGTTACCCG 60.461 55.000 10.83 0.00 0.00 5.28
2615 2649 5.215160 GTGGATAGATTTTAAAGGCGCATG 58.785 41.667 10.83 0.00 0.00 4.06
2616 2650 4.278419 GGTGGATAGATTTTAAAGGCGCAT 59.722 41.667 10.83 0.00 0.00 4.73
2617 2651 3.630312 GGTGGATAGATTTTAAAGGCGCA 59.370 43.478 10.83 0.00 0.00 6.09
2626 2660 2.582636 ACAGCCTGGGTGGATAGATTTT 59.417 45.455 27.75 2.54 38.35 1.82
2646 2680 4.032786 GCTTTTGATGGTGTTGTTTGTGAC 59.967 41.667 0.00 0.00 0.00 3.67
2662 2696 3.431055 CGGCACCACTGCTTTTGA 58.569 55.556 0.00 0.00 43.66 2.69
2677 2711 1.168407 AATGGCGATCATGGAAGCGG 61.168 55.000 0.00 0.00 35.99 5.52
2680 2714 2.289820 CTGTCAATGGCGATCATGGAAG 59.710 50.000 0.00 0.00 37.54 3.46
2685 2719 2.711711 GCCTGTCAATGGCGATCAT 58.288 52.632 0.00 0.00 41.03 2.45
2686 2720 4.223800 GCCTGTCAATGGCGATCA 57.776 55.556 0.00 0.00 41.03 2.92
2692 2726 0.179073 CTAGACCCGCCTGTCAATGG 60.179 60.000 3.40 0.00 37.73 3.16
2695 2729 1.255667 GGTCTAGACCCGCCTGTCAA 61.256 60.000 28.87 0.00 45.68 3.18
2745 2780 2.124736 CGGGACAATGCGGGTGAT 60.125 61.111 0.00 0.00 0.00 3.06
2760 2795 1.006220 GAAAAGGCACCAAAGGCGG 60.006 57.895 0.00 0.00 39.37 6.13
2773 2808 4.559153 CCAGTGTTGGGCAATAAGAAAAG 58.441 43.478 0.00 0.00 41.05 2.27
2801 2836 5.885352 CACAATATTGACATGGAGGTTGGTA 59.115 40.000 22.16 0.00 0.00 3.25
2803 2838 4.706476 ACACAATATTGACATGGAGGTTGG 59.294 41.667 22.16 0.00 0.00 3.77
2804 2839 5.643664 CACACAATATTGACATGGAGGTTG 58.356 41.667 22.16 7.96 0.00 3.77
2810 2845 2.101249 GGGGCACACAATATTGACATGG 59.899 50.000 22.16 8.05 0.00 3.66
2830 2865 3.541713 GCGTAGGAGGCTGAGGGG 61.542 72.222 0.00 0.00 0.00 4.79
2860 2895 0.179137 TCAAGCATGTAGAGACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
2863 2898 5.931532 ACAAAAATCAAGCATGTAGAGACG 58.068 37.500 0.00 0.00 0.00 4.18
2864 2899 7.362662 TCAACAAAAATCAAGCATGTAGAGAC 58.637 34.615 0.00 0.00 0.00 3.36
2874 2909 5.055812 TGGGAACATCAACAAAAATCAAGC 58.944 37.500 0.00 0.00 33.40 4.01
2897 2932 6.058183 GGATATTAGAAGTGGCAGACAACAT 58.942 40.000 0.00 0.00 0.00 2.71
2904 2939 4.346418 AGAGTGGGATATTAGAAGTGGCAG 59.654 45.833 0.00 0.00 0.00 4.85
2920 2955 4.504132 GCTTGACGCTAGAGTGGG 57.496 61.111 2.99 0.00 35.14 4.61
2943 2978 2.149578 GATGAAATGAGGCGGGATCAG 58.850 52.381 0.00 0.00 0.00 2.90
2958 2993 1.228228 GCATGGGCTGAGGGATGAA 59.772 57.895 0.00 0.00 36.96 2.57
2996 3031 1.118838 GTCATCAGGGTGAGAGGGAG 58.881 60.000 0.00 0.00 0.00 4.30
2997 3032 0.684479 CGTCATCAGGGTGAGAGGGA 60.684 60.000 0.00 0.00 0.00 4.20
2998 3033 1.819229 CGTCATCAGGGTGAGAGGG 59.181 63.158 0.00 0.00 0.00 4.30
3005 3040 1.961180 GCAGGTAGCGTCATCAGGGT 61.961 60.000 0.00 0.00 0.00 4.34
3047 3082 2.205074 GTCCATGGAGTCGTAGCAATG 58.795 52.381 16.81 0.00 0.00 2.82
3048 3083 1.202417 CGTCCATGGAGTCGTAGCAAT 60.202 52.381 16.81 0.00 0.00 3.56
3053 3088 1.404035 CATGACGTCCATGGAGTCGTA 59.596 52.381 25.30 15.93 46.85 3.43
3067 3102 2.500369 GCACAACGCAGCATGACG 60.500 61.111 0.00 0.00 39.69 4.35
3077 3112 3.725459 TGCATCAGCGGCACAACG 61.725 61.111 1.45 0.00 46.23 4.10
3082 3117 3.057548 CAAGGTGCATCAGCGGCA 61.058 61.111 0.00 0.00 46.23 5.69
3083 3118 3.818787 CCAAGGTGCATCAGCGGC 61.819 66.667 0.00 0.00 46.23 6.53
3084 3119 3.818787 GCCAAGGTGCATCAGCGG 61.819 66.667 0.00 0.00 46.23 5.52
3085 3120 2.749044 AGCCAAGGTGCATCAGCG 60.749 61.111 0.00 0.00 46.23 5.18
3086 3121 2.882876 CAGCCAAGGTGCATCAGC 59.117 61.111 0.00 0.00 42.57 4.26
3108 3143 4.030452 GCGTGAAGTGCAGGGTGC 62.030 66.667 0.00 0.00 45.29 5.01
3109 3144 3.357079 GGCGTGAAGTGCAGGGTG 61.357 66.667 0.00 0.00 33.10 4.61
3110 3145 4.643387 GGGCGTGAAGTGCAGGGT 62.643 66.667 0.00 0.00 33.10 4.34
3112 3147 4.988598 ACGGGCGTGAAGTGCAGG 62.989 66.667 0.00 0.00 35.53 4.85
3128 3163 1.160137 GTGGTGATTGTGGCTCTCAC 58.840 55.000 1.56 1.56 46.23 3.51
3129 3164 1.002430 GAGTGGTGATTGTGGCTCTCA 59.998 52.381 0.00 0.00 0.00 3.27
3130 3165 1.677217 GGAGTGGTGATTGTGGCTCTC 60.677 57.143 0.00 0.00 0.00 3.20
3131 3166 0.326264 GGAGTGGTGATTGTGGCTCT 59.674 55.000 0.00 0.00 0.00 4.09
3132 3167 0.326264 AGGAGTGGTGATTGTGGCTC 59.674 55.000 0.00 0.00 0.00 4.70
3133 3168 1.279271 GTAGGAGTGGTGATTGTGGCT 59.721 52.381 0.00 0.00 0.00 4.75
3134 3169 1.739067 GTAGGAGTGGTGATTGTGGC 58.261 55.000 0.00 0.00 0.00 5.01
3135 3170 1.548719 TCGTAGGAGTGGTGATTGTGG 59.451 52.381 0.00 0.00 0.00 4.17
3136 3171 2.492088 TCTCGTAGGAGTGGTGATTGTG 59.508 50.000 11.97 0.00 41.26 3.33
3137 3172 2.755655 CTCTCGTAGGAGTGGTGATTGT 59.244 50.000 11.97 0.00 41.26 2.71
3138 3173 2.755655 ACTCTCGTAGGAGTGGTGATTG 59.244 50.000 16.38 1.73 43.89 2.67
3139 3174 3.088789 ACTCTCGTAGGAGTGGTGATT 57.911 47.619 16.38 0.00 43.89 2.57
3140 3175 2.810870 ACTCTCGTAGGAGTGGTGAT 57.189 50.000 16.38 0.00 43.89 3.06
3146 3181 1.025647 GTCGGCACTCTCGTAGGAGT 61.026 60.000 11.97 0.20 46.14 3.85
3147 3182 0.745128 AGTCGGCACTCTCGTAGGAG 60.745 60.000 6.08 6.08 41.89 3.69
3148 3183 0.538584 TAGTCGGCACTCTCGTAGGA 59.461 55.000 0.00 0.00 33.62 2.94
3149 3184 1.595466 ATAGTCGGCACTCTCGTAGG 58.405 55.000 0.00 0.00 33.62 3.18
3150 3185 4.691685 AGAATATAGTCGGCACTCTCGTAG 59.308 45.833 0.00 0.00 33.62 3.51
3151 3186 4.639334 AGAATATAGTCGGCACTCTCGTA 58.361 43.478 0.00 0.00 33.62 3.43
3152 3187 3.478509 AGAATATAGTCGGCACTCTCGT 58.521 45.455 0.00 0.00 33.62 4.18
3153 3188 3.498777 TGAGAATATAGTCGGCACTCTCG 59.501 47.826 0.00 0.00 33.62 4.04
3154 3189 5.398169 CATGAGAATATAGTCGGCACTCTC 58.602 45.833 0.00 0.00 33.62 3.20
3155 3190 4.219507 CCATGAGAATATAGTCGGCACTCT 59.780 45.833 0.00 0.00 33.62 3.24
3156 3191 4.218635 TCCATGAGAATATAGTCGGCACTC 59.781 45.833 0.00 0.00 33.62 3.51
3157 3192 4.021894 GTCCATGAGAATATAGTCGGCACT 60.022 45.833 0.00 0.00 36.55 4.40
3158 3193 4.238514 GTCCATGAGAATATAGTCGGCAC 58.761 47.826 0.00 0.00 0.00 5.01
3159 3194 3.895041 TGTCCATGAGAATATAGTCGGCA 59.105 43.478 0.00 0.00 0.00 5.69
3160 3195 4.238514 GTGTCCATGAGAATATAGTCGGC 58.761 47.826 0.00 0.00 0.00 5.54
3161 3196 4.322049 GGGTGTCCATGAGAATATAGTCGG 60.322 50.000 0.00 0.00 0.00 4.79
3162 3197 4.322049 GGGGTGTCCATGAGAATATAGTCG 60.322 50.000 0.00 0.00 35.00 4.18
3163 3198 4.020128 GGGGGTGTCCATGAGAATATAGTC 60.020 50.000 0.00 0.00 37.22 2.59
3164 3199 3.910627 GGGGGTGTCCATGAGAATATAGT 59.089 47.826 0.00 0.00 37.22 2.12
3165 3200 3.909995 TGGGGGTGTCCATGAGAATATAG 59.090 47.826 0.00 0.00 37.22 1.31
3166 3201 3.650942 GTGGGGGTGTCCATGAGAATATA 59.349 47.826 0.00 0.00 39.26 0.86
3167 3202 2.443255 GTGGGGGTGTCCATGAGAATAT 59.557 50.000 0.00 0.00 39.26 1.28
3168 3203 1.843851 GTGGGGGTGTCCATGAGAATA 59.156 52.381 0.00 0.00 39.26 1.75
3169 3204 0.625849 GTGGGGGTGTCCATGAGAAT 59.374 55.000 0.00 0.00 39.26 2.40
3170 3205 0.770166 TGTGGGGGTGTCCATGAGAA 60.770 55.000 0.00 0.00 39.26 2.87
3171 3206 0.770166 TTGTGGGGGTGTCCATGAGA 60.770 55.000 0.00 0.00 39.26 3.27
3172 3207 0.112218 TTTGTGGGGGTGTCCATGAG 59.888 55.000 0.00 0.00 39.26 2.90
3173 3208 0.558220 TTTTGTGGGGGTGTCCATGA 59.442 50.000 0.00 0.00 39.26 3.07
3174 3209 1.418334 TTTTTGTGGGGGTGTCCATG 58.582 50.000 0.00 0.00 39.26 3.66
3175 3210 3.957188 TTTTTGTGGGGGTGTCCAT 57.043 47.368 0.00 0.00 39.26 3.41


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

AutoCloner maintained by Alex Coulton.