Multiple sequence alignment - TraesCS3B01G010600

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G010600 chr3B 100.000 2724 0 0 1 2724 4801109 4798386 0.000000e+00 5031.0
1 TraesCS3B01G010600 chr3B 98.754 1926 15 4 1 1919 3913110 3911187 0.000000e+00 3415.0
2 TraesCS3B01G010600 chr3B 90.554 307 19 5 1957 2263 3911187 3910891 5.470000e-107 398.0
3 TraesCS3B01G010600 chr3B 93.293 164 4 4 2263 2424 201491346 201491188 4.530000e-58 235.0
4 TraesCS3B01G010600 chr3B 82.051 234 15 15 689 922 3960142 3959936 1.000000e-39 174.0
5 TraesCS3B01G010600 chr3B 81.435 237 14 18 689 922 4819686 4819477 1.680000e-37 167.0
6 TraesCS3B01G010600 chr3B 76.562 192 25 7 1632 1820 3910222 3910048 1.340000e-13 87.9
7 TraesCS3B01G010600 chr3B 90.909 55 3 2 1216 1269 534166319 534166372 3.760000e-09 73.1
8 TraesCS3B01G010600 chr3D 83.586 1651 118 70 662 2263 1762810 1761264 0.000000e+00 1406.0
9 TraesCS3B01G010600 chr3D 93.617 141 7 1 1 139 48297586 48297446 2.750000e-50 209.0
10 TraesCS3B01G010600 chr3D 95.402 87 4 0 372 458 490836982 490836896 3.660000e-29 139.0
11 TraesCS3B01G010600 chr3A 84.119 806 46 35 1000 1774 7261141 7261895 0.000000e+00 704.0
12 TraesCS3B01G010600 chr4A 93.293 164 5 4 2263 2424 141128584 141128425 1.260000e-58 237.0
13 TraesCS3B01G010600 chr4A 88.983 118 9 2 343 460 722340132 722340019 2.830000e-30 143.0
14 TraesCS3B01G010600 chrUn 93.293 164 4 4 2263 2424 406224077 406224235 4.530000e-58 235.0
15 TraesCS3B01G010600 chrUn 93.293 164 4 4 2263 2424 468750348 468750506 4.530000e-58 235.0
16 TraesCS3B01G010600 chr5D 93.293 164 4 4 2263 2424 503329254 503329096 4.530000e-58 235.0
17 TraesCS3B01G010600 chr5D 89.565 115 9 1 345 459 70665526 70665415 2.830000e-30 143.0
18 TraesCS3B01G010600 chr2D 93.293 164 4 4 2263 2424 33931364 33931522 4.530000e-58 235.0
19 TraesCS3B01G010600 chr2D 93.293 164 4 4 2263 2424 630265609 630265451 4.530000e-58 235.0
20 TraesCS3B01G010600 chr1A 94.268 157 3 3 2263 2418 545402456 545402305 4.530000e-58 235.0
21 TraesCS3B01G010600 chr1A 89.091 55 5 1 2502 2556 247354338 247354285 1.750000e-07 67.6
22 TraesCS3B01G010600 chr1D 92.683 164 7 4 2263 2424 244766834 244766674 5.870000e-57 231.0
23 TraesCS3B01G010600 chr6B 79.598 348 40 16 1216 1544 255100987 255100652 1.270000e-53 220.0
24 TraesCS3B01G010600 chr6B 84.906 106 16 0 356 461 94585353 94585248 1.030000e-19 108.0
25 TraesCS3B01G010600 chr4D 92.908 141 8 1 1 139 11497485 11497345 1.280000e-48 204.0
26 TraesCS3B01G010600 chr4D 79.882 169 20 10 2556 2722 49803693 49803537 7.970000e-21 111.0
27 TraesCS3B01G010600 chr2A 90.141 142 11 2 1 139 166082936 166083077 5.990000e-42 182.0
28 TraesCS3B01G010600 chr2A 88.136 59 5 2 2502 2559 571462229 571462286 4.870000e-08 69.4
29 TraesCS3B01G010600 chr7D 88.889 117 10 1 345 461 29600927 29601040 1.020000e-29 141.0
30 TraesCS3B01G010600 chr7D 88.034 117 11 1 345 461 4288857 4288744 4.730000e-28 135.0
31 TraesCS3B01G010600 chr2B 85.849 106 15 0 356 461 717039714 717039609 2.220000e-21 113.0
32 TraesCS3B01G010600 chr2B 85.714 105 15 0 356 460 19847750 19847646 7.970000e-21 111.0
33 TraesCS3B01G010600 chr6D 82.677 127 18 3 16 139 102399901 102400026 2.870000e-20 110.0
34 TraesCS3B01G010600 chr7B 90.909 55 3 2 1216 1269 126787109 126787162 3.760000e-09 73.1
35 TraesCS3B01G010600 chr7A 90.909 55 3 2 1216 1269 636231021 636230968 3.760000e-09 73.1
36 TraesCS3B01G010600 chr7A 86.885 61 7 1 2499 2559 479854494 479854553 1.750000e-07 67.6
37 TraesCS3B01G010600 chr7A 85.484 62 7 2 2499 2559 543441756 543441696 2.260000e-06 63.9
38 TraesCS3B01G010600 chr5B 90.909 55 3 2 1216 1269 672818187 672818134 3.760000e-09 73.1
39 TraesCS3B01G010600 chr1B 90.909 55 3 2 1216 1269 47170184 47170237 3.760000e-09 73.1
40 TraesCS3B01G010600 chr5A 85.484 62 8 1 2498 2559 520440998 520441058 2.260000e-06 63.9


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 TraesCS3B01G010600 chr3B 4798386 4801109 2723 True 5031.0 5031 100.000000 1 2724 1 chr3B.!!$R2 2723
1 TraesCS3B01G010600 chr3B 3910048 3913110 3062 True 1300.3 3415 88.623333 1 2263 3 chr3B.!!$R5 2262
2 TraesCS3B01G010600 chr3D 1761264 1762810 1546 True 1406.0 1406 83.586000 662 2263 1 chr3D.!!$R1 1601
3 TraesCS3B01G010600 chr3A 7261141 7261895 754 False 704.0 704 84.119000 1000 1774 1 chr3A.!!$F1 774

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
433 434 0.389296 TCATCCGCACTACAACACCG 60.389 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2000 0.511221 CGTACCTGTTTCGGCACTTG 59.489 55.0 0.0 0.0 0.0 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
433 434 0.389296 TCATCCGCACTACAACACCG 60.389 55.000 0.00 0.00 0.00 4.94
451 452 2.165845 ACCGTACAATACTGCAGAGGAC 59.834 50.000 23.35 12.53 0.00 3.85
561 562 6.848069 TGATCCGGGAATCTTAATTACCATT 58.152 36.000 0.00 0.00 45.19 3.16
801 814 3.369388 GTCCCTCCCTCCCTCCCT 61.369 72.222 0.00 0.00 0.00 4.20
804 817 3.039526 CCTCCCTCCCTCCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
807 820 3.039526 CCCTCCCTCCCTCCTCCT 61.040 72.222 0.00 0.00 0.00 3.69
808 821 2.612251 CCTCCCTCCCTCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
809 822 2.612251 CTCCCTCCCTCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
907 921 2.892425 CGCTCGCTCACCAATCCC 60.892 66.667 0.00 0.00 0.00 3.85
1035 1049 2.750350 GTGGTGGTGGTGGAGGAG 59.250 66.667 0.00 0.00 0.00 3.69
1933 1999 3.979495 GCATCGCCATGATTGATCTTTTC 59.021 43.478 0.00 0.00 34.13 2.29
1934 2000 4.543692 CATCGCCATGATTGATCTTTTCC 58.456 43.478 0.00 0.00 34.13 3.13
1946 2012 3.004315 TGATCTTTTCCAAGTGCCGAAAC 59.996 43.478 0.00 0.00 0.00 2.78
1951 2017 0.759959 TCCAAGTGCCGAAACAGGTA 59.240 50.000 0.00 0.00 0.00 3.08
2028 2094 4.340950 AGTTCGTCCATCCACAACAAAAAT 59.659 37.500 0.00 0.00 0.00 1.82
2030 2096 6.039941 AGTTCGTCCATCCACAACAAAAATAA 59.960 34.615 0.00 0.00 0.00 1.40
2031 2097 6.007936 TCGTCCATCCACAACAAAAATAAG 57.992 37.500 0.00 0.00 0.00 1.73
2159 2237 0.029300 GCTGCGCAACACAAAAGAGA 59.971 50.000 13.05 0.00 0.00 3.10
2160 2238 1.533756 GCTGCGCAACACAAAAGAGAA 60.534 47.619 13.05 0.00 0.00 2.87
2161 2239 2.796304 CTGCGCAACACAAAAGAGAAA 58.204 42.857 13.05 0.00 0.00 2.52
2162 2240 3.178267 CTGCGCAACACAAAAGAGAAAA 58.822 40.909 13.05 0.00 0.00 2.29
2191 2269 3.605726 AAATGCAGGGATCCATGATGA 57.394 42.857 29.91 12.67 0.00 2.92
2209 2287 2.821546 TGACACTGTCTCTGTTTTCGG 58.178 47.619 10.54 0.00 33.15 4.30
2214 2292 0.878523 TGTCTCTGTTTTCGGCACCG 60.879 55.000 1.73 1.73 41.35 4.94
2227 2306 2.867472 CACCGGAAATGCGTGTCC 59.133 61.111 9.46 4.87 0.00 4.02
2250 2329 1.487976 TCTGATGGACAGGCAGAATCC 59.512 52.381 5.52 0.00 45.76 3.01
2263 2342 3.084039 GCAGAATCCACATGTTCTTCCA 58.916 45.455 0.00 0.00 32.60 3.53
2264 2343 3.507233 GCAGAATCCACATGTTCTTCCAA 59.493 43.478 0.00 0.00 32.60 3.53
2266 2345 4.520111 CAGAATCCACATGTTCTTCCAACA 59.480 41.667 0.00 0.00 32.60 3.33
2267 2346 4.520492 AGAATCCACATGTTCTTCCAACAC 59.480 41.667 0.00 0.00 30.84 3.32
2268 2347 2.582052 TCCACATGTTCTTCCAACACC 58.418 47.619 0.00 0.00 32.37 4.16
2269 2348 1.266718 CCACATGTTCTTCCAACACCG 59.733 52.381 0.00 0.00 32.37 4.94
2271 2350 2.813754 CACATGTTCTTCCAACACCGAT 59.186 45.455 0.00 0.00 32.37 4.18
2272 2351 3.253188 CACATGTTCTTCCAACACCGATT 59.747 43.478 0.00 0.00 32.37 3.34
2273 2352 3.888930 ACATGTTCTTCCAACACCGATTT 59.111 39.130 0.00 0.00 32.37 2.17
2274 2353 4.340950 ACATGTTCTTCCAACACCGATTTT 59.659 37.500 0.00 0.00 32.37 1.82
2275 2354 5.533154 ACATGTTCTTCCAACACCGATTTTA 59.467 36.000 0.00 0.00 32.37 1.52
2276 2355 6.208599 ACATGTTCTTCCAACACCGATTTTAT 59.791 34.615 0.00 0.00 32.37 1.40
2277 2356 6.642707 TGTTCTTCCAACACCGATTTTATT 57.357 33.333 0.00 0.00 0.00 1.40
2279 2358 5.539582 TCTTCCAACACCGATTTTATTCG 57.460 39.130 0.00 0.00 38.83 3.34
2280 2359 5.239351 TCTTCCAACACCGATTTTATTCGA 58.761 37.500 0.00 0.00 41.62 3.71
2281 2360 5.701750 TCTTCCAACACCGATTTTATTCGAA 59.298 36.000 0.00 0.00 41.62 3.71
2282 2361 5.539582 TCCAACACCGATTTTATTCGAAG 57.460 39.130 3.35 0.00 41.62 3.79
2283 2362 4.998672 TCCAACACCGATTTTATTCGAAGT 59.001 37.500 3.35 0.00 41.62 3.01
2284 2363 5.121142 TCCAACACCGATTTTATTCGAAGTC 59.879 40.000 3.35 0.00 41.62 3.01
2285 2364 5.106869 CCAACACCGATTTTATTCGAAGTCA 60.107 40.000 3.35 0.00 41.62 3.41
2286 2365 6.367421 CAACACCGATTTTATTCGAAGTCAA 58.633 36.000 3.35 0.00 41.62 3.18
2287 2366 6.165659 ACACCGATTTTATTCGAAGTCAAG 57.834 37.500 3.35 0.00 41.62 3.02
2288 2367 5.121768 ACACCGATTTTATTCGAAGTCAAGG 59.878 40.000 3.35 3.86 41.62 3.61
2289 2368 5.350365 CACCGATTTTATTCGAAGTCAAGGA 59.650 40.000 3.35 0.00 41.62 3.36
2290 2369 5.935789 ACCGATTTTATTCGAAGTCAAGGAA 59.064 36.000 3.35 0.00 41.62 3.36
2292 2371 7.767198 ACCGATTTTATTCGAAGTCAAGGAATA 59.233 33.333 3.35 0.00 41.62 1.75
2293 2372 8.774586 CCGATTTTATTCGAAGTCAAGGAATAT 58.225 33.333 3.35 0.00 41.62 1.28
2301 2380 8.857694 TTCGAAGTCAAGGAATATTTTTAGGT 57.142 30.769 0.00 0.00 0.00 3.08
2302 2381 8.857694 TCGAAGTCAAGGAATATTTTTAGGTT 57.142 30.769 0.00 0.00 0.00 3.50
2304 2383 8.947115 CGAAGTCAAGGAATATTTTTAGGTTCT 58.053 33.333 0.00 0.00 0.00 3.01
2320 2399 7.900782 TTAGGTTCTTTTCCTAGATGAAACG 57.099 36.000 0.00 0.00 38.55 3.60
2321 2400 5.246307 AGGTTCTTTTCCTAGATGAAACGG 58.754 41.667 0.00 0.00 34.13 4.44
2322 2401 5.012768 AGGTTCTTTTCCTAGATGAAACGGA 59.987 40.000 0.00 0.00 34.13 4.69
2323 2402 5.704053 GGTTCTTTTCCTAGATGAAACGGAA 59.296 40.000 0.00 0.00 34.13 4.30
2325 2404 7.551617 GGTTCTTTTCCTAGATGAAACGGAATA 59.448 37.037 0.00 0.00 35.63 1.75
2326 2405 8.388853 GTTCTTTTCCTAGATGAAACGGAATAC 58.611 37.037 0.00 0.00 35.63 1.89
2327 2406 7.046033 TCTTTTCCTAGATGAAACGGAATACC 58.954 38.462 0.00 0.00 35.63 2.73
2328 2407 6.555463 TTTCCTAGATGAAACGGAATACCT 57.445 37.500 0.00 0.00 35.63 3.08
2329 2408 7.664552 TTTCCTAGATGAAACGGAATACCTA 57.335 36.000 0.00 0.00 35.63 3.08
2330 2409 7.850935 TTCCTAGATGAAACGGAATACCTAT 57.149 36.000 0.00 0.00 31.00 2.57
2331 2410 7.850935 TCCTAGATGAAACGGAATACCTATT 57.149 36.000 0.00 0.00 0.00 1.73
2332 2411 8.258850 TCCTAGATGAAACGGAATACCTATTT 57.741 34.615 0.00 0.00 0.00 1.40
2333 2412 9.370930 TCCTAGATGAAACGGAATACCTATTTA 57.629 33.333 0.00 0.00 0.00 1.40
2367 2446 9.693739 TTCCTAATTATACAAAAGCATTCCAGA 57.306 29.630 0.00 0.00 0.00 3.86
2368 2447 9.866655 TCCTAATTATACAAAAGCATTCCAGAT 57.133 29.630 0.00 0.00 0.00 2.90
2407 2609 4.908601 AAAGGGTTTCATTTGGATTCCC 57.091 40.909 0.00 0.00 38.37 3.97
2408 2610 2.832838 AGGGTTTCATTTGGATTCCCC 58.167 47.619 0.00 0.00 38.67 4.81
2409 2611 2.386811 AGGGTTTCATTTGGATTCCCCT 59.613 45.455 0.00 0.00 38.67 4.79
2411 2613 4.235164 AGGGTTTCATTTGGATTCCCCTAT 59.765 41.667 0.00 0.00 38.67 2.57
2414 2616 6.069673 GGGTTTCATTTGGATTCCCCTATTTT 60.070 38.462 0.00 0.00 34.59 1.82
2415 2617 7.047891 GGTTTCATTTGGATTCCCCTATTTTC 58.952 38.462 0.00 0.00 35.38 2.29
2416 2618 7.310983 GGTTTCATTTGGATTCCCCTATTTTCA 60.311 37.037 0.00 0.00 35.38 2.69
2418 2620 7.181569 TCATTTGGATTCCCCTATTTTCAAC 57.818 36.000 0.00 0.00 35.38 3.18
2419 2621 6.728164 TCATTTGGATTCCCCTATTTTCAACA 59.272 34.615 0.00 0.00 35.38 3.33
2420 2622 5.993748 TTGGATTCCCCTATTTTCAACAC 57.006 39.130 0.00 0.00 35.38 3.32
2421 2623 4.013728 TGGATTCCCCTATTTTCAACACG 58.986 43.478 0.00 0.00 35.38 4.49
2422 2624 3.181490 GGATTCCCCTATTTTCAACACGC 60.181 47.826 0.00 0.00 0.00 5.34
2423 2625 2.570415 TCCCCTATTTTCAACACGCA 57.430 45.000 0.00 0.00 0.00 5.24
2424 2626 2.156098 TCCCCTATTTTCAACACGCAC 58.844 47.619 0.00 0.00 0.00 5.34
2426 2628 2.161609 CCCCTATTTTCAACACGCACTC 59.838 50.000 0.00 0.00 0.00 3.51
2427 2629 3.074412 CCCTATTTTCAACACGCACTCT 58.926 45.455 0.00 0.00 0.00 3.24
2428 2630 4.250464 CCCTATTTTCAACACGCACTCTA 58.750 43.478 0.00 0.00 0.00 2.43
2429 2631 4.693566 CCCTATTTTCAACACGCACTCTAA 59.306 41.667 0.00 0.00 0.00 2.10
2430 2632 5.390567 CCCTATTTTCAACACGCACTCTAAC 60.391 44.000 0.00 0.00 0.00 2.34
2432 2634 2.212869 TTCAACACGCACTCTAACGT 57.787 45.000 0.00 0.00 44.75 3.99
2441 2643 1.442769 CACTCTAACGTGCCATTGCT 58.557 50.000 0.00 0.00 38.71 3.91
2445 2647 1.003118 TCTAACGTGCCATTGCTTCCT 59.997 47.619 0.00 0.00 38.71 3.36
2446 2648 1.131126 CTAACGTGCCATTGCTTCCTG 59.869 52.381 0.00 0.00 38.71 3.86
2447 2649 1.526575 AACGTGCCATTGCTTCCTGG 61.527 55.000 0.00 0.00 38.71 4.45
2448 2650 1.675310 CGTGCCATTGCTTCCTGGA 60.675 57.895 0.00 0.00 38.71 3.86
2449 2651 1.033746 CGTGCCATTGCTTCCTGGAT 61.034 55.000 0.00 0.00 38.71 3.41
2450 2652 1.188863 GTGCCATTGCTTCCTGGATT 58.811 50.000 0.00 0.00 38.71 3.01
2453 2655 3.195396 GTGCCATTGCTTCCTGGATTTTA 59.805 43.478 0.00 0.00 38.71 1.52
2464 2821 6.401537 TTCCTGGATTTTATCAAGAAGGGA 57.598 37.500 0.00 0.00 31.67 4.20
2465 2822 6.401537 TCCTGGATTTTATCAAGAAGGGAA 57.598 37.500 0.00 0.00 31.67 3.97
2466 2823 6.799827 TCCTGGATTTTATCAAGAAGGGAAA 58.200 36.000 0.00 0.00 31.67 3.13
2467 2824 6.663523 TCCTGGATTTTATCAAGAAGGGAAAC 59.336 38.462 0.00 0.00 31.67 2.78
2468 2825 6.127338 CCTGGATTTTATCAAGAAGGGAAACC 60.127 42.308 0.00 0.00 41.30 3.27
2469 2826 6.127338 CTGGATTTTATCAAGAAGGGAAACCC 60.127 42.308 0.00 0.00 41.71 4.11
2480 2837 3.256281 GGAAACCCCAGCTTCAGAG 57.744 57.895 0.00 0.00 34.14 3.35
2481 2838 0.322906 GGAAACCCCAGCTTCAGAGG 60.323 60.000 0.00 0.00 34.14 3.69
2483 2840 0.402121 AAACCCCAGCTTCAGAGGAC 59.598 55.000 0.00 0.00 0.00 3.85
2487 2844 1.909302 CCCCAGCTTCAGAGGACTTTA 59.091 52.381 0.00 0.00 0.00 1.85
2488 2845 2.507471 CCCCAGCTTCAGAGGACTTTAT 59.493 50.000 0.00 0.00 0.00 1.40
2491 2848 5.163152 CCCCAGCTTCAGAGGACTTTATTAT 60.163 44.000 0.00 0.00 0.00 1.28
2492 2849 5.762218 CCCAGCTTCAGAGGACTTTATTATG 59.238 44.000 0.00 0.00 0.00 1.90
2494 2851 5.819379 CAGCTTCAGAGGACTTTATTATGCA 59.181 40.000 0.00 0.00 0.00 3.96
2496 2853 6.051717 GCTTCAGAGGACTTTATTATGCAGA 58.948 40.000 0.00 0.00 0.00 4.26
2497 2854 6.540189 GCTTCAGAGGACTTTATTATGCAGAA 59.460 38.462 0.00 0.00 0.00 3.02
2498 2855 7.066284 GCTTCAGAGGACTTTATTATGCAGAAA 59.934 37.037 0.00 0.00 0.00 2.52
2499 2856 8.862325 TTCAGAGGACTTTATTATGCAGAAAA 57.138 30.769 0.00 0.00 0.00 2.29
2500 2857 8.268850 TCAGAGGACTTTATTATGCAGAAAAC 57.731 34.615 0.00 0.00 0.00 2.43
2501 2858 7.882791 TCAGAGGACTTTATTATGCAGAAAACA 59.117 33.333 0.00 0.00 0.00 2.83
2502 2859 8.180267 CAGAGGACTTTATTATGCAGAAAACAG 58.820 37.037 0.00 0.00 0.00 3.16
2503 2860 8.103305 AGAGGACTTTATTATGCAGAAAACAGA 58.897 33.333 0.00 0.00 0.00 3.41
2505 2862 8.103305 AGGACTTTATTATGCAGAAAACAGAGA 58.897 33.333 0.00 0.00 0.00 3.10
2506 2863 8.730680 GGACTTTATTATGCAGAAAACAGAGAA 58.269 33.333 0.00 0.00 0.00 2.87
2508 2865 9.289782 ACTTTATTATGCAGAAAACAGAGAAGT 57.710 29.630 0.00 0.00 0.00 3.01
2511 2868 2.642427 TGCAGAAAACAGAGAAGTGCA 58.358 42.857 0.00 0.00 37.12 4.57
2512 2869 3.216800 TGCAGAAAACAGAGAAGTGCAT 58.783 40.909 0.00 0.00 34.65 3.96
2513 2870 4.388485 TGCAGAAAACAGAGAAGTGCATA 58.612 39.130 0.00 0.00 34.65 3.14
2515 2872 5.474532 TGCAGAAAACAGAGAAGTGCATATT 59.525 36.000 0.00 0.00 34.65 1.28
2516 2873 6.654582 TGCAGAAAACAGAGAAGTGCATATTA 59.345 34.615 0.00 0.00 34.65 0.98
2518 2875 7.361201 GCAGAAAACAGAGAAGTGCATATTACA 60.361 37.037 0.00 0.00 0.00 2.41
2519 2876 7.959651 CAGAAAACAGAGAAGTGCATATTACAC 59.040 37.037 0.00 0.00 38.35 2.90
2520 2877 6.743575 AAACAGAGAAGTGCATATTACACC 57.256 37.500 0.00 0.00 38.87 4.16
2521 2878 4.770795 ACAGAGAAGTGCATATTACACCC 58.229 43.478 0.00 0.00 38.87 4.61
2523 2880 4.040755 AGAGAAGTGCATATTACACCCCT 58.959 43.478 0.00 1.15 38.87 4.79
2525 2882 3.780294 AGAAGTGCATATTACACCCCTCA 59.220 43.478 0.00 0.00 38.87 3.86
2526 2883 4.227300 AGAAGTGCATATTACACCCCTCAA 59.773 41.667 0.00 0.00 38.87 3.02
2527 2884 4.796110 AGTGCATATTACACCCCTCAAT 57.204 40.909 0.00 0.00 38.87 2.57
2528 2885 5.129368 AGTGCATATTACACCCCTCAATT 57.871 39.130 0.00 0.00 38.87 2.32
2529 2886 5.133221 AGTGCATATTACACCCCTCAATTC 58.867 41.667 0.00 0.00 38.87 2.17
2530 2887 5.103940 AGTGCATATTACACCCCTCAATTCT 60.104 40.000 0.00 0.00 38.87 2.40
2531 2888 6.101150 AGTGCATATTACACCCCTCAATTCTA 59.899 38.462 0.00 0.00 38.87 2.10
2532 2889 6.428159 GTGCATATTACACCCCTCAATTCTAG 59.572 42.308 0.00 0.00 31.67 2.43
2533 2890 5.412904 GCATATTACACCCCTCAATTCTAGC 59.587 44.000 0.00 0.00 0.00 3.42
2534 2891 6.533730 CATATTACACCCCTCAATTCTAGCA 58.466 40.000 0.00 0.00 0.00 3.49
2535 2892 5.653255 ATTACACCCCTCAATTCTAGCAT 57.347 39.130 0.00 0.00 0.00 3.79
2536 2893 5.450818 TTACACCCCTCAATTCTAGCATT 57.549 39.130 0.00 0.00 0.00 3.56
2537 2894 4.322057 ACACCCCTCAATTCTAGCATTT 57.678 40.909 0.00 0.00 0.00 2.32
2538 2895 4.019174 ACACCCCTCAATTCTAGCATTTG 58.981 43.478 0.00 0.00 0.00 2.32
2539 2896 4.019174 CACCCCTCAATTCTAGCATTTGT 58.981 43.478 0.00 0.00 0.00 2.83
2540 2897 4.463891 CACCCCTCAATTCTAGCATTTGTT 59.536 41.667 0.00 0.00 0.00 2.83
2541 2898 5.047092 CACCCCTCAATTCTAGCATTTGTTT 60.047 40.000 0.00 0.00 0.00 2.83
2542 2899 6.152661 CACCCCTCAATTCTAGCATTTGTTTA 59.847 38.462 0.00 0.00 0.00 2.01
2543 2900 6.723977 ACCCCTCAATTCTAGCATTTGTTTAA 59.276 34.615 0.00 0.00 0.00 1.52
2544 2901 7.093771 ACCCCTCAATTCTAGCATTTGTTTAAG 60.094 37.037 0.00 0.00 0.00 1.85
2545 2902 7.122650 CCCCTCAATTCTAGCATTTGTTTAAGA 59.877 37.037 0.00 0.00 0.00 2.10
2546 2903 8.522830 CCCTCAATTCTAGCATTTGTTTAAGAA 58.477 33.333 0.00 0.00 0.00 2.52
2553 2910 8.276252 TCTAGCATTTGTTTAAGAATACACCC 57.724 34.615 0.00 0.00 0.00 4.61
2554 2911 6.280855 AGCATTTGTTTAAGAATACACCCC 57.719 37.500 0.00 0.00 0.00 4.95
2555 2912 5.186992 AGCATTTGTTTAAGAATACACCCCC 59.813 40.000 0.00 0.00 0.00 5.40
2556 2913 5.046950 GCATTTGTTTAAGAATACACCCCCA 60.047 40.000 0.00 0.00 0.00 4.96
2557 2914 6.519213 GCATTTGTTTAAGAATACACCCCCAA 60.519 38.462 0.00 0.00 0.00 4.12
2558 2915 6.408107 TTTGTTTAAGAATACACCCCCAAC 57.592 37.500 0.00 0.00 0.00 3.77
2559 2916 5.063017 TGTTTAAGAATACACCCCCAACA 57.937 39.130 0.00 0.00 0.00 3.33
2560 2917 5.455872 TGTTTAAGAATACACCCCCAACAA 58.544 37.500 0.00 0.00 0.00 2.83
2561 2918 5.302313 TGTTTAAGAATACACCCCCAACAAC 59.698 40.000 0.00 0.00 0.00 3.32
2562 2919 2.597578 AGAATACACCCCCAACAACC 57.402 50.000 0.00 0.00 0.00 3.77
2563 2920 1.783979 AGAATACACCCCCAACAACCA 59.216 47.619 0.00 0.00 0.00 3.67
2564 2921 2.167662 GAATACACCCCCAACAACCAG 58.832 52.381 0.00 0.00 0.00 4.00
2565 2922 1.451449 ATACACCCCCAACAACCAGA 58.549 50.000 0.00 0.00 0.00 3.86
2566 2923 0.475044 TACACCCCCAACAACCAGAC 59.525 55.000 0.00 0.00 0.00 3.51
2567 2924 1.228793 CACCCCCAACAACCAGACA 59.771 57.895 0.00 0.00 0.00 3.41
2568 2925 0.823356 CACCCCCAACAACCAGACAG 60.823 60.000 0.00 0.00 0.00 3.51
2569 2926 0.991355 ACCCCCAACAACCAGACAGA 60.991 55.000 0.00 0.00 0.00 3.41
2570 2927 0.184933 CCCCCAACAACCAGACAGAA 59.815 55.000 0.00 0.00 0.00 3.02
2571 2928 1.203050 CCCCCAACAACCAGACAGAAT 60.203 52.381 0.00 0.00 0.00 2.40
2572 2929 2.041081 CCCCCAACAACCAGACAGAATA 59.959 50.000 0.00 0.00 0.00 1.75
2573 2930 3.081804 CCCCAACAACCAGACAGAATAC 58.918 50.000 0.00 0.00 0.00 1.89
2574 2931 3.497763 CCCCAACAACCAGACAGAATACA 60.498 47.826 0.00 0.00 0.00 2.29
2575 2932 4.141287 CCCAACAACCAGACAGAATACAA 58.859 43.478 0.00 0.00 0.00 2.41
2576 2933 4.023193 CCCAACAACCAGACAGAATACAAC 60.023 45.833 0.00 0.00 0.00 3.32
2577 2934 4.023193 CCAACAACCAGACAGAATACAACC 60.023 45.833 0.00 0.00 0.00 3.77
2578 2935 3.751518 ACAACCAGACAGAATACAACCC 58.248 45.455 0.00 0.00 0.00 4.11
2579 2936 3.394606 ACAACCAGACAGAATACAACCCT 59.605 43.478 0.00 0.00 0.00 4.34
2580 2937 3.983044 ACCAGACAGAATACAACCCTC 57.017 47.619 0.00 0.00 0.00 4.30
2581 2938 2.572104 ACCAGACAGAATACAACCCTCC 59.428 50.000 0.00 0.00 0.00 4.30
2582 2939 2.840651 CCAGACAGAATACAACCCTCCT 59.159 50.000 0.00 0.00 0.00 3.69
2583 2940 3.118592 CCAGACAGAATACAACCCTCCTC 60.119 52.174 0.00 0.00 0.00 3.71
2584 2941 3.772025 CAGACAGAATACAACCCTCCTCT 59.228 47.826 0.00 0.00 0.00 3.69
2585 2942 4.027437 AGACAGAATACAACCCTCCTCTC 58.973 47.826 0.00 0.00 0.00 3.20
2586 2943 3.108376 ACAGAATACAACCCTCCTCTCC 58.892 50.000 0.00 0.00 0.00 3.71
2587 2944 2.436173 CAGAATACAACCCTCCTCTCCC 59.564 54.545 0.00 0.00 0.00 4.30
2588 2945 1.769465 GAATACAACCCTCCTCTCCCC 59.231 57.143 0.00 0.00 0.00 4.81
2589 2946 0.398664 ATACAACCCTCCTCTCCCCG 60.399 60.000 0.00 0.00 0.00 5.73
2590 2947 1.807771 TACAACCCTCCTCTCCCCGT 61.808 60.000 0.00 0.00 0.00 5.28
2591 2948 1.918800 CAACCCTCCTCTCCCCGTT 60.919 63.158 0.00 0.00 0.00 4.44
2592 2949 1.918800 AACCCTCCTCTCCCCGTTG 60.919 63.158 0.00 0.00 0.00 4.10
2593 2950 2.038975 CCCTCCTCTCCCCGTTGA 59.961 66.667 0.00 0.00 0.00 3.18
2594 2951 2.359967 CCCTCCTCTCCCCGTTGAC 61.360 68.421 0.00 0.00 0.00 3.18
2595 2952 2.359967 CCTCCTCTCCCCGTTGACC 61.360 68.421 0.00 0.00 0.00 4.02
2596 2953 2.678934 TCCTCTCCCCGTTGACCG 60.679 66.667 0.00 0.00 0.00 4.79
2607 2964 1.458746 CGTTGACCGGTTTTGAAACG 58.541 50.000 9.42 16.03 39.77 3.60
2608 2965 1.202054 CGTTGACCGGTTTTGAAACGT 60.202 47.619 21.78 0.00 39.77 3.99
2609 2966 2.728535 CGTTGACCGGTTTTGAAACGTT 60.729 45.455 21.78 0.00 39.77 3.99
2610 2967 2.546195 TGACCGGTTTTGAAACGTTG 57.454 45.000 9.42 0.00 39.77 4.10
2611 2968 2.082231 TGACCGGTTTTGAAACGTTGA 58.918 42.857 9.42 0.00 39.77 3.18
2612 2969 2.159544 TGACCGGTTTTGAAACGTTGAC 60.160 45.455 9.42 0.00 39.77 3.18
2613 2970 2.086094 ACCGGTTTTGAAACGTTGACT 58.914 42.857 0.00 0.00 39.77 3.41
2614 2971 2.159490 ACCGGTTTTGAAACGTTGACTG 60.159 45.455 0.00 1.53 39.77 3.51
2615 2972 2.446282 CGGTTTTGAAACGTTGACTGG 58.554 47.619 0.00 0.00 39.77 4.00
2616 2973 2.096174 CGGTTTTGAAACGTTGACTGGA 59.904 45.455 0.00 0.00 39.77 3.86
2617 2974 3.691498 GGTTTTGAAACGTTGACTGGAG 58.309 45.455 0.00 0.00 39.77 3.86
2618 2975 3.128068 GGTTTTGAAACGTTGACTGGAGT 59.872 43.478 0.00 0.00 39.77 3.85
2619 2976 4.095610 GTTTTGAAACGTTGACTGGAGTG 58.904 43.478 0.00 0.00 0.00 3.51
2620 2977 2.971660 TGAAACGTTGACTGGAGTGA 57.028 45.000 0.00 0.00 0.00 3.41
2621 2978 3.254470 TGAAACGTTGACTGGAGTGAA 57.746 42.857 0.00 0.00 0.00 3.18
2622 2979 2.933906 TGAAACGTTGACTGGAGTGAAC 59.066 45.455 0.00 0.00 38.49 3.18
2623 2980 2.684001 AACGTTGACTGGAGTGAACA 57.316 45.000 0.00 0.00 41.23 3.18
2624 2981 2.225068 ACGTTGACTGGAGTGAACAG 57.775 50.000 9.37 5.16 41.23 3.16
2633 2990 5.209818 ACTGGAGTGAACAGTAAATTCGA 57.790 39.130 0.00 0.00 46.62 3.71
2634 2991 5.607477 ACTGGAGTGAACAGTAAATTCGAA 58.393 37.500 0.00 0.00 46.62 3.71
2635 2992 6.053005 ACTGGAGTGAACAGTAAATTCGAAA 58.947 36.000 0.00 0.00 46.62 3.46
2636 2993 6.202954 ACTGGAGTGAACAGTAAATTCGAAAG 59.797 38.462 0.00 0.00 46.62 2.62
2637 2994 6.285224 TGGAGTGAACAGTAAATTCGAAAGA 58.715 36.000 0.00 0.00 39.20 2.52
2692 3049 9.790344 ACAATTTTCATTATTTCATTGGGTGAA 57.210 25.926 0.00 0.00 44.87 3.18
2695 3052 8.830201 TTTTCATTATTTCATTGGGTGAACAG 57.170 30.769 0.00 0.00 46.14 3.16
2697 3054 8.642935 TTCATTATTTCATTGGGTGAACAGTA 57.357 30.769 0.00 0.00 46.14 2.74
2698 3055 8.642935 TCATTATTTCATTGGGTGAACAGTAA 57.357 30.769 0.00 0.00 46.14 2.24
2699 3056 9.083422 TCATTATTTCATTGGGTGAACAGTAAA 57.917 29.630 0.00 0.00 46.14 2.01
2700 3057 9.139174 CATTATTTCATTGGGTGAACAGTAAAC 57.861 33.333 0.00 0.00 46.14 2.01
2703 3060 5.042463 TCATTGGGTGAACAGTAAACTGA 57.958 39.130 16.74 0.00 46.36 3.41
2705 3062 5.888724 TCATTGGGTGAACAGTAAACTGAAA 59.111 36.000 16.74 0.00 46.36 2.69
2707 3064 5.828299 TGGGTGAACAGTAAACTGAAAAG 57.172 39.130 16.74 0.00 46.59 2.27
2708 3065 5.502079 TGGGTGAACAGTAAACTGAAAAGA 58.498 37.500 16.74 0.00 46.59 2.52
2709 3066 5.946972 TGGGTGAACAGTAAACTGAAAAGAA 59.053 36.000 16.74 0.00 46.59 2.52
2710 3067 6.434652 TGGGTGAACAGTAAACTGAAAAGAAA 59.565 34.615 16.74 0.00 46.59 2.52
2711 3068 7.123547 TGGGTGAACAGTAAACTGAAAAGAAAT 59.876 33.333 16.74 0.00 46.59 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
346 347 4.553467 GCTACTGCAGAGGACGATCCTAA 61.553 52.174 23.35 0.00 42.63 2.69
433 434 3.447586 TGAGGTCCTCTGCAGTATTGTAC 59.552 47.826 19.82 4.91 0.00 2.90
451 452 0.682852 TGACGTACTTGGGGTTGAGG 59.317 55.000 0.00 0.00 0.00 3.86
561 562 7.920160 TGCTCATGATCAAACTATAACAACA 57.080 32.000 0.00 0.00 0.00 3.33
797 810 2.019272 GTAGGGGGAGGAGGAGGGA 61.019 68.421 0.00 0.00 0.00 4.20
799 812 2.021652 AGGTAGGGGGAGGAGGAGG 61.022 68.421 0.00 0.00 0.00 4.30
801 814 1.000041 GAGAGGTAGGGGGAGGAGGA 61.000 65.000 0.00 0.00 0.00 3.71
804 817 0.048117 AGAGAGAGGTAGGGGGAGGA 59.952 60.000 0.00 0.00 0.00 3.71
807 820 0.555369 ACCAGAGAGAGGTAGGGGGA 60.555 60.000 0.00 0.00 37.67 4.81
808 821 0.105913 GACCAGAGAGAGGTAGGGGG 60.106 65.000 0.00 0.00 40.09 5.40
809 822 0.105913 GGACCAGAGAGAGGTAGGGG 60.106 65.000 0.00 0.00 40.09 4.79
907 921 3.072468 TAGTCGGGCAAGACGGGG 61.072 66.667 6.69 0.00 45.26 5.73
1933 1999 0.872388 GTACCTGTTTCGGCACTTGG 59.128 55.000 0.00 0.00 0.00 3.61
1934 2000 0.511221 CGTACCTGTTTCGGCACTTG 59.489 55.000 0.00 0.00 0.00 3.16
1946 2012 4.889832 AAATACTACTCGACCGTACCTG 57.110 45.455 0.00 0.00 0.00 4.00
1951 2017 6.512415 CGAGGAAATAAATACTACTCGACCGT 60.512 42.308 5.35 0.00 46.44 4.83
2030 2096 7.692705 CGTCGTTTCTTTTCTTTTCTTTTCTCT 59.307 33.333 0.00 0.00 0.00 3.10
2031 2097 7.511659 GCGTCGTTTCTTTTCTTTTCTTTTCTC 60.512 37.037 0.00 0.00 0.00 2.87
2191 2269 1.134521 TGCCGAAAACAGAGACAGTGT 60.135 47.619 0.00 0.00 0.00 3.55
2209 2287 2.175811 GACACGCATTTCCGGTGC 59.824 61.111 0.00 2.80 39.18 5.01
2214 2292 0.798776 CAGACAGGACACGCATTTCC 59.201 55.000 0.00 0.00 0.00 3.13
2242 2321 3.084039 TGGAAGAACATGTGGATTCTGC 58.916 45.455 0.00 0.00 35.34 4.26
2250 2329 2.217750 TCGGTGTTGGAAGAACATGTG 58.782 47.619 0.00 0.00 32.23 3.21
2263 2342 6.348213 CCTTGACTTCGAATAAAATCGGTGTT 60.348 38.462 0.00 0.00 42.92 3.32
2264 2343 5.121768 CCTTGACTTCGAATAAAATCGGTGT 59.878 40.000 0.00 0.00 42.92 4.16
2266 2345 5.484715 TCCTTGACTTCGAATAAAATCGGT 58.515 37.500 0.00 0.00 42.92 4.69
2267 2346 6.417191 TTCCTTGACTTCGAATAAAATCGG 57.583 37.500 0.00 0.00 42.92 4.18
2275 2354 9.462606 ACCTAAAAATATTCCTTGACTTCGAAT 57.537 29.630 0.00 0.00 0.00 3.34
2276 2355 8.857694 ACCTAAAAATATTCCTTGACTTCGAA 57.142 30.769 0.00 0.00 0.00 3.71
2277 2356 8.857694 AACCTAAAAATATTCCTTGACTTCGA 57.142 30.769 0.00 0.00 0.00 3.71
2294 2373 8.780249 CGTTTCATCTAGGAAAAGAACCTAAAA 58.220 33.333 0.00 0.00 38.13 1.52
2295 2374 7.389607 CCGTTTCATCTAGGAAAAGAACCTAAA 59.610 37.037 4.92 0.00 38.13 1.85
2296 2375 6.877322 CCGTTTCATCTAGGAAAAGAACCTAA 59.123 38.462 4.92 0.00 38.13 2.69
2298 2377 5.012768 TCCGTTTCATCTAGGAAAAGAACCT 59.987 40.000 4.92 0.00 38.13 3.50
2300 2379 6.796705 TTCCGTTTCATCTAGGAAAAGAAC 57.203 37.500 4.92 0.00 39.53 3.01
2301 2380 7.551617 GGTATTCCGTTTCATCTAGGAAAAGAA 59.448 37.037 4.92 5.74 44.71 2.52
2302 2381 7.046033 GGTATTCCGTTTCATCTAGGAAAAGA 58.954 38.462 4.92 0.00 44.71 2.52
2304 2383 6.954232 AGGTATTCCGTTTCATCTAGGAAAA 58.046 36.000 0.00 0.00 44.71 2.29
2306 2385 7.850935 ATAGGTATTCCGTTTCATCTAGGAA 57.149 36.000 0.00 0.00 45.49 3.36
2307 2386 7.850935 AATAGGTATTCCGTTTCATCTAGGA 57.149 36.000 0.00 0.00 39.05 2.94
2350 2429 9.553064 CTAAGTCTATCTGGAATGCTTTTGTAT 57.447 33.333 0.00 0.00 0.00 2.29
2351 2430 7.495934 GCTAAGTCTATCTGGAATGCTTTTGTA 59.504 37.037 0.00 0.00 0.00 2.41
2353 2432 6.317140 TGCTAAGTCTATCTGGAATGCTTTTG 59.683 38.462 0.00 0.00 0.00 2.44
2354 2433 6.418101 TGCTAAGTCTATCTGGAATGCTTTT 58.582 36.000 0.00 0.00 0.00 2.27
2355 2434 5.994250 TGCTAAGTCTATCTGGAATGCTTT 58.006 37.500 0.00 0.00 0.00 3.51
2356 2435 5.620738 TGCTAAGTCTATCTGGAATGCTT 57.379 39.130 0.00 0.00 0.00 3.91
2357 2436 5.620738 TTGCTAAGTCTATCTGGAATGCT 57.379 39.130 0.00 0.00 0.00 3.79
2358 2437 6.683974 TTTTGCTAAGTCTATCTGGAATGC 57.316 37.500 0.00 0.00 0.00 3.56
2385 2587 4.042809 GGGGAATCCAAATGAAACCCTTTT 59.957 41.667 0.09 0.00 40.26 2.27
2387 2589 3.181329 GGGGAATCCAAATGAAACCCTT 58.819 45.455 0.09 0.00 40.26 3.95
2388 2590 2.386811 AGGGGAATCCAAATGAAACCCT 59.613 45.455 0.09 0.00 40.26 4.34
2389 2591 2.832838 AGGGGAATCCAAATGAAACCC 58.167 47.619 0.09 0.00 39.91 4.11
2393 2595 7.236432 TGTTGAAAATAGGGGAATCCAAATGAA 59.764 33.333 0.09 0.00 38.24 2.57
2394 2596 6.728164 TGTTGAAAATAGGGGAATCCAAATGA 59.272 34.615 0.09 0.00 38.24 2.57
2395 2597 6.818142 GTGTTGAAAATAGGGGAATCCAAATG 59.182 38.462 0.09 0.00 38.24 2.32
2403 2605 2.554893 GTGCGTGTTGAAAATAGGGGAA 59.445 45.455 0.00 0.00 0.00 3.97
2404 2606 2.156098 GTGCGTGTTGAAAATAGGGGA 58.844 47.619 0.00 0.00 0.00 4.81
2405 2607 2.159382 AGTGCGTGTTGAAAATAGGGG 58.841 47.619 0.00 0.00 0.00 4.79
2406 2608 3.074412 AGAGTGCGTGTTGAAAATAGGG 58.926 45.455 0.00 0.00 0.00 3.53
2407 2609 5.618561 GTTAGAGTGCGTGTTGAAAATAGG 58.381 41.667 0.00 0.00 0.00 2.57
2408 2610 5.107607 ACGTTAGAGTGCGTGTTGAAAATAG 60.108 40.000 0.00 0.00 40.03 1.73
2409 2611 4.746115 ACGTTAGAGTGCGTGTTGAAAATA 59.254 37.500 0.00 0.00 40.03 1.40
2411 2613 2.931325 ACGTTAGAGTGCGTGTTGAAAA 59.069 40.909 0.00 0.00 40.03 2.29
2414 2616 3.951115 ACGTTAGAGTGCGTGTTGA 57.049 47.368 0.00 0.00 40.03 3.18
2422 2624 1.442769 AGCAATGGCACGTTAGAGTG 58.557 50.000 0.00 0.00 44.61 3.51
2423 2625 2.076863 GAAGCAATGGCACGTTAGAGT 58.923 47.619 0.00 0.00 44.61 3.24
2424 2626 1.398390 GGAAGCAATGGCACGTTAGAG 59.602 52.381 0.00 0.00 44.61 2.43
2426 2628 1.131126 CAGGAAGCAATGGCACGTTAG 59.869 52.381 0.00 0.00 44.61 2.34
2427 2629 1.164411 CAGGAAGCAATGGCACGTTA 58.836 50.000 0.00 0.00 44.61 3.18
2428 2630 1.526575 CCAGGAAGCAATGGCACGTT 61.527 55.000 0.00 0.00 44.61 3.99
2429 2631 1.973281 CCAGGAAGCAATGGCACGT 60.973 57.895 0.00 0.00 44.61 4.49
2430 2632 1.033746 ATCCAGGAAGCAATGGCACG 61.034 55.000 0.00 0.00 44.61 5.34
2432 2634 1.941377 AAATCCAGGAAGCAATGGCA 58.059 45.000 0.00 0.00 44.61 4.92
2433 2635 4.099881 TGATAAAATCCAGGAAGCAATGGC 59.900 41.667 0.00 0.00 36.47 4.40
2434 2636 5.857471 TGATAAAATCCAGGAAGCAATGG 57.143 39.130 0.00 0.00 37.97 3.16
2435 2637 7.104043 TCTTGATAAAATCCAGGAAGCAATG 57.896 36.000 0.00 0.00 0.00 2.82
2437 2639 6.153340 CCTTCTTGATAAAATCCAGGAAGCAA 59.847 38.462 0.00 0.00 41.94 3.91
2438 2640 5.653769 CCTTCTTGATAAAATCCAGGAAGCA 59.346 40.000 0.00 0.00 41.94 3.91
2439 2641 5.068329 CCCTTCTTGATAAAATCCAGGAAGC 59.932 44.000 0.00 0.00 41.94 3.86
2441 2643 6.401537 TCCCTTCTTGATAAAATCCAGGAA 57.598 37.500 0.00 0.00 0.00 3.36
2445 2647 5.719563 GGGTTTCCCTTCTTGATAAAATCCA 59.280 40.000 0.00 0.00 41.34 3.41
2446 2648 6.222038 GGGTTTCCCTTCTTGATAAAATCC 57.778 41.667 0.00 0.00 41.34 3.01
2464 2821 0.402121 GTCCTCTGAAGCTGGGGTTT 59.598 55.000 0.00 0.00 0.00 3.27
2465 2822 0.474660 AGTCCTCTGAAGCTGGGGTT 60.475 55.000 0.00 0.00 0.00 4.11
2466 2823 0.474660 AAGTCCTCTGAAGCTGGGGT 60.475 55.000 0.00 0.00 0.00 4.95
2467 2824 0.695347 AAAGTCCTCTGAAGCTGGGG 59.305 55.000 0.00 0.00 0.00 4.96
2468 2825 3.922171 ATAAAGTCCTCTGAAGCTGGG 57.078 47.619 0.00 0.00 0.00 4.45
2469 2826 5.238214 GCATAATAAAGTCCTCTGAAGCTGG 59.762 44.000 0.00 0.00 0.00 4.85
2472 2829 6.051717 TCTGCATAATAAAGTCCTCTGAAGC 58.948 40.000 0.00 0.00 0.00 3.86
2473 2830 8.498054 TTTCTGCATAATAAAGTCCTCTGAAG 57.502 34.615 0.00 0.00 0.00 3.02
2474 2831 8.730680 GTTTTCTGCATAATAAAGTCCTCTGAA 58.269 33.333 0.00 0.00 0.00 3.02
2475 2832 7.882791 TGTTTTCTGCATAATAAAGTCCTCTGA 59.117 33.333 0.00 0.00 0.00 3.27
2477 2834 8.103305 TCTGTTTTCTGCATAATAAAGTCCTCT 58.897 33.333 0.00 0.00 0.00 3.69
2478 2835 8.268850 TCTGTTTTCTGCATAATAAAGTCCTC 57.731 34.615 0.00 0.00 0.00 3.71
2479 2836 8.103305 TCTCTGTTTTCTGCATAATAAAGTCCT 58.897 33.333 0.00 0.00 0.00 3.85
2480 2837 8.268850 TCTCTGTTTTCTGCATAATAAAGTCC 57.731 34.615 0.00 0.00 0.00 3.85
2481 2838 9.766277 CTTCTCTGTTTTCTGCATAATAAAGTC 57.234 33.333 0.00 0.00 0.00 3.01
2483 2840 9.552114 CACTTCTCTGTTTTCTGCATAATAAAG 57.448 33.333 0.00 0.00 0.00 1.85
2487 2844 5.474532 TGCACTTCTCTGTTTTCTGCATAAT 59.525 36.000 0.00 0.00 0.00 1.28
2488 2845 4.821260 TGCACTTCTCTGTTTTCTGCATAA 59.179 37.500 0.00 0.00 0.00 1.90
2491 2848 2.642427 TGCACTTCTCTGTTTTCTGCA 58.358 42.857 0.00 0.00 0.00 4.41
2492 2849 3.911661 ATGCACTTCTCTGTTTTCTGC 57.088 42.857 0.00 0.00 0.00 4.26
2494 2851 7.119846 GGTGTAATATGCACTTCTCTGTTTTCT 59.880 37.037 9.60 0.00 37.07 2.52
2496 2853 6.151144 GGGTGTAATATGCACTTCTCTGTTTT 59.849 38.462 9.60 0.00 37.07 2.43
2497 2854 5.648092 GGGTGTAATATGCACTTCTCTGTTT 59.352 40.000 9.60 0.00 37.07 2.83
2498 2855 5.186198 GGGTGTAATATGCACTTCTCTGTT 58.814 41.667 9.60 0.00 37.07 3.16
2499 2856 4.384208 GGGGTGTAATATGCACTTCTCTGT 60.384 45.833 9.60 0.00 37.07 3.41
2500 2857 4.130118 GGGGTGTAATATGCACTTCTCTG 58.870 47.826 9.60 0.00 37.07 3.35
2501 2858 4.040755 AGGGGTGTAATATGCACTTCTCT 58.959 43.478 9.60 0.00 37.07 3.10
2502 2859 4.141711 TGAGGGGTGTAATATGCACTTCTC 60.142 45.833 16.64 16.64 36.92 2.87
2503 2860 3.780294 TGAGGGGTGTAATATGCACTTCT 59.220 43.478 9.60 7.75 37.07 2.85
2505 2862 4.584638 TTGAGGGGTGTAATATGCACTT 57.415 40.909 9.60 0.00 37.07 3.16
2506 2863 4.796110 ATTGAGGGGTGTAATATGCACT 57.204 40.909 9.60 0.00 37.07 4.40
2508 2865 5.387113 AGAATTGAGGGGTGTAATATGCA 57.613 39.130 0.00 0.00 0.00 3.96
2511 2868 6.763715 TGCTAGAATTGAGGGGTGTAATAT 57.236 37.500 0.00 0.00 0.00 1.28
2512 2869 6.763715 ATGCTAGAATTGAGGGGTGTAATA 57.236 37.500 0.00 0.00 0.00 0.98
2513 2870 5.653255 ATGCTAGAATTGAGGGGTGTAAT 57.347 39.130 0.00 0.00 0.00 1.89
2515 2872 5.192927 CAAATGCTAGAATTGAGGGGTGTA 58.807 41.667 0.00 0.00 0.00 2.90
2516 2873 4.019174 CAAATGCTAGAATTGAGGGGTGT 58.981 43.478 0.00 0.00 0.00 4.16
2518 2875 4.322057 ACAAATGCTAGAATTGAGGGGT 57.678 40.909 0.00 0.00 0.00 4.95
2519 2876 5.665916 AAACAAATGCTAGAATTGAGGGG 57.334 39.130 0.00 0.00 0.00 4.79
2520 2877 8.055279 TCTTAAACAAATGCTAGAATTGAGGG 57.945 34.615 0.00 0.00 0.00 4.30
2527 2884 8.736244 GGGTGTATTCTTAAACAAATGCTAGAA 58.264 33.333 0.00 0.00 0.00 2.10
2528 2885 7.338449 GGGGTGTATTCTTAAACAAATGCTAGA 59.662 37.037 0.00 0.00 0.00 2.43
2529 2886 7.416326 GGGGGTGTATTCTTAAACAAATGCTAG 60.416 40.741 0.00 0.00 0.00 3.42
2530 2887 6.378848 GGGGGTGTATTCTTAAACAAATGCTA 59.621 38.462 0.00 0.00 0.00 3.49
2531 2888 5.186992 GGGGGTGTATTCTTAAACAAATGCT 59.813 40.000 0.00 0.00 0.00 3.79
2532 2889 5.046950 TGGGGGTGTATTCTTAAACAAATGC 60.047 40.000 0.00 0.00 0.00 3.56
2533 2890 6.597832 TGGGGGTGTATTCTTAAACAAATG 57.402 37.500 0.00 0.00 0.00 2.32
2534 2891 6.555360 TGTTGGGGGTGTATTCTTAAACAAAT 59.445 34.615 0.00 0.00 0.00 2.32
2535 2892 5.897824 TGTTGGGGGTGTATTCTTAAACAAA 59.102 36.000 0.00 0.00 0.00 2.83
2536 2893 5.455872 TGTTGGGGGTGTATTCTTAAACAA 58.544 37.500 0.00 0.00 0.00 2.83
2537 2894 5.063017 TGTTGGGGGTGTATTCTTAAACA 57.937 39.130 0.00 0.00 0.00 2.83
2538 2895 5.279106 GGTTGTTGGGGGTGTATTCTTAAAC 60.279 44.000 0.00 0.00 0.00 2.01
2539 2896 4.833938 GGTTGTTGGGGGTGTATTCTTAAA 59.166 41.667 0.00 0.00 0.00 1.52
2540 2897 4.140994 TGGTTGTTGGGGGTGTATTCTTAA 60.141 41.667 0.00 0.00 0.00 1.85
2541 2898 3.398292 TGGTTGTTGGGGGTGTATTCTTA 59.602 43.478 0.00 0.00 0.00 2.10
2542 2899 2.178106 TGGTTGTTGGGGGTGTATTCTT 59.822 45.455 0.00 0.00 0.00 2.52
2543 2900 1.783979 TGGTTGTTGGGGGTGTATTCT 59.216 47.619 0.00 0.00 0.00 2.40
2544 2901 2.167662 CTGGTTGTTGGGGGTGTATTC 58.832 52.381 0.00 0.00 0.00 1.75
2545 2902 1.783979 TCTGGTTGTTGGGGGTGTATT 59.216 47.619 0.00 0.00 0.00 1.89
2546 2903 1.074889 GTCTGGTTGTTGGGGGTGTAT 59.925 52.381 0.00 0.00 0.00 2.29
2547 2904 0.475044 GTCTGGTTGTTGGGGGTGTA 59.525 55.000 0.00 0.00 0.00 2.90
2548 2905 1.229076 GTCTGGTTGTTGGGGGTGT 59.771 57.895 0.00 0.00 0.00 4.16
2549 2906 0.823356 CTGTCTGGTTGTTGGGGGTG 60.823 60.000 0.00 0.00 0.00 4.61
2550 2907 0.991355 TCTGTCTGGTTGTTGGGGGT 60.991 55.000 0.00 0.00 0.00 4.95
2551 2908 0.184933 TTCTGTCTGGTTGTTGGGGG 59.815 55.000 0.00 0.00 0.00 5.40
2552 2909 2.292828 ATTCTGTCTGGTTGTTGGGG 57.707 50.000 0.00 0.00 0.00 4.96
2553 2910 3.750371 TGTATTCTGTCTGGTTGTTGGG 58.250 45.455 0.00 0.00 0.00 4.12
2554 2911 4.023193 GGTTGTATTCTGTCTGGTTGTTGG 60.023 45.833 0.00 0.00 0.00 3.77
2555 2912 4.023193 GGGTTGTATTCTGTCTGGTTGTTG 60.023 45.833 0.00 0.00 0.00 3.33
2556 2913 4.141251 AGGGTTGTATTCTGTCTGGTTGTT 60.141 41.667 0.00 0.00 0.00 2.83
2557 2914 3.394606 AGGGTTGTATTCTGTCTGGTTGT 59.605 43.478 0.00 0.00 0.00 3.32
2558 2915 4.003648 GAGGGTTGTATTCTGTCTGGTTG 58.996 47.826 0.00 0.00 0.00 3.77
2559 2916 3.009143 GGAGGGTTGTATTCTGTCTGGTT 59.991 47.826 0.00 0.00 0.00 3.67
2560 2917 2.572104 GGAGGGTTGTATTCTGTCTGGT 59.428 50.000 0.00 0.00 0.00 4.00
2561 2918 2.840651 AGGAGGGTTGTATTCTGTCTGG 59.159 50.000 0.00 0.00 0.00 3.86
2562 2919 3.772025 AGAGGAGGGTTGTATTCTGTCTG 59.228 47.826 0.00 0.00 0.00 3.51
2563 2920 4.027437 GAGAGGAGGGTTGTATTCTGTCT 58.973 47.826 0.00 0.00 0.00 3.41
2564 2921 3.133183 GGAGAGGAGGGTTGTATTCTGTC 59.867 52.174 0.00 0.00 0.00 3.51
2565 2922 3.108376 GGAGAGGAGGGTTGTATTCTGT 58.892 50.000 0.00 0.00 0.00 3.41
2566 2923 2.436173 GGGAGAGGAGGGTTGTATTCTG 59.564 54.545 0.00 0.00 0.00 3.02
2567 2924 2.629909 GGGGAGAGGAGGGTTGTATTCT 60.630 54.545 0.00 0.00 0.00 2.40
2568 2925 1.769465 GGGGAGAGGAGGGTTGTATTC 59.231 57.143 0.00 0.00 0.00 1.75
2569 2926 1.894699 GGGGAGAGGAGGGTTGTATT 58.105 55.000 0.00 0.00 0.00 1.89
2570 2927 0.398664 CGGGGAGAGGAGGGTTGTAT 60.399 60.000 0.00 0.00 0.00 2.29
2571 2928 1.001248 CGGGGAGAGGAGGGTTGTA 59.999 63.158 0.00 0.00 0.00 2.41
2572 2929 2.284699 CGGGGAGAGGAGGGTTGT 60.285 66.667 0.00 0.00 0.00 3.32
2573 2930 1.918800 AACGGGGAGAGGAGGGTTG 60.919 63.158 0.00 0.00 0.00 3.77
2574 2931 1.918800 CAACGGGGAGAGGAGGGTT 60.919 63.158 0.00 0.00 0.00 4.11
2575 2932 2.284699 CAACGGGGAGAGGAGGGT 60.285 66.667 0.00 0.00 0.00 4.34
2576 2933 2.038975 TCAACGGGGAGAGGAGGG 59.961 66.667 0.00 0.00 0.00 4.30
2577 2934 2.359967 GGTCAACGGGGAGAGGAGG 61.360 68.421 0.00 0.00 0.00 4.30
2578 2935 2.711922 CGGTCAACGGGGAGAGGAG 61.712 68.421 0.00 0.00 39.42 3.69
2579 2936 2.678934 CGGTCAACGGGGAGAGGA 60.679 66.667 0.00 0.00 39.42 3.71
2588 2945 1.202054 ACGTTTCAAAACCGGTCAACG 60.202 47.619 23.32 23.32 42.05 4.10
2589 2946 2.547913 ACGTTTCAAAACCGGTCAAC 57.452 45.000 8.04 5.55 35.51 3.18
2590 2947 2.486982 TCAACGTTTCAAAACCGGTCAA 59.513 40.909 8.04 0.00 35.51 3.18
2591 2948 2.082231 TCAACGTTTCAAAACCGGTCA 58.918 42.857 8.04 0.00 35.51 4.02
2592 2949 2.096335 AGTCAACGTTTCAAAACCGGTC 59.904 45.455 8.04 0.00 35.51 4.79
2593 2950 2.086094 AGTCAACGTTTCAAAACCGGT 58.914 42.857 0.00 0.00 35.51 5.28
2594 2951 2.446282 CAGTCAACGTTTCAAAACCGG 58.554 47.619 0.00 0.00 35.51 5.28
2595 2952 2.096174 TCCAGTCAACGTTTCAAAACCG 59.904 45.455 0.00 0.00 35.51 4.44
2596 2953 3.128068 ACTCCAGTCAACGTTTCAAAACC 59.872 43.478 0.00 0.00 35.51 3.27
2597 2954 4.095610 CACTCCAGTCAACGTTTCAAAAC 58.904 43.478 0.00 0.00 35.59 2.43
2598 2955 4.004314 TCACTCCAGTCAACGTTTCAAAA 58.996 39.130 0.00 0.00 0.00 2.44
2599 2956 3.601435 TCACTCCAGTCAACGTTTCAAA 58.399 40.909 0.00 0.00 0.00 2.69
2600 2957 3.254470 TCACTCCAGTCAACGTTTCAA 57.746 42.857 0.00 0.00 0.00 2.69
2601 2958 2.933906 GTTCACTCCAGTCAACGTTTCA 59.066 45.455 0.00 0.00 0.00 2.69
2602 2959 2.933906 TGTTCACTCCAGTCAACGTTTC 59.066 45.455 0.00 0.00 31.32 2.78
2603 2960 2.936498 CTGTTCACTCCAGTCAACGTTT 59.064 45.455 0.00 0.00 31.32 3.60
2604 2961 2.093658 ACTGTTCACTCCAGTCAACGTT 60.094 45.455 0.00 0.00 38.81 3.99
2605 2962 1.480954 ACTGTTCACTCCAGTCAACGT 59.519 47.619 0.00 0.00 38.81 3.99
2606 2963 2.225068 ACTGTTCACTCCAGTCAACG 57.775 50.000 0.00 0.00 38.81 4.10
2607 2964 6.564125 CGAATTTACTGTTCACTCCAGTCAAC 60.564 42.308 0.00 0.00 42.03 3.18
2608 2965 5.465390 CGAATTTACTGTTCACTCCAGTCAA 59.535 40.000 0.00 0.00 42.03 3.18
2609 2966 4.988540 CGAATTTACTGTTCACTCCAGTCA 59.011 41.667 0.00 0.00 42.03 3.41
2610 2967 5.227908 TCGAATTTACTGTTCACTCCAGTC 58.772 41.667 0.00 0.00 42.03 3.51
2611 2968 5.209818 TCGAATTTACTGTTCACTCCAGT 57.790 39.130 0.00 0.00 44.90 4.00
2612 2969 6.423905 TCTTTCGAATTTACTGTTCACTCCAG 59.576 38.462 0.00 0.00 36.01 3.86
2613 2970 6.285224 TCTTTCGAATTTACTGTTCACTCCA 58.715 36.000 0.00 0.00 0.00 3.86
2614 2971 6.780706 TCTTTCGAATTTACTGTTCACTCC 57.219 37.500 0.00 0.00 0.00 3.85
2665 3022 9.790344 TCACCCAATGAAATAATGAAAATTGTT 57.210 25.926 0.00 0.00 33.02 2.83
2680 3037 5.441500 TCAGTTTACTGTTCACCCAATGAA 58.558 37.500 9.53 0.00 42.58 2.57
2681 3038 5.042463 TCAGTTTACTGTTCACCCAATGA 57.958 39.130 9.53 0.00 44.12 2.57
2682 3039 5.766150 TTCAGTTTACTGTTCACCCAATG 57.234 39.130 9.53 0.00 44.12 2.82
2683 3040 6.605594 TCTTTTCAGTTTACTGTTCACCCAAT 59.394 34.615 9.53 0.00 44.12 3.16
2686 3043 6.445357 TTCTTTTCAGTTTACTGTTCACCC 57.555 37.500 9.53 0.00 44.12 4.61
2687 3044 8.926715 AATTTCTTTTCAGTTTACTGTTCACC 57.073 30.769 9.53 0.00 44.12 4.02


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

AutoCloner maintained by Alex Coulton.