Multiple sequence alignment - TraesCS2D01G371700

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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 TraesCS2D01G371700 chr2D 100.000 2932 0 0 1 2932 476016520 476019451 0.000000e+00 5415.0
1 TraesCS2D01G371700 chr2D 77.753 454 79 20 1467 1909 475985216 475985658 2.900000e-65 259.0
2 TraesCS2D01G371700 chr2D 77.243 457 82 20 1467 1912 475877262 475877707 6.270000e-62 248.0
3 TraesCS2D01G371700 chr2D 91.379 174 14 1 2398 2571 618294604 618294776 1.360000e-58 237.0
4 TraesCS2D01G371700 chr2D 90.230 174 16 1 2398 2571 575230411 575230583 2.940000e-55 226.0
5 TraesCS2D01G371700 chr2D 85.714 56 5 3 2341 2394 410234293 410234239 4.080000e-04 56.5
6 TraesCS2D01G371700 chr2A 93.458 2308 91 17 1 2268 617822848 617825135 0.000000e+00 3371.0
7 TraesCS2D01G371700 chr2A 89.456 294 26 3 2613 2906 617825130 617825418 1.660000e-97 366.0
8 TraesCS2D01G371700 chr2A 89.773 176 15 2 2398 2571 197420156 197419982 3.800000e-54 222.0
9 TraesCS2D01G371700 chr2B 91.408 2386 83 34 1 2329 556692218 556694538 0.000000e+00 3158.0
10 TraesCS2D01G371700 chr2B 88.745 231 20 6 2570 2799 556694525 556694750 8.000000e-71 278.0
11 TraesCS2D01G371700 chr2B 77.974 454 82 16 1467 1911 556596098 556596542 4.820000e-68 268.0
12 TraesCS2D01G371700 chr2B 77.706 462 80 20 1467 1917 556517600 556518049 8.060000e-66 261.0
13 TraesCS2D01G371700 chr2B 90.230 174 16 1 2398 2571 105849922 105849750 2.940000e-55 226.0
14 TraesCS2D01G371700 chr6A 87.104 442 57 0 1467 1908 441807244 441806803 4.360000e-138 501.0
15 TraesCS2D01G371700 chr6A 76.445 467 93 16 1463 1921 442037406 442036949 1.360000e-58 237.0
16 TraesCS2D01G371700 chr6D 86.652 442 59 0 1467 1908 306203578 306203137 9.440000e-135 490.0
17 TraesCS2D01G371700 chr6D 89.714 175 16 2 2398 2571 471006798 471006971 3.800000e-54 222.0
18 TraesCS2D01G371700 chr6B 86.199 442 61 0 1467 1908 473215316 473214875 2.040000e-131 479.0
19 TraesCS2D01G371700 chr7D 90.909 176 15 1 2398 2573 201830970 201831144 4.890000e-58 235.0
20 TraesCS2D01G371700 chr7D 92.857 56 3 1 2342 2396 440595310 440595255 2.420000e-11 80.5
21 TraesCS2D01G371700 chr1B 90.286 175 15 2 2398 2571 683992000 683992173 8.170000e-56 228.0
22 TraesCS2D01G371700 chr3D 90.230 174 16 1 2398 2571 287339498 287339670 2.940000e-55 226.0
23 TraesCS2D01G371700 chr3D 89.143 175 18 1 2398 2571 21444225 21444399 1.770000e-52 217.0
24 TraesCS2D01G371700 chr4B 89.474 57 4 2 2339 2394 574227963 574228018 1.460000e-08 71.3
25 TraesCS2D01G371700 chr5D 88.889 54 5 1 2342 2394 521623277 521623224 6.780000e-07 65.8
26 TraesCS2D01G371700 chr1A 88.889 54 5 1 2342 2394 493297323 493297270 6.780000e-07 65.8
27 TraesCS2D01G371700 chr4A 87.500 56 6 1 2342 2396 130499781 130499726 2.440000e-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 TraesCS2D01G371700 chr2D 476016520 476019451 2931 False 5415.0 5415 100.0000 1 2932 1 chr2D.!!$F3 2931
1 TraesCS2D01G371700 chr2A 617822848 617825418 2570 False 1868.5 3371 91.4570 1 2906 2 chr2A.!!$F1 2905
2 TraesCS2D01G371700 chr2B 556692218 556694750 2532 False 1718.0 3158 90.0765 1 2799 2 chr2B.!!$F3 2798

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
830 917 0.039618 AAAAGGATCCACCACCGCAT 59.96 50.0 15.82 0.0 42.04 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2440 0.033228 CAATTGGTTTGCGGCCTGAA 59.967 50.0 0.0 0.0 0.0 3.02 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
43 44 2.949644 AGTACCAACTGCCAAACTGTTC 59.050 45.455 0.00 0.00 38.27 3.18
129 130 0.666374 GTTTTCCCTGGTTCCACGTG 59.334 55.000 9.08 9.08 0.00 4.49
150 151 4.219944 GTGGATGAATTGATGGATCATGGG 59.780 45.833 0.00 0.00 36.56 4.00
202 226 2.030562 CCTTGCGTTGGACCGTCT 59.969 61.111 0.00 0.00 0.00 4.18
268 295 5.579904 GTGCATGCAGATATATGGTCTACAG 59.420 44.000 23.41 0.00 0.00 2.74
273 300 6.010219 TGCAGATATATGGTCTACAGCTACA 58.990 40.000 0.00 0.00 0.00 2.74
338 397 2.153039 TGCAATGCACGAGACGAAG 58.847 52.632 2.72 0.00 31.71 3.79
339 398 0.319469 TGCAATGCACGAGACGAAGA 60.319 50.000 2.72 0.00 31.71 2.87
340 399 0.790207 GCAATGCACGAGACGAAGAA 59.210 50.000 0.00 0.00 0.00 2.52
372 431 1.970114 GGCATGGCATCGATCCCTG 60.970 63.158 15.47 10.10 0.00 4.45
381 440 2.478539 GCATCGATCCCTGCAAGAAAAC 60.479 50.000 3.89 0.00 38.28 2.43
382 441 2.859165 TCGATCCCTGCAAGAAAACT 57.141 45.000 0.00 0.00 34.07 2.66
383 442 3.140325 TCGATCCCTGCAAGAAAACTT 57.860 42.857 0.00 0.00 34.07 2.66
384 443 4.280436 TCGATCCCTGCAAGAAAACTTA 57.720 40.909 0.00 0.00 34.07 2.24
385 444 4.843728 TCGATCCCTGCAAGAAAACTTAT 58.156 39.130 0.00 0.00 34.07 1.73
386 445 4.635765 TCGATCCCTGCAAGAAAACTTATG 59.364 41.667 0.00 0.00 34.07 1.90
387 446 4.676546 GATCCCTGCAAGAAAACTTATGC 58.323 43.478 0.00 0.00 39.22 3.14
388 447 3.495331 TCCCTGCAAGAAAACTTATGCA 58.505 40.909 0.00 0.00 45.75 3.96
389 448 4.088634 TCCCTGCAAGAAAACTTATGCAT 58.911 39.130 3.79 3.79 46.59 3.96
390 449 4.158394 TCCCTGCAAGAAAACTTATGCATC 59.842 41.667 0.19 0.00 46.59 3.91
391 450 4.427312 CCTGCAAGAAAACTTATGCATCC 58.573 43.478 0.19 0.00 46.59 3.51
392 451 4.159135 CCTGCAAGAAAACTTATGCATCCT 59.841 41.667 0.19 0.00 46.59 3.24
393 452 5.357878 CCTGCAAGAAAACTTATGCATCCTA 59.642 40.000 0.19 0.00 46.59 2.94
706 783 3.840437 GGCCATGCCGAATTAGCA 58.160 55.556 0.00 5.19 45.94 3.49
712 789 1.067516 CATGCCGAATTAGCAAAGGGG 59.932 52.381 6.72 0.00 44.83 4.79
829 916 0.893270 CAAAAGGATCCACCACCGCA 60.893 55.000 15.82 0.00 42.04 5.69
830 917 0.039618 AAAAGGATCCACCACCGCAT 59.960 50.000 15.82 0.00 42.04 4.73
920 1007 2.156917 GCTAAGTTAACCCACCACCAC 58.843 52.381 0.88 0.00 0.00 4.16
923 1010 0.476771 AGTTAACCCACCACCACCAG 59.523 55.000 0.88 0.00 0.00 4.00
925 1012 2.684192 TTAACCCACCACCACCAGCG 62.684 60.000 0.00 0.00 0.00 5.18
962 1057 2.499685 GCGGGCCTAGTTGATCGT 59.500 61.111 0.84 0.00 0.00 3.73
963 1058 1.737816 GCGGGCCTAGTTGATCGTA 59.262 57.895 0.84 0.00 0.00 3.43
1056 1151 1.079336 GGTGACCTCCAAGGCGTAC 60.079 63.158 0.00 0.00 39.63 3.67
1062 1157 1.111116 CCTCCAAGGCGTACGGGATA 61.111 60.000 18.39 0.00 0.00 2.59
1110 1205 1.738099 CCAGTCGTTCAGGAAGGCG 60.738 63.158 0.00 0.00 0.00 5.52
1384 1482 3.786809 TGAGTAGCACACGCACTAC 57.213 52.632 0.00 0.00 42.27 2.73
1385 1483 0.242825 TGAGTAGCACACGCACTACC 59.757 55.000 0.00 0.00 39.69 3.18
1413 1511 7.112565 GTGCATATATGTTTCTTCTGCAATTCG 59.887 37.037 14.14 0.00 39.56 3.34
1423 1530 0.516877 CTGCAATTCGACGGCTTGAA 59.483 50.000 12.52 3.47 0.00 2.69
1424 1531 0.947960 TGCAATTCGACGGCTTGAAA 59.052 45.000 12.52 0.00 0.00 2.69
1493 1600 1.298382 ACCCTGGGTCCCAAGATATCT 59.702 52.381 14.05 0.00 30.80 1.98
1717 1824 1.074090 TCACTGTCACCTCCCCCAA 60.074 57.895 0.00 0.00 0.00 4.12
1829 1936 1.132643 GAGAAGTACATCCACGTCGCT 59.867 52.381 0.00 0.00 32.91 4.93
2023 2133 2.983725 AAGTGGAGTTGTGGGCTGCC 62.984 60.000 11.05 11.05 0.00 4.85
2024 2134 4.641645 TGGAGTTGTGGGCTGCCG 62.642 66.667 13.40 0.00 0.00 5.69
2107 2217 3.717707 TCTTATTTCGGATCGGAGCAAG 58.282 45.455 2.99 8.18 0.00 4.01
2110 2220 3.536956 ATTTCGGATCGGAGCAAGTTA 57.463 42.857 2.99 0.00 0.00 2.24
2133 2243 1.426041 CCTTCCGCGTACGATTTGGG 61.426 60.000 21.65 10.78 43.93 4.12
2241 2351 9.255304 GAAAGGCAGTTGTTCAAAATTATTGTA 57.745 29.630 0.00 0.00 0.00 2.41
2328 2438 6.583562 ACAATTGAACCTACTAGTATCAGGC 58.416 40.000 13.59 0.00 32.31 4.85
2329 2439 6.156256 ACAATTGAACCTACTAGTATCAGGCA 59.844 38.462 13.59 0.00 32.31 4.75
2330 2440 7.147479 ACAATTGAACCTACTAGTATCAGGCAT 60.147 37.037 13.59 0.34 32.31 4.40
2331 2441 6.808321 TTGAACCTACTAGTATCAGGCATT 57.192 37.500 9.70 0.00 32.31 3.56
2332 2442 6.406692 TGAACCTACTAGTATCAGGCATTC 57.593 41.667 9.70 7.92 32.31 2.67
2333 2443 5.897250 TGAACCTACTAGTATCAGGCATTCA 59.103 40.000 9.70 9.99 32.31 2.57
2334 2444 6.040955 TGAACCTACTAGTATCAGGCATTCAG 59.959 42.308 9.70 0.00 32.31 3.02
2335 2445 4.835615 ACCTACTAGTATCAGGCATTCAGG 59.164 45.833 9.70 4.53 32.31 3.86
2336 2446 3.760580 ACTAGTATCAGGCATTCAGGC 57.239 47.619 0.00 0.00 44.61 4.85
2343 2453 2.125952 GGCATTCAGGCCGCAAAC 60.126 61.111 0.00 0.00 45.40 2.93
2344 2454 2.125952 GCATTCAGGCCGCAAACC 60.126 61.111 0.00 0.00 0.00 3.27
2345 2455 2.929903 GCATTCAGGCCGCAAACCA 61.930 57.895 0.00 0.00 0.00 3.67
2346 2456 1.664873 CATTCAGGCCGCAAACCAA 59.335 52.632 0.00 0.00 0.00 3.67
2347 2457 0.247185 CATTCAGGCCGCAAACCAAT 59.753 50.000 0.00 0.00 0.00 3.16
2348 2458 0.975887 ATTCAGGCCGCAAACCAATT 59.024 45.000 0.00 0.00 0.00 2.32
2349 2459 0.033228 TTCAGGCCGCAAACCAATTG 59.967 50.000 0.00 0.00 42.21 2.32
2350 2460 1.112315 TCAGGCCGCAAACCAATTGT 61.112 50.000 4.43 0.00 41.32 2.71
2351 2461 0.945265 CAGGCCGCAAACCAATTGTG 60.945 55.000 4.43 0.00 46.78 3.33
2366 2476 5.314923 CAATTGTGGTTGGATGGTTAGAG 57.685 43.478 0.00 0.00 0.00 2.43
2367 2477 4.927267 ATTGTGGTTGGATGGTTAGAGA 57.073 40.909 0.00 0.00 0.00 3.10
2368 2478 3.981071 TGTGGTTGGATGGTTAGAGAG 57.019 47.619 0.00 0.00 0.00 3.20
2369 2479 3.516586 TGTGGTTGGATGGTTAGAGAGA 58.483 45.455 0.00 0.00 0.00 3.10
2370 2480 3.260884 TGTGGTTGGATGGTTAGAGAGAC 59.739 47.826 0.00 0.00 0.00 3.36
2371 2481 3.515901 GTGGTTGGATGGTTAGAGAGACT 59.484 47.826 0.00 0.00 0.00 3.24
2372 2482 4.710375 GTGGTTGGATGGTTAGAGAGACTA 59.290 45.833 0.00 0.00 0.00 2.59
2373 2483 5.364157 GTGGTTGGATGGTTAGAGAGACTAT 59.636 44.000 0.00 0.00 0.00 2.12
2374 2484 5.363868 TGGTTGGATGGTTAGAGAGACTATG 59.636 44.000 0.00 0.00 0.00 2.23
2375 2485 5.221541 GGTTGGATGGTTAGAGAGACTATGG 60.222 48.000 0.00 0.00 0.00 2.74
2376 2486 5.144159 TGGATGGTTAGAGAGACTATGGT 57.856 43.478 0.00 0.00 0.00 3.55
2377 2487 6.275692 TGGATGGTTAGAGAGACTATGGTA 57.724 41.667 0.00 0.00 0.00 3.25
2378 2488 6.864421 TGGATGGTTAGAGAGACTATGGTAT 58.136 40.000 0.00 0.00 0.00 2.73
2379 2489 7.306013 TGGATGGTTAGAGAGACTATGGTATT 58.694 38.462 0.00 0.00 0.00 1.89
2380 2490 7.451877 TGGATGGTTAGAGAGACTATGGTATTC 59.548 40.741 0.00 0.00 0.00 1.75
2381 2491 7.093684 GGATGGTTAGAGAGACTATGGTATTCC 60.094 44.444 0.00 0.00 0.00 3.01
2393 2503 3.380471 TGGTATTCCAAACCCATCAGG 57.620 47.619 0.00 0.00 41.25 3.86
2394 2504 2.922955 TGGTATTCCAAACCCATCAGGA 59.077 45.455 0.00 0.00 41.25 3.86
2395 2505 3.531397 TGGTATTCCAAACCCATCAGGAT 59.469 43.478 0.00 0.00 41.25 3.24
2396 2506 4.729370 TGGTATTCCAAACCCATCAGGATA 59.271 41.667 0.00 0.00 41.25 2.59
2397 2507 5.163099 TGGTATTCCAAACCCATCAGGATAG 60.163 44.000 0.00 0.00 41.25 2.08
2398 2508 5.073144 GGTATTCCAAACCCATCAGGATAGA 59.927 44.000 0.00 0.00 39.89 1.98
2399 2509 4.778213 TTCCAAACCCATCAGGATAGAG 57.222 45.455 0.00 0.00 39.89 2.43
2400 2510 4.007581 TCCAAACCCATCAGGATAGAGA 57.992 45.455 0.00 0.00 39.89 3.10
2401 2511 4.570926 TCCAAACCCATCAGGATAGAGAT 58.429 43.478 0.00 0.00 39.89 2.75
2402 2512 4.349048 TCCAAACCCATCAGGATAGAGATG 59.651 45.833 0.00 0.00 40.94 2.90
2403 2513 4.103785 CCAAACCCATCAGGATAGAGATGT 59.896 45.833 0.00 0.00 39.92 3.06
2404 2514 5.398353 CCAAACCCATCAGGATAGAGATGTT 60.398 44.000 0.00 0.00 39.92 2.71
2405 2515 5.559148 AACCCATCAGGATAGAGATGTTC 57.441 43.478 0.00 0.00 39.92 3.18
2406 2516 3.906846 ACCCATCAGGATAGAGATGTTCC 59.093 47.826 0.00 0.00 39.92 3.62
2407 2517 3.262915 CCCATCAGGATAGAGATGTTCCC 59.737 52.174 0.00 0.00 39.92 3.97
2408 2518 3.056250 CCATCAGGATAGAGATGTTCCCG 60.056 52.174 0.00 0.00 39.92 5.14
2409 2519 3.314307 TCAGGATAGAGATGTTCCCGT 57.686 47.619 0.00 0.00 0.00 5.28
2410 2520 3.223435 TCAGGATAGAGATGTTCCCGTC 58.777 50.000 0.00 0.00 0.00 4.79
2411 2521 2.030717 CAGGATAGAGATGTTCCCGTCG 60.031 54.545 0.00 0.00 0.00 5.12
2412 2522 2.158652 AGGATAGAGATGTTCCCGTCGA 60.159 50.000 0.00 0.00 0.00 4.20
2413 2523 2.030981 GGATAGAGATGTTCCCGTCGAC 60.031 54.545 5.18 5.18 0.00 4.20
2414 2524 1.012086 TAGAGATGTTCCCGTCGACG 58.988 55.000 30.33 30.33 39.44 5.12
2415 2525 0.675837 AGAGATGTTCCCGTCGACGA 60.676 55.000 37.65 18.99 43.02 4.20
2416 2526 0.522915 GAGATGTTCCCGTCGACGAC 60.523 60.000 37.65 27.09 43.02 4.34
2428 2538 0.926155 TCGACGACGAGATTCCTACG 59.074 55.000 5.75 0.00 43.81 3.51
2429 2539 0.042361 CGACGACGAGATTCCTACGG 60.042 60.000 0.00 0.00 42.66 4.02
2430 2540 1.012841 GACGACGAGATTCCTACGGT 58.987 55.000 0.00 0.00 0.00 4.83
2431 2541 0.731417 ACGACGAGATTCCTACGGTG 59.269 55.000 0.00 0.00 0.00 4.94
2432 2542 0.591741 CGACGAGATTCCTACGGTGC 60.592 60.000 0.00 0.00 0.00 5.01
2433 2543 0.248949 GACGAGATTCCTACGGTGCC 60.249 60.000 0.00 0.00 0.00 5.01
2434 2544 0.683504 ACGAGATTCCTACGGTGCCT 60.684 55.000 0.00 0.00 0.00 4.75
2435 2545 0.460311 CGAGATTCCTACGGTGCCTT 59.540 55.000 0.00 0.00 0.00 4.35
2436 2546 1.536284 CGAGATTCCTACGGTGCCTTC 60.536 57.143 0.00 0.00 0.00 3.46
2437 2547 1.480954 GAGATTCCTACGGTGCCTTCA 59.519 52.381 0.00 0.00 0.00 3.02
2438 2548 2.103263 GAGATTCCTACGGTGCCTTCAT 59.897 50.000 0.00 0.00 0.00 2.57
2439 2549 3.305720 AGATTCCTACGGTGCCTTCATA 58.694 45.455 0.00 0.00 0.00 2.15
2440 2550 3.709653 AGATTCCTACGGTGCCTTCATAA 59.290 43.478 0.00 0.00 0.00 1.90
2441 2551 3.985019 TTCCTACGGTGCCTTCATAAA 57.015 42.857 0.00 0.00 0.00 1.40
2442 2552 4.497291 TTCCTACGGTGCCTTCATAAAT 57.503 40.909 0.00 0.00 0.00 1.40
2443 2553 4.497291 TCCTACGGTGCCTTCATAAATT 57.503 40.909 0.00 0.00 0.00 1.82
2444 2554 4.850680 TCCTACGGTGCCTTCATAAATTT 58.149 39.130 0.00 0.00 0.00 1.82
2445 2555 4.879545 TCCTACGGTGCCTTCATAAATTTC 59.120 41.667 0.00 0.00 0.00 2.17
2446 2556 4.638421 CCTACGGTGCCTTCATAAATTTCA 59.362 41.667 0.00 0.00 0.00 2.69
2447 2557 5.124776 CCTACGGTGCCTTCATAAATTTCAA 59.875 40.000 0.00 0.00 0.00 2.69
2448 2558 5.059404 ACGGTGCCTTCATAAATTTCAAG 57.941 39.130 0.00 0.00 0.00 3.02
2449 2559 4.764823 ACGGTGCCTTCATAAATTTCAAGA 59.235 37.500 0.00 0.00 0.00 3.02
2450 2560 5.418840 ACGGTGCCTTCATAAATTTCAAGAT 59.581 36.000 0.00 0.00 0.00 2.40
2451 2561 5.745294 CGGTGCCTTCATAAATTTCAAGATG 59.255 40.000 0.00 0.00 0.00 2.90
2452 2562 6.044682 GGTGCCTTCATAAATTTCAAGATGG 58.955 40.000 0.00 4.74 0.00 3.51
2453 2563 6.351286 GGTGCCTTCATAAATTTCAAGATGGT 60.351 38.462 14.96 0.00 0.00 3.55
2454 2564 7.147915 GGTGCCTTCATAAATTTCAAGATGGTA 60.148 37.037 14.96 10.83 0.00 3.25
2455 2565 8.416329 GTGCCTTCATAAATTTCAAGATGGTAT 58.584 33.333 14.96 0.00 0.00 2.73
2456 2566 8.415553 TGCCTTCATAAATTTCAAGATGGTATG 58.584 33.333 14.96 4.34 0.00 2.39
2457 2567 7.383300 GCCTTCATAAATTTCAAGATGGTATGC 59.617 37.037 14.96 5.29 0.00 3.14
2458 2568 7.869429 CCTTCATAAATTTCAAGATGGTATGCC 59.131 37.037 0.00 0.00 0.00 4.40
2459 2569 6.969366 TCATAAATTTCAAGATGGTATGCCG 58.031 36.000 0.00 0.00 37.67 5.69
2460 2570 4.654091 AAATTTCAAGATGGTATGCCGG 57.346 40.909 0.00 0.00 37.67 6.13
2461 2571 1.388547 TTTCAAGATGGTATGCCGGC 58.611 50.000 22.73 22.73 37.67 6.13
2462 2572 0.546122 TTCAAGATGGTATGCCGGCT 59.454 50.000 29.70 15.76 37.67 5.52
2463 2573 0.106708 TCAAGATGGTATGCCGGCTC 59.893 55.000 29.70 15.82 37.67 4.70
2464 2574 0.179048 CAAGATGGTATGCCGGCTCA 60.179 55.000 29.70 19.88 37.67 4.26
2465 2575 0.107456 AAGATGGTATGCCGGCTCAG 59.893 55.000 29.70 0.00 37.67 3.35
2466 2576 1.050988 AGATGGTATGCCGGCTCAGT 61.051 55.000 29.70 13.44 37.67 3.41
2467 2577 0.601311 GATGGTATGCCGGCTCAGTC 60.601 60.000 29.70 14.01 37.67 3.51
2468 2578 1.050988 ATGGTATGCCGGCTCAGTCT 61.051 55.000 29.70 5.58 37.67 3.24
2469 2579 1.264749 TGGTATGCCGGCTCAGTCTT 61.265 55.000 29.70 6.03 37.67 3.01
2470 2580 0.107654 GGTATGCCGGCTCAGTCTTT 60.108 55.000 29.70 4.59 0.00 2.52
2471 2581 1.291132 GTATGCCGGCTCAGTCTTTC 58.709 55.000 29.70 4.01 0.00 2.62
2472 2582 0.179111 TATGCCGGCTCAGTCTTTCG 60.179 55.000 29.70 0.00 0.00 3.46
2473 2583 2.815647 GCCGGCTCAGTCTTTCGG 60.816 66.667 22.15 0.00 43.13 4.30
2474 2584 2.970639 CCGGCTCAGTCTTTCGGA 59.029 61.111 0.00 0.00 42.94 4.55
2475 2585 1.153745 CCGGCTCAGTCTTTCGGAG 60.154 63.158 0.00 0.00 42.94 4.63
2476 2586 1.595993 CCGGCTCAGTCTTTCGGAGA 61.596 60.000 0.00 0.00 42.94 3.71
2477 2587 0.457851 CGGCTCAGTCTTTCGGAGAT 59.542 55.000 0.00 0.00 40.01 2.75
2478 2588 1.800655 CGGCTCAGTCTTTCGGAGATG 60.801 57.143 0.00 0.00 40.01 2.90
2479 2589 1.285578 GCTCAGTCTTTCGGAGATGC 58.714 55.000 0.00 0.00 40.01 3.91
2480 2590 1.134848 GCTCAGTCTTTCGGAGATGCT 60.135 52.381 0.00 0.00 40.01 3.79
2481 2591 2.808244 CTCAGTCTTTCGGAGATGCTC 58.192 52.381 0.00 0.00 40.01 4.26
2482 2592 2.165234 CTCAGTCTTTCGGAGATGCTCA 59.835 50.000 0.00 0.00 40.01 4.26
2483 2593 2.762887 TCAGTCTTTCGGAGATGCTCAT 59.237 45.455 0.00 0.00 36.61 2.90
2484 2594 3.954258 TCAGTCTTTCGGAGATGCTCATA 59.046 43.478 0.00 0.00 36.61 2.15
2485 2595 4.037327 TCAGTCTTTCGGAGATGCTCATAG 59.963 45.833 0.00 0.00 36.61 2.23
2486 2596 3.320541 AGTCTTTCGGAGATGCTCATAGG 59.679 47.826 0.00 0.00 36.61 2.57
2487 2597 2.630098 TCTTTCGGAGATGCTCATAGGG 59.370 50.000 0.00 0.00 35.04 3.53
2488 2598 2.381752 TTCGGAGATGCTCATAGGGA 57.618 50.000 0.00 0.00 35.04 4.20
2489 2599 2.612285 TCGGAGATGCTCATAGGGAT 57.388 50.000 0.00 0.00 31.08 3.85
2490 2600 3.739401 TCGGAGATGCTCATAGGGATA 57.261 47.619 0.00 0.00 31.08 2.59
2491 2601 3.625853 TCGGAGATGCTCATAGGGATAG 58.374 50.000 0.00 0.00 31.08 2.08
2492 2602 2.692557 CGGAGATGCTCATAGGGATAGG 59.307 54.545 0.00 0.00 31.08 2.57
2493 2603 3.037549 GGAGATGCTCATAGGGATAGGG 58.962 54.545 0.00 0.00 31.08 3.53
2494 2604 3.567663 GGAGATGCTCATAGGGATAGGGT 60.568 52.174 0.00 0.00 31.08 4.34
2495 2605 3.448934 AGATGCTCATAGGGATAGGGTG 58.551 50.000 0.00 0.00 0.00 4.61
2496 2606 2.795291 TGCTCATAGGGATAGGGTGT 57.205 50.000 0.00 0.00 0.00 4.16
2497 2607 2.329267 TGCTCATAGGGATAGGGTGTG 58.671 52.381 0.00 0.00 0.00 3.82
2498 2608 1.002544 GCTCATAGGGATAGGGTGTGC 59.997 57.143 0.00 0.00 0.00 4.57
2499 2609 1.273606 CTCATAGGGATAGGGTGTGCG 59.726 57.143 0.00 0.00 0.00 5.34
2500 2610 1.048601 CATAGGGATAGGGTGTGCGT 58.951 55.000 0.00 0.00 0.00 5.24
2501 2611 1.048601 ATAGGGATAGGGTGTGCGTG 58.951 55.000 0.00 0.00 0.00 5.34
2502 2612 0.324923 TAGGGATAGGGTGTGCGTGT 60.325 55.000 0.00 0.00 0.00 4.49
2503 2613 1.449601 GGGATAGGGTGTGCGTGTG 60.450 63.158 0.00 0.00 0.00 3.82
2504 2614 1.295423 GGATAGGGTGTGCGTGTGT 59.705 57.895 0.00 0.00 0.00 3.72
2505 2615 0.533491 GGATAGGGTGTGCGTGTGTA 59.467 55.000 0.00 0.00 0.00 2.90
2506 2616 1.636988 GATAGGGTGTGCGTGTGTAC 58.363 55.000 0.00 0.00 0.00 2.90
2518 2628 3.508744 CGTGTGTACGTTTATAGGGGT 57.491 47.619 0.00 0.00 44.99 4.95
2519 2629 3.181397 CGTGTGTACGTTTATAGGGGTG 58.819 50.000 0.00 0.00 44.99 4.61
2520 2630 3.119531 CGTGTGTACGTTTATAGGGGTGA 60.120 47.826 0.00 0.00 44.99 4.02
2521 2631 4.427312 GTGTGTACGTTTATAGGGGTGAG 58.573 47.826 0.00 0.00 0.00 3.51
2522 2632 4.082026 GTGTGTACGTTTATAGGGGTGAGT 60.082 45.833 0.00 0.00 0.00 3.41
2523 2633 4.082081 TGTGTACGTTTATAGGGGTGAGTG 60.082 45.833 0.00 0.00 0.00 3.51
2524 2634 4.082026 GTGTACGTTTATAGGGGTGAGTGT 60.082 45.833 0.00 0.00 0.00 3.55
2525 2635 5.125417 GTGTACGTTTATAGGGGTGAGTGTA 59.875 44.000 0.00 0.00 0.00 2.90
2526 2636 5.893255 TGTACGTTTATAGGGGTGAGTGTAT 59.107 40.000 0.00 0.00 0.00 2.29
2527 2637 5.272283 ACGTTTATAGGGGTGAGTGTATG 57.728 43.478 0.00 0.00 0.00 2.39
2528 2638 4.957954 ACGTTTATAGGGGTGAGTGTATGA 59.042 41.667 0.00 0.00 0.00 2.15
2529 2639 5.422970 ACGTTTATAGGGGTGAGTGTATGAA 59.577 40.000 0.00 0.00 0.00 2.57
2530 2640 5.751990 CGTTTATAGGGGTGAGTGTATGAAC 59.248 44.000 0.00 0.00 0.00 3.18
2531 2641 5.524971 TTATAGGGGTGAGTGTATGAACG 57.475 43.478 0.00 0.00 0.00 3.95
2532 2642 1.640917 AGGGGTGAGTGTATGAACGT 58.359 50.000 0.00 0.00 0.00 3.99
2533 2643 1.275291 AGGGGTGAGTGTATGAACGTG 59.725 52.381 0.00 0.00 0.00 4.49
2534 2644 1.001633 GGGGTGAGTGTATGAACGTGT 59.998 52.381 0.00 0.00 0.00 4.49
2535 2645 2.231964 GGGGTGAGTGTATGAACGTGTA 59.768 50.000 0.00 0.00 0.00 2.90
2536 2646 3.118884 GGGGTGAGTGTATGAACGTGTAT 60.119 47.826 0.00 0.00 0.00 2.29
2537 2647 4.098349 GGGGTGAGTGTATGAACGTGTATA 59.902 45.833 0.00 0.00 0.00 1.47
2538 2648 5.221382 GGGGTGAGTGTATGAACGTGTATAT 60.221 44.000 0.00 0.00 0.00 0.86
2539 2649 5.690409 GGGTGAGTGTATGAACGTGTATATG 59.310 44.000 0.00 0.00 0.00 1.78
2540 2650 6.460537 GGGTGAGTGTATGAACGTGTATATGA 60.461 42.308 0.00 0.00 0.00 2.15
2541 2651 6.976349 GGTGAGTGTATGAACGTGTATATGAA 59.024 38.462 0.00 0.00 0.00 2.57
2542 2652 7.043590 GGTGAGTGTATGAACGTGTATATGAAC 60.044 40.741 0.00 0.00 0.00 3.18
2543 2653 6.689669 TGAGTGTATGAACGTGTATATGAACG 59.310 38.462 9.65 9.65 45.15 3.95
2544 2654 5.457799 AGTGTATGAACGTGTATATGAACGC 59.542 40.000 10.80 0.00 43.49 4.84
2545 2655 5.457799 GTGTATGAACGTGTATATGAACGCT 59.542 40.000 10.80 0.77 43.49 5.07
2546 2656 6.020121 GTGTATGAACGTGTATATGAACGCTT 60.020 38.462 10.80 5.99 43.49 4.68
2547 2657 6.532302 TGTATGAACGTGTATATGAACGCTTT 59.468 34.615 10.80 0.00 43.49 3.51
2548 2658 5.198116 TGAACGTGTATATGAACGCTTTG 57.802 39.130 10.80 0.00 43.49 2.77
2549 2659 3.651562 ACGTGTATATGAACGCTTTGC 57.348 42.857 10.80 0.00 43.49 3.68
2562 2672 1.217882 GCTTTGCGTCTGTACTGTGT 58.782 50.000 0.00 0.00 0.00 3.72
2563 2673 1.597663 GCTTTGCGTCTGTACTGTGTT 59.402 47.619 0.00 0.00 0.00 3.32
2564 2674 2.031683 GCTTTGCGTCTGTACTGTGTTT 59.968 45.455 0.00 0.00 0.00 2.83
2565 2675 3.246699 GCTTTGCGTCTGTACTGTGTTTA 59.753 43.478 0.00 0.00 0.00 2.01
2566 2676 4.260456 GCTTTGCGTCTGTACTGTGTTTAA 60.260 41.667 0.00 0.00 0.00 1.52
2567 2677 5.728344 GCTTTGCGTCTGTACTGTGTTTAAA 60.728 40.000 0.00 0.00 0.00 1.52
2568 2678 5.798015 TTGCGTCTGTACTGTGTTTAAAA 57.202 34.783 0.00 0.00 0.00 1.52
2569 2679 5.798015 TGCGTCTGTACTGTGTTTAAAAA 57.202 34.783 0.00 0.00 0.00 1.94
2610 2720 1.595929 GGGGTGCAAACGAGTCGAA 60.596 57.895 21.50 0.00 0.00 3.71
2632 2742 6.237755 CGAATTTAAGCAACCTAGACTTACCG 60.238 42.308 0.00 0.00 0.00 4.02
2646 2756 1.950973 TTACCGCGGCTCAGCACATA 61.951 55.000 28.58 3.16 36.85 2.29
2647 2757 2.349969 TACCGCGGCTCAGCACATAG 62.350 60.000 28.58 0.00 36.85 2.23
2648 2758 2.202797 CGCGGCTCAGCACATAGT 60.203 61.111 0.00 0.00 36.85 2.12
2654 2764 3.807622 GCGGCTCAGCACATAGTATTAAA 59.192 43.478 0.00 0.00 37.05 1.52
2657 2767 6.513393 GCGGCTCAGCACATAGTATTAAAAAT 60.513 38.462 0.00 0.00 37.05 1.82
2661 2771 8.616076 GCTCAGCACATAGTATTAAAAATGAGT 58.384 33.333 0.00 0.00 33.53 3.41
2685 2795 2.353605 GCTCAACAGAACTCTAGCTGCT 60.354 50.000 7.57 7.57 35.57 4.24
2738 2848 3.077359 ACTGCAAAGTTGGCTGATAGTC 58.923 45.455 15.42 0.00 34.70 2.59
2758 2868 4.631813 AGTCGGTTTGTAATGATCTTGAGC 59.368 41.667 0.00 0.00 0.00 4.26
2763 2873 5.066505 GGTTTGTAATGATCTTGAGCCGATT 59.933 40.000 0.00 0.00 0.00 3.34
2868 2978 3.437395 TGTGTGTTTCTGTGTAAAACGCT 59.563 39.130 11.97 0.00 43.88 5.07
2929 3039 7.377766 TCACTCCAAAACATAAGAATGTAGC 57.622 36.000 0.00 0.00 45.79 3.58
2930 3040 6.939730 TCACTCCAAAACATAAGAATGTAGCA 59.060 34.615 0.00 0.00 45.79 3.49
2931 3041 7.446931 TCACTCCAAAACATAAGAATGTAGCAA 59.553 33.333 0.00 0.00 45.79 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.249661 GCTAAAGCCTAGGCATAGCTAAG 58.750 47.826 38.54 25.90 46.08 2.18
129 130 4.219944 CACCCATGATCCATCAATTCATCC 59.780 45.833 0.00 0.00 40.69 3.51
150 151 4.899239 CCGAGATCGCTGCCCCAC 62.899 72.222 0.00 0.00 38.18 4.61
202 226 9.811995 GTACACATCATCTAGGTTTGTATTGTA 57.188 33.333 0.00 0.00 0.00 2.41
241 268 4.220602 AGACCATATATCTGCATGCACGTA 59.779 41.667 18.46 12.79 0.00 3.57
273 300 8.570068 TCATAATATCAGTAACATGCATGCAT 57.430 30.769 27.46 27.46 37.08 3.96
338 397 3.182967 CATGCCTCTGTAGACGACTTTC 58.817 50.000 0.00 0.00 0.00 2.62
339 398 2.093973 CCATGCCTCTGTAGACGACTTT 60.094 50.000 0.00 0.00 0.00 2.66
340 399 1.478510 CCATGCCTCTGTAGACGACTT 59.521 52.381 0.00 0.00 0.00 3.01
372 431 6.261118 CAGTAGGATGCATAAGTTTTCTTGC 58.739 40.000 0.00 0.00 40.70 4.01
381 440 2.975489 AGGGACCAGTAGGATGCATAAG 59.025 50.000 0.00 0.00 38.69 1.73
382 441 2.705658 CAGGGACCAGTAGGATGCATAA 59.294 50.000 0.00 0.00 38.69 1.90
383 442 2.329267 CAGGGACCAGTAGGATGCATA 58.671 52.381 0.00 0.00 38.69 3.14
384 443 1.135094 CAGGGACCAGTAGGATGCAT 58.865 55.000 0.00 0.00 38.69 3.96
385 444 1.626356 GCAGGGACCAGTAGGATGCA 61.626 60.000 0.00 0.00 38.69 3.96
386 445 1.147153 GCAGGGACCAGTAGGATGC 59.853 63.158 0.00 0.00 38.69 3.91
387 446 0.179000 GTGCAGGGACCAGTAGGATG 59.821 60.000 0.00 0.00 38.69 3.51
388 447 0.043334 AGTGCAGGGACCAGTAGGAT 59.957 55.000 0.00 0.00 38.69 3.24
389 448 0.904865 CAGTGCAGGGACCAGTAGGA 60.905 60.000 0.00 0.00 38.69 2.94
390 449 1.599047 CAGTGCAGGGACCAGTAGG 59.401 63.158 0.00 0.00 42.21 3.18
391 450 1.078848 GCAGTGCAGGGACCAGTAG 60.079 63.158 11.09 0.00 0.00 2.57
392 451 1.841103 TGCAGTGCAGGGACCAGTA 60.841 57.895 15.37 0.00 33.32 2.74
393 452 3.170672 TGCAGTGCAGGGACCAGT 61.171 61.111 15.37 0.00 33.32 4.00
425 497 2.671619 CGTGTCGGGGGCAACAAT 60.672 61.111 0.00 0.00 39.74 2.71
694 771 0.039035 ACCCCTTTGCTAATTCGGCA 59.961 50.000 2.44 2.44 37.97 5.69
706 783 3.552384 TGTCCGCGTCACCCCTTT 61.552 61.111 4.92 0.00 0.00 3.11
712 789 3.749373 CGTTCGTGTCCGCGTCAC 61.749 66.667 17.63 17.63 0.00 3.67
949 1040 3.417690 AGAACGTACGATCAACTAGGC 57.582 47.619 24.41 0.00 0.00 3.93
1056 1151 1.960612 CGCCTTCTCCTCTATCCCG 59.039 63.158 0.00 0.00 0.00 5.14
1062 1157 3.453679 GACGGCGCCTTCTCCTCT 61.454 66.667 26.68 0.00 0.00 3.69
1110 1205 3.195698 GCAAGGTGATCGCCGTCC 61.196 66.667 19.45 2.61 0.00 4.79
1380 1478 5.546621 AGAAACATATATGCACGGGTAGT 57.453 39.130 12.79 0.00 0.00 2.73
1382 1480 5.989168 CAGAAGAAACATATATGCACGGGTA 59.011 40.000 12.79 0.00 0.00 3.69
1384 1482 4.319766 GCAGAAGAAACATATATGCACGGG 60.320 45.833 12.79 0.00 32.58 5.28
1385 1483 4.273235 TGCAGAAGAAACATATATGCACGG 59.727 41.667 12.79 1.20 37.28 4.94
1394 1492 4.092821 CCGTCGAATTGCAGAAGAAACATA 59.907 41.667 0.00 0.00 0.00 2.29
1413 1511 1.333791 CCTTTCACGTTTCAAGCCGTC 60.334 52.381 0.00 0.00 34.59 4.79
1423 1530 1.459450 ACACAAGCACCTTTCACGTT 58.541 45.000 0.00 0.00 0.00 3.99
1424 1531 1.400494 GAACACAAGCACCTTTCACGT 59.600 47.619 0.00 0.00 0.00 4.49
1493 1600 1.827399 GCTTCCCCTTCACGGTCTCA 61.827 60.000 0.00 0.00 0.00 3.27
1915 2022 4.527157 GTCATTGCAGCTCCGCGC 62.527 66.667 0.00 0.00 39.57 6.86
1957 2064 2.101770 CCTCGCGTACGTCTTCCC 59.898 66.667 17.90 0.00 41.18 3.97
2107 2217 1.331756 TCGTACGCGGAAGGATCTAAC 59.668 52.381 12.47 0.00 38.89 2.34
2110 2220 1.030457 AATCGTACGCGGAAGGATCT 58.970 50.000 12.47 3.70 38.89 2.75
2133 2243 3.428534 CGCTTGGAAAAACATAAGCCAAC 59.571 43.478 0.00 0.00 41.77 3.77
2241 2351 9.050601 GCTTAAGAGTTAAGATCATGCATAAGT 57.949 33.333 6.67 0.00 44.19 2.24
2315 2425 4.873746 GCCTGAATGCCTGATACTAGTA 57.126 45.455 4.77 4.77 0.00 1.82
2327 2437 2.125952 GGTTTGCGGCCTGAATGC 60.126 61.111 0.00 0.00 0.00 3.56
2328 2438 0.247185 ATTGGTTTGCGGCCTGAATG 59.753 50.000 0.00 0.00 0.00 2.67
2329 2439 0.975887 AATTGGTTTGCGGCCTGAAT 59.024 45.000 0.00 0.00 0.00 2.57
2330 2440 0.033228 CAATTGGTTTGCGGCCTGAA 59.967 50.000 0.00 0.00 0.00 3.02
2331 2441 1.112315 ACAATTGGTTTGCGGCCTGA 61.112 50.000 10.83 0.00 39.03 3.86
2332 2442 0.945265 CACAATTGGTTTGCGGCCTG 60.945 55.000 10.83 0.00 39.03 4.85
2333 2443 1.367102 CACAATTGGTTTGCGGCCT 59.633 52.632 10.83 0.00 39.03 5.19
2334 2444 1.667510 CCACAATTGGTTTGCGGCC 60.668 57.895 10.83 0.00 39.03 6.13
2335 2445 3.949855 CCACAATTGGTTTGCGGC 58.050 55.556 10.83 0.00 39.03 6.53
2344 2454 5.009631 TCTCTAACCATCCAACCACAATTG 58.990 41.667 3.24 3.24 0.00 2.32
2345 2455 5.014123 TCTCTCTAACCATCCAACCACAATT 59.986 40.000 0.00 0.00 0.00 2.32
2346 2456 4.536090 TCTCTCTAACCATCCAACCACAAT 59.464 41.667 0.00 0.00 0.00 2.71
2347 2457 3.907474 TCTCTCTAACCATCCAACCACAA 59.093 43.478 0.00 0.00 0.00 3.33
2348 2458 3.260884 GTCTCTCTAACCATCCAACCACA 59.739 47.826 0.00 0.00 0.00 4.17
2349 2459 3.515901 AGTCTCTCTAACCATCCAACCAC 59.484 47.826 0.00 0.00 0.00 4.16
2350 2460 3.791320 AGTCTCTCTAACCATCCAACCA 58.209 45.455 0.00 0.00 0.00 3.67
2351 2461 5.221541 CCATAGTCTCTCTAACCATCCAACC 60.222 48.000 0.00 0.00 31.94 3.77
2352 2462 5.364157 ACCATAGTCTCTCTAACCATCCAAC 59.636 44.000 0.00 0.00 31.94 3.77
2353 2463 5.529289 ACCATAGTCTCTCTAACCATCCAA 58.471 41.667 0.00 0.00 31.94 3.53
2354 2464 5.144159 ACCATAGTCTCTCTAACCATCCA 57.856 43.478 0.00 0.00 31.94 3.41
2355 2465 7.093684 GGAATACCATAGTCTCTCTAACCATCC 60.094 44.444 0.00 0.00 35.97 3.51
2356 2466 7.451877 TGGAATACCATAGTCTCTCTAACCATC 59.548 40.741 0.00 0.00 41.77 3.51
2357 2467 7.306013 TGGAATACCATAGTCTCTCTAACCAT 58.694 38.462 0.00 0.00 41.77 3.55
2358 2468 6.679542 TGGAATACCATAGTCTCTCTAACCA 58.320 40.000 0.00 0.00 41.77 3.67
2359 2469 7.598759 TTGGAATACCATAGTCTCTCTAACC 57.401 40.000 0.00 0.00 46.34 2.85
2360 2470 7.927092 GGTTTGGAATACCATAGTCTCTCTAAC 59.073 40.741 0.00 0.00 46.34 2.34
2361 2471 7.070821 GGGTTTGGAATACCATAGTCTCTCTAA 59.929 40.741 0.00 0.00 46.34 2.10
2362 2472 6.553852 GGGTTTGGAATACCATAGTCTCTCTA 59.446 42.308 0.00 0.00 46.34 2.43
2363 2473 5.367060 GGGTTTGGAATACCATAGTCTCTCT 59.633 44.000 0.00 0.00 46.34 3.10
2364 2474 5.130477 TGGGTTTGGAATACCATAGTCTCTC 59.870 44.000 0.00 0.00 46.34 3.20
2365 2475 5.036916 TGGGTTTGGAATACCATAGTCTCT 58.963 41.667 0.00 0.00 46.34 3.10
2366 2476 5.367945 TGGGTTTGGAATACCATAGTCTC 57.632 43.478 0.00 0.00 46.34 3.36
2367 2477 5.431731 TGATGGGTTTGGAATACCATAGTCT 59.568 40.000 0.00 0.00 46.34 3.24
2368 2478 5.690865 TGATGGGTTTGGAATACCATAGTC 58.309 41.667 0.00 0.00 46.34 2.59
2369 2479 5.399038 CCTGATGGGTTTGGAATACCATAGT 60.399 44.000 0.00 0.00 46.34 2.12
2370 2480 5.072741 CCTGATGGGTTTGGAATACCATAG 58.927 45.833 0.00 0.00 46.34 2.23
2371 2481 4.729370 TCCTGATGGGTTTGGAATACCATA 59.271 41.667 0.00 0.00 43.40 2.74
2372 2482 3.531397 TCCTGATGGGTTTGGAATACCAT 59.469 43.478 0.00 0.00 45.87 3.55
2373 2483 2.922955 TCCTGATGGGTTTGGAATACCA 59.077 45.455 0.00 0.00 39.31 3.25
2374 2484 3.662759 TCCTGATGGGTTTGGAATACC 57.337 47.619 0.00 0.00 36.25 2.73
2375 2485 6.043243 TCTCTATCCTGATGGGTTTGGAATAC 59.957 42.308 0.00 0.00 36.25 1.89
2376 2486 6.150332 TCTCTATCCTGATGGGTTTGGAATA 58.850 40.000 0.00 0.00 36.25 1.75
2377 2487 4.977739 TCTCTATCCTGATGGGTTTGGAAT 59.022 41.667 0.00 0.00 36.25 3.01
2378 2488 4.370776 TCTCTATCCTGATGGGTTTGGAA 58.629 43.478 0.00 0.00 36.25 3.53
2379 2489 4.007581 TCTCTATCCTGATGGGTTTGGA 57.992 45.455 0.00 0.00 36.25 3.53
2380 2490 4.103785 ACATCTCTATCCTGATGGGTTTGG 59.896 45.833 7.69 0.00 42.96 3.28
2381 2491 5.301835 ACATCTCTATCCTGATGGGTTTG 57.698 43.478 7.69 0.00 42.96 2.93
2382 2492 5.163152 GGAACATCTCTATCCTGATGGGTTT 60.163 44.000 7.69 0.00 42.96 3.27
2383 2493 4.349342 GGAACATCTCTATCCTGATGGGTT 59.651 45.833 7.69 0.00 42.96 4.11
2384 2494 3.906846 GGAACATCTCTATCCTGATGGGT 59.093 47.826 7.69 0.00 42.96 4.51
2385 2495 3.262915 GGGAACATCTCTATCCTGATGGG 59.737 52.174 7.69 0.00 42.96 4.00
2386 2496 3.056250 CGGGAACATCTCTATCCTGATGG 60.056 52.174 7.69 0.00 42.96 3.51
2387 2497 3.576118 ACGGGAACATCTCTATCCTGATG 59.424 47.826 6.86 0.00 41.31 3.07
2388 2498 3.829601 GACGGGAACATCTCTATCCTGAT 59.170 47.826 6.86 0.00 41.31 2.90
2389 2499 3.223435 GACGGGAACATCTCTATCCTGA 58.777 50.000 6.86 0.00 41.31 3.86
2390 2500 2.030717 CGACGGGAACATCTCTATCCTG 60.031 54.545 0.00 0.00 43.83 3.86
2391 2501 2.158652 TCGACGGGAACATCTCTATCCT 60.159 50.000 0.00 0.00 33.61 3.24
2392 2502 2.030981 GTCGACGGGAACATCTCTATCC 60.031 54.545 0.00 0.00 0.00 2.59
2393 2503 2.349627 CGTCGACGGGAACATCTCTATC 60.350 54.545 29.70 0.00 35.37 2.08
2394 2504 1.602851 CGTCGACGGGAACATCTCTAT 59.397 52.381 29.70 0.00 35.37 1.98
2395 2505 1.012086 CGTCGACGGGAACATCTCTA 58.988 55.000 29.70 0.00 35.37 2.43
2396 2506 0.675837 TCGTCGACGGGAACATCTCT 60.676 55.000 35.05 0.00 40.29 3.10
2397 2507 0.522915 GTCGTCGACGGGAACATCTC 60.523 60.000 35.05 12.17 40.29 2.75
2398 2508 1.505353 GTCGTCGACGGGAACATCT 59.495 57.895 35.05 0.00 40.29 2.90
2399 2509 4.068302 GTCGTCGACGGGAACATC 57.932 61.111 35.05 14.32 40.29 3.06
2408 2518 1.331854 CGTAGGAATCTCGTCGTCGAC 60.332 57.143 15.51 15.51 41.35 4.20
2409 2519 0.926155 CGTAGGAATCTCGTCGTCGA 59.074 55.000 4.42 4.42 44.12 4.20
2410 2520 3.417619 CGTAGGAATCTCGTCGTCG 57.582 57.895 0.00 0.00 38.55 5.12
2424 2534 5.811399 TGAAATTTATGAAGGCACCGTAG 57.189 39.130 0.00 0.00 0.00 3.51
2425 2535 5.941058 TCTTGAAATTTATGAAGGCACCGTA 59.059 36.000 0.00 0.00 0.00 4.02
2426 2536 4.764823 TCTTGAAATTTATGAAGGCACCGT 59.235 37.500 0.00 0.00 0.00 4.83
2427 2537 5.309323 TCTTGAAATTTATGAAGGCACCG 57.691 39.130 0.00 0.00 0.00 4.94
2428 2538 6.044682 CCATCTTGAAATTTATGAAGGCACC 58.955 40.000 0.00 0.00 0.00 5.01
2429 2539 6.633856 ACCATCTTGAAATTTATGAAGGCAC 58.366 36.000 0.00 0.00 0.00 5.01
2430 2540 6.855763 ACCATCTTGAAATTTATGAAGGCA 57.144 33.333 0.00 0.00 0.00 4.75
2431 2541 7.383300 GCATACCATCTTGAAATTTATGAAGGC 59.617 37.037 0.00 0.00 0.00 4.35
2432 2542 7.869429 GGCATACCATCTTGAAATTTATGAAGG 59.131 37.037 0.00 0.00 35.26 3.46
2433 2543 7.592533 CGGCATACCATCTTGAAATTTATGAAG 59.407 37.037 0.00 0.00 34.57 3.02
2434 2544 7.424803 CGGCATACCATCTTGAAATTTATGAA 58.575 34.615 0.00 0.00 34.57 2.57
2435 2545 6.016360 CCGGCATACCATCTTGAAATTTATGA 60.016 38.462 0.00 0.00 34.57 2.15
2436 2546 6.151691 CCGGCATACCATCTTGAAATTTATG 58.848 40.000 0.00 0.00 34.57 1.90
2437 2547 5.278957 GCCGGCATACCATCTTGAAATTTAT 60.279 40.000 24.80 0.00 34.57 1.40
2438 2548 4.037446 GCCGGCATACCATCTTGAAATTTA 59.963 41.667 24.80 0.00 34.57 1.40
2439 2549 3.181476 GCCGGCATACCATCTTGAAATTT 60.181 43.478 24.80 0.00 34.57 1.82
2440 2550 2.362077 GCCGGCATACCATCTTGAAATT 59.638 45.455 24.80 0.00 34.57 1.82
2441 2551 1.956477 GCCGGCATACCATCTTGAAAT 59.044 47.619 24.80 0.00 34.57 2.17
2442 2552 1.064758 AGCCGGCATACCATCTTGAAA 60.065 47.619 31.54 0.00 34.57 2.69
2443 2553 0.546122 AGCCGGCATACCATCTTGAA 59.454 50.000 31.54 0.00 34.57 2.69
2444 2554 0.106708 GAGCCGGCATACCATCTTGA 59.893 55.000 31.54 0.00 34.57 3.02
2445 2555 0.179048 TGAGCCGGCATACCATCTTG 60.179 55.000 31.54 0.00 34.57 3.02
2446 2556 0.107456 CTGAGCCGGCATACCATCTT 59.893 55.000 31.54 3.33 34.57 2.40
2447 2557 1.050988 ACTGAGCCGGCATACCATCT 61.051 55.000 31.54 4.27 34.57 2.90
2448 2558 0.601311 GACTGAGCCGGCATACCATC 60.601 60.000 31.54 16.99 34.57 3.51
2449 2559 1.050988 AGACTGAGCCGGCATACCAT 61.051 55.000 31.54 6.18 34.57 3.55
2450 2560 1.264749 AAGACTGAGCCGGCATACCA 61.265 55.000 31.54 18.81 34.57 3.25
2451 2561 0.107654 AAAGACTGAGCCGGCATACC 60.108 55.000 31.54 14.98 0.00 2.73
2452 2562 1.291132 GAAAGACTGAGCCGGCATAC 58.709 55.000 31.54 19.58 0.00 2.39
2453 2563 0.179111 CGAAAGACTGAGCCGGCATA 60.179 55.000 31.54 16.21 0.00 3.14
2454 2564 1.448540 CGAAAGACTGAGCCGGCAT 60.449 57.895 31.54 14.28 0.00 4.40
2455 2565 2.048222 CGAAAGACTGAGCCGGCA 60.048 61.111 31.54 7.98 0.00 5.69
2456 2566 2.815647 CCGAAAGACTGAGCCGGC 60.816 66.667 21.89 21.89 33.47 6.13
2457 2567 1.153745 CTCCGAAAGACTGAGCCGG 60.154 63.158 0.00 0.00 41.36 6.13
2458 2568 0.457851 ATCTCCGAAAGACTGAGCCG 59.542 55.000 0.00 0.00 36.65 5.52
2459 2569 1.933247 CATCTCCGAAAGACTGAGCC 58.067 55.000 0.00 0.00 36.65 4.70
2460 2570 1.134848 AGCATCTCCGAAAGACTGAGC 60.135 52.381 0.00 0.00 36.65 4.26
2461 2571 2.165234 TGAGCATCTCCGAAAGACTGAG 59.835 50.000 0.00 0.00 36.65 3.35
2462 2572 2.171003 TGAGCATCTCCGAAAGACTGA 58.829 47.619 0.00 0.00 36.65 3.41
2463 2573 2.662006 TGAGCATCTCCGAAAGACTG 57.338 50.000 0.00 0.00 36.65 3.51
2464 2574 3.320541 CCTATGAGCATCTCCGAAAGACT 59.679 47.826 0.00 0.00 36.65 3.24
2465 2575 3.553922 CCCTATGAGCATCTCCGAAAGAC 60.554 52.174 0.00 0.00 36.65 3.01
2466 2576 2.630098 CCCTATGAGCATCTCCGAAAGA 59.370 50.000 0.00 0.00 38.72 2.52
2467 2577 2.630098 TCCCTATGAGCATCTCCGAAAG 59.370 50.000 0.00 0.00 34.92 2.62
2468 2578 2.677914 TCCCTATGAGCATCTCCGAAA 58.322 47.619 0.00 0.00 34.92 3.46
2469 2579 2.381752 TCCCTATGAGCATCTCCGAA 57.618 50.000 0.00 0.00 34.92 4.30
2470 2580 2.612285 ATCCCTATGAGCATCTCCGA 57.388 50.000 0.00 0.00 34.92 4.55
2471 2581 2.692557 CCTATCCCTATGAGCATCTCCG 59.307 54.545 0.00 0.00 34.92 4.63
2472 2582 3.037549 CCCTATCCCTATGAGCATCTCC 58.962 54.545 0.00 0.00 34.92 3.71
2473 2583 3.450457 CACCCTATCCCTATGAGCATCTC 59.550 52.174 0.00 0.00 34.92 2.75
2474 2584 3.181402 ACACCCTATCCCTATGAGCATCT 60.181 47.826 0.00 0.00 34.92 2.90
2475 2585 3.055530 CACACCCTATCCCTATGAGCATC 60.056 52.174 0.00 0.00 0.00 3.91
2476 2586 2.909006 CACACCCTATCCCTATGAGCAT 59.091 50.000 0.00 0.00 0.00 3.79
2477 2587 2.329267 CACACCCTATCCCTATGAGCA 58.671 52.381 0.00 0.00 0.00 4.26
2478 2588 1.002544 GCACACCCTATCCCTATGAGC 59.997 57.143 0.00 0.00 0.00 4.26
2479 2589 1.273606 CGCACACCCTATCCCTATGAG 59.726 57.143 0.00 0.00 0.00 2.90
2480 2590 1.338107 CGCACACCCTATCCCTATGA 58.662 55.000 0.00 0.00 0.00 2.15
2481 2591 1.048601 ACGCACACCCTATCCCTATG 58.951 55.000 0.00 0.00 0.00 2.23
2482 2592 1.048601 CACGCACACCCTATCCCTAT 58.951 55.000 0.00 0.00 0.00 2.57
2483 2593 0.324923 ACACGCACACCCTATCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
2484 2594 1.612442 ACACGCACACCCTATCCCT 60.612 57.895 0.00 0.00 0.00 4.20
2485 2595 1.449601 CACACGCACACCCTATCCC 60.450 63.158 0.00 0.00 0.00 3.85
2486 2596 0.533491 TACACACGCACACCCTATCC 59.467 55.000 0.00 0.00 0.00 2.59
2487 2597 1.636988 GTACACACGCACACCCTATC 58.363 55.000 0.00 0.00 0.00 2.08
2488 2598 0.108992 CGTACACACGCACACCCTAT 60.109 55.000 0.00 0.00 42.05 2.57
2489 2599 1.286570 CGTACACACGCACACCCTA 59.713 57.895 0.00 0.00 42.05 3.53
2490 2600 2.028484 CGTACACACGCACACCCT 59.972 61.111 0.00 0.00 42.05 4.34
2499 2609 4.082026 ACTCACCCCTATAAACGTACACAC 60.082 45.833 0.00 0.00 0.00 3.82
2500 2610 4.082081 CACTCACCCCTATAAACGTACACA 60.082 45.833 0.00 0.00 0.00 3.72
2501 2611 4.082026 ACACTCACCCCTATAAACGTACAC 60.082 45.833 0.00 0.00 0.00 2.90
2502 2612 4.088634 ACACTCACCCCTATAAACGTACA 58.911 43.478 0.00 0.00 0.00 2.90
2503 2613 4.725790 ACACTCACCCCTATAAACGTAC 57.274 45.455 0.00 0.00 0.00 3.67
2504 2614 6.128486 TCATACACTCACCCCTATAAACGTA 58.872 40.000 0.00 0.00 0.00 3.57
2505 2615 4.957954 TCATACACTCACCCCTATAAACGT 59.042 41.667 0.00 0.00 0.00 3.99
2506 2616 5.524971 TCATACACTCACCCCTATAAACG 57.475 43.478 0.00 0.00 0.00 3.60
2507 2617 5.751990 CGTTCATACACTCACCCCTATAAAC 59.248 44.000 0.00 0.00 0.00 2.01
2508 2618 5.422970 ACGTTCATACACTCACCCCTATAAA 59.577 40.000 0.00 0.00 0.00 1.40
2509 2619 4.957954 ACGTTCATACACTCACCCCTATAA 59.042 41.667 0.00 0.00 0.00 0.98
2510 2620 4.340097 CACGTTCATACACTCACCCCTATA 59.660 45.833 0.00 0.00 0.00 1.31
2511 2621 3.132289 CACGTTCATACACTCACCCCTAT 59.868 47.826 0.00 0.00 0.00 2.57
2512 2622 2.494471 CACGTTCATACACTCACCCCTA 59.506 50.000 0.00 0.00 0.00 3.53
2513 2623 1.275291 CACGTTCATACACTCACCCCT 59.725 52.381 0.00 0.00 0.00 4.79
2514 2624 1.001633 ACACGTTCATACACTCACCCC 59.998 52.381 0.00 0.00 0.00 4.95
2515 2625 2.450609 ACACGTTCATACACTCACCC 57.549 50.000 0.00 0.00 0.00 4.61
2516 2626 6.500910 TCATATACACGTTCATACACTCACC 58.499 40.000 0.00 0.00 0.00 4.02
2517 2627 7.305247 CGTTCATATACACGTTCATACACTCAC 60.305 40.741 0.00 0.00 0.00 3.51
2518 2628 6.689669 CGTTCATATACACGTTCATACACTCA 59.310 38.462 0.00 0.00 0.00 3.41
2519 2629 6.344780 GCGTTCATATACACGTTCATACACTC 60.345 42.308 7.48 0.00 38.70 3.51
2520 2630 5.457799 GCGTTCATATACACGTTCATACACT 59.542 40.000 7.48 0.00 38.70 3.55
2521 2631 5.457799 AGCGTTCATATACACGTTCATACAC 59.542 40.000 7.48 0.00 38.70 2.90
2522 2632 5.584442 AGCGTTCATATACACGTTCATACA 58.416 37.500 7.48 0.00 38.70 2.29
2523 2633 6.506464 AAGCGTTCATATACACGTTCATAC 57.494 37.500 7.48 0.00 38.70 2.39
2524 2634 6.508880 GCAAAGCGTTCATATACACGTTCATA 60.509 38.462 7.48 0.00 38.70 2.15
2525 2635 5.726688 GCAAAGCGTTCATATACACGTTCAT 60.727 40.000 7.48 0.00 38.70 2.57
2526 2636 4.434989 GCAAAGCGTTCATATACACGTTCA 60.435 41.667 7.48 0.00 38.70 3.18
2527 2637 4.019867 GCAAAGCGTTCATATACACGTTC 58.980 43.478 7.48 0.00 38.70 3.95
2528 2638 3.998522 GCAAAGCGTTCATATACACGTT 58.001 40.909 7.48 0.00 38.70 3.99
2529 2639 3.651562 GCAAAGCGTTCATATACACGT 57.348 42.857 7.48 0.00 38.70 4.49
2543 2653 1.217882 ACACAGTACAGACGCAAAGC 58.782 50.000 0.00 0.00 0.00 3.51
2544 2654 3.944422 AAACACAGTACAGACGCAAAG 57.056 42.857 0.00 0.00 0.00 2.77
2545 2655 5.798015 TTTAAACACAGTACAGACGCAAA 57.202 34.783 0.00 0.00 0.00 3.68
2546 2656 5.798015 TTTTAAACACAGTACAGACGCAA 57.202 34.783 0.00 0.00 0.00 4.85
2547 2657 5.798015 TTTTTAAACACAGTACAGACGCA 57.202 34.783 0.00 0.00 0.00 5.24
2566 2676 5.193679 AGAAGCGGCCTGATATTAGTTTTT 58.806 37.500 0.00 0.00 0.00 1.94
2567 2677 4.781934 AGAAGCGGCCTGATATTAGTTTT 58.218 39.130 0.00 0.00 0.00 2.43
2568 2678 4.423625 AGAAGCGGCCTGATATTAGTTT 57.576 40.909 0.00 0.00 0.00 2.66
2569 2679 4.021016 CCTAGAAGCGGCCTGATATTAGTT 60.021 45.833 0.00 0.00 0.00 2.24
2570 2680 3.511934 CCTAGAAGCGGCCTGATATTAGT 59.488 47.826 0.00 0.00 0.00 2.24
2571 2681 3.118956 CCCTAGAAGCGGCCTGATATTAG 60.119 52.174 0.00 0.00 0.00 1.73
2572 2682 2.832129 CCCTAGAAGCGGCCTGATATTA 59.168 50.000 0.00 0.00 0.00 0.98
2573 2683 1.625818 CCCTAGAAGCGGCCTGATATT 59.374 52.381 0.00 0.00 0.00 1.28
2574 2684 1.270907 CCCTAGAAGCGGCCTGATAT 58.729 55.000 0.00 0.00 0.00 1.63
2610 2720 4.874396 GCGGTAAGTCTAGGTTGCTTAAAT 59.126 41.667 0.00 0.00 0.00 1.40
2632 2742 1.871080 AATACTATGTGCTGAGCCGC 58.129 50.000 0.23 0.00 0.00 6.53
2661 2771 3.445450 CAGCTAGAGTTCTGTTGAGCCTA 59.555 47.826 0.00 0.00 0.00 3.93
2662 2772 2.233431 CAGCTAGAGTTCTGTTGAGCCT 59.767 50.000 0.00 0.00 0.00 4.58
2663 2773 2.615869 CAGCTAGAGTTCTGTTGAGCC 58.384 52.381 0.00 0.00 0.00 4.70
2709 2819 5.049167 CAGCCAACTTTGCAGTTTTGATTA 58.951 37.500 5.15 0.00 40.66 1.75
2713 2823 2.891112 TCAGCCAACTTTGCAGTTTTG 58.109 42.857 0.00 0.00 40.66 2.44
2715 2825 3.891366 ACTATCAGCCAACTTTGCAGTTT 59.109 39.130 0.00 0.00 40.66 2.66
2718 2828 2.094894 CGACTATCAGCCAACTTTGCAG 59.905 50.000 0.00 0.00 0.00 4.41
2738 2848 3.242413 CGGCTCAAGATCATTACAAACCG 60.242 47.826 0.00 0.00 0.00 4.44
2758 2868 4.981806 TCTAAAAATGGCCTGAAATCGG 57.018 40.909 3.32 0.00 0.00 4.18
2786 2896 9.157104 TCGTGCATGAGATTTTTGTAGTATTTA 57.843 29.630 3.97 0.00 0.00 1.40
2840 2950 9.015577 CGTTTTACACAGAAACACACATAATTT 57.984 29.630 0.00 0.00 36.94 1.82
2906 3016 7.144722 TGCTACATTCTTATGTTTTGGAGTG 57.855 36.000 0.00 0.00 42.29 3.51
2907 3017 7.759489 TTGCTACATTCTTATGTTTTGGAGT 57.241 32.000 0.00 0.00 42.29 3.85


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

AutoCloner maintained by Alex Coulton.