Multiple sequence alignment - TraesCS3D01G401900

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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 TraesCS3D01G401900 chr3D 100.000 2739 0 0 1 2739 516403665 516400927 0.000000e+00 5059
1 TraesCS3D01G401900 chr3D 97.321 2352 61 2 1 2351 465175690 465178040 0.000000e+00 3993
2 TraesCS3D01G401900 chr1D 97.657 2347 54 1 1 2346 487307375 487305029 0.000000e+00 4028
3 TraesCS3D01G401900 chr1D 97.070 2355 63 4 1 2354 30698306 30695957 0.000000e+00 3962
4 TraesCS3D01G401900 chr1D 95.226 398 10 1 2351 2739 120098607 120099004 3.000000e-174 621
5 TraesCS3D01G401900 chr2B 96.562 2356 75 4 1 2352 431355 433708 0.000000e+00 3897
6 TraesCS3D01G401900 chr7A 96.299 2351 86 1 1 2351 303752227 303749878 0.000000e+00 3858
7 TraesCS3D01G401900 chr5A 95.499 2355 82 14 1 2351 168957344 168959678 0.000000e+00 3740
8 TraesCS3D01G401900 chr1B 93.970 2073 112 10 2 2072 40302773 40300712 0.000000e+00 3123
9 TraesCS3D01G401900 chr4B 93.298 2074 131 7 1 2072 272432848 272430781 0.000000e+00 3053
10 TraesCS3D01G401900 chr4B 91.339 254 21 1 2098 2351 657005635 657005887 2.020000e-91 346
11 TraesCS3D01G401900 chr3A 96.915 1556 47 1 1 1555 706202315 706203870 0.000000e+00 2606
12 TraesCS3D01G401900 chr1A 96.078 765 30 0 1588 2352 347417584 347416820 0.000000e+00 1247
13 TraesCS3D01G401900 chr6D 95.477 398 7 2 2351 2739 274615087 274615482 2.320000e-175 625
14 TraesCS3D01G401900 chr6D 95.226 398 9 2 2351 2739 326343737 326343341 3.000000e-174 621
15 TraesCS3D01G401900 chr6D 95.202 396 10 1 2353 2739 67174450 67174055 3.880000e-173 617
16 TraesCS3D01G401900 chr7D 94.344 389 21 1 2351 2739 46460001 46459614 1.820000e-166 595
17 TraesCS3D01G401900 chr5B 94.087 389 23 0 2351 2739 667933494 667933882 2.350000e-165 592
18 TraesCS3D01G401900 chr5D 94.087 389 18 2 2351 2739 478128416 478128799 1.090000e-163 586
19 TraesCS3D01G401900 chr5D 89.950 398 27 2 2351 2739 486505103 486505496 4.070000e-138 501
20 TraesCS3D01G401900 chr5D 86.269 335 29 5 2351 2670 323113771 323114103 5.610000e-92 348
21 TraesCS3D01G401900 chr6B 93.573 389 23 1 2351 2739 224825318 224824932 1.830000e-161 579
22 TraesCS3D01G401900 chr6B 91.960 398 19 4 2351 2739 234576021 234575628 1.850000e-151 545
23 TraesCS3D01G401900 chr2D 93.367 392 20 4 2351 2739 304651008 304651396 2.370000e-160 575
24 TraesCS3D01G401900 chr2D 86.930 329 29 2 2351 2670 413134710 413134387 9.330000e-95 357
25 TraesCS3D01G401900 chr4A 85.750 400 45 7 2351 2739 238082444 238082046 1.960000e-111 412


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 TraesCS3D01G401900 chr3D 516400927 516403665 2738 True 5059 5059 100.000 1 2739 1 chr3D.!!$R1 2738
1 TraesCS3D01G401900 chr3D 465175690 465178040 2350 False 3993 3993 97.321 1 2351 1 chr3D.!!$F1 2350
2 TraesCS3D01G401900 chr1D 487305029 487307375 2346 True 4028 4028 97.657 1 2346 1 chr1D.!!$R2 2345
3 TraesCS3D01G401900 chr1D 30695957 30698306 2349 True 3962 3962 97.070 1 2354 1 chr1D.!!$R1 2353
4 TraesCS3D01G401900 chr2B 431355 433708 2353 False 3897 3897 96.562 1 2352 1 chr2B.!!$F1 2351
5 TraesCS3D01G401900 chr7A 303749878 303752227 2349 True 3858 3858 96.299 1 2351 1 chr7A.!!$R1 2350
6 TraesCS3D01G401900 chr5A 168957344 168959678 2334 False 3740 3740 95.499 1 2351 1 chr5A.!!$F1 2350
7 TraesCS3D01G401900 chr1B 40300712 40302773 2061 True 3123 3123 93.970 2 2072 1 chr1B.!!$R1 2070
8 TraesCS3D01G401900 chr4B 272430781 272432848 2067 True 3053 3053 93.298 1 2072 1 chr4B.!!$R1 2071
9 TraesCS3D01G401900 chr3A 706202315 706203870 1555 False 2606 2606 96.915 1 1555 1 chr3A.!!$F1 1554
10 TraesCS3D01G401900 chr1A 347416820 347417584 764 True 1247 1247 96.078 1588 2352 1 chr1A.!!$R1 764

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
661 672 2.18402 ATACACCGGCAGCAGCTCAA 62.184 55.0 0.0 0.0 41.7 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2625 2648 0.322008 GGGAGGTGAGTGCTTGAAGG 60.322 60.0 0.0 0.0 0.0 3.46 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
45 47 3.049912 GTTGATTGAAACCAAACGCCTC 58.950 45.455 0.00 0.00 0.00 4.70
207 210 2.747446 GTCCACTGCATCGGTTAAATGT 59.253 45.455 1.76 0.00 0.00 2.71
470 473 7.273320 AGTCAATGCAAAGGATTCATCTATG 57.727 36.000 0.00 0.00 0.00 2.23
661 672 2.184020 ATACACCGGCAGCAGCTCAA 62.184 55.000 0.00 0.00 41.70 3.02
1065 1079 1.995484 CAAGATACAGCAGTGTCCGTG 59.005 52.381 2.32 0.00 36.63 4.94
1208 1223 5.395657 CCACTGAGCTCATACCACTTTGATA 60.396 44.000 18.63 0.00 0.00 2.15
1261 1276 6.815089 TCTTGCTGTCATGGTTTGTAAATTT 58.185 32.000 0.00 0.00 0.00 1.82
1272 1287 7.938563 TGGTTTGTAAATTTCTGAATTTCCG 57.061 32.000 0.00 0.00 42.80 4.30
1306 1321 3.244387 TGCACTGTTCCATACAAGCAGTA 60.244 43.478 0.00 0.00 40.69 2.74
1316 1331 9.712305 GTTCCATACAAGCAGTATCTATTATGT 57.288 33.333 0.00 0.00 41.47 2.29
1392 1407 6.451393 GCCACAACCACATCTGTTTATTTTA 58.549 36.000 0.00 0.00 0.00 1.52
1601 1616 7.096353 GCATCATGTCAATGCATTGTGTATTAC 60.096 37.037 32.67 23.83 46.93 1.89
1919 1940 8.650143 ATCAACTATTGTAATCCCACAGTTTT 57.350 30.769 0.00 0.00 0.00 2.43
2145 2168 2.443632 TCCTGGACATTAACCACCAACA 59.556 45.455 0.00 0.00 33.57 3.33
2340 2363 1.070134 GCGTTGCTATATGAGGGGTCA 59.930 52.381 0.00 0.00 0.00 4.02
2354 2377 1.812571 GGGGTCATGTTGTAGTGCTTG 59.187 52.381 0.00 0.00 0.00 4.01
2355 2378 2.504367 GGGTCATGTTGTAGTGCTTGT 58.496 47.619 0.00 0.00 0.00 3.16
2356 2379 2.226437 GGGTCATGTTGTAGTGCTTGTG 59.774 50.000 0.00 0.00 0.00 3.33
2357 2380 2.226437 GGTCATGTTGTAGTGCTTGTGG 59.774 50.000 0.00 0.00 0.00 4.17
2358 2381 1.879380 TCATGTTGTAGTGCTTGTGGC 59.121 47.619 0.00 0.00 42.22 5.01
2359 2382 1.881973 CATGTTGTAGTGCTTGTGGCT 59.118 47.619 0.00 0.00 42.39 4.75
2360 2383 2.051334 TGTTGTAGTGCTTGTGGCTT 57.949 45.000 0.00 0.00 42.39 4.35
2361 2384 2.374184 TGTTGTAGTGCTTGTGGCTTT 58.626 42.857 0.00 0.00 42.39 3.51
2362 2385 2.098934 TGTTGTAGTGCTTGTGGCTTTG 59.901 45.455 0.00 0.00 42.39 2.77
2363 2386 0.667993 TGTAGTGCTTGTGGCTTTGC 59.332 50.000 0.00 0.00 42.39 3.68
2364 2387 0.667993 GTAGTGCTTGTGGCTTTGCA 59.332 50.000 0.00 0.00 42.39 4.08
2365 2388 1.270550 GTAGTGCTTGTGGCTTTGCAT 59.729 47.619 0.00 0.00 42.39 3.96
2366 2389 1.619654 AGTGCTTGTGGCTTTGCATA 58.380 45.000 0.00 0.00 42.39 3.14
2367 2390 2.173519 AGTGCTTGTGGCTTTGCATAT 58.826 42.857 0.00 0.00 42.39 1.78
2368 2391 2.165030 AGTGCTTGTGGCTTTGCATATC 59.835 45.455 0.00 0.00 42.39 1.63
2369 2392 2.094597 GTGCTTGTGGCTTTGCATATCA 60.095 45.455 0.00 0.00 42.39 2.15
2370 2393 2.761767 TGCTTGTGGCTTTGCATATCAT 59.238 40.909 0.00 0.00 42.39 2.45
2371 2394 3.196039 TGCTTGTGGCTTTGCATATCATT 59.804 39.130 0.00 0.00 42.39 2.57
2372 2395 4.401837 TGCTTGTGGCTTTGCATATCATTA 59.598 37.500 0.00 0.00 42.39 1.90
2373 2396 4.980434 GCTTGTGGCTTTGCATATCATTAG 59.020 41.667 0.00 0.00 38.06 1.73
2374 2397 4.572985 TGTGGCTTTGCATATCATTAGC 57.427 40.909 0.00 0.00 34.10 3.09
2375 2398 3.952967 TGTGGCTTTGCATATCATTAGCA 59.047 39.130 0.00 0.00 35.59 3.49
2376 2399 4.585581 TGTGGCTTTGCATATCATTAGCAT 59.414 37.500 0.00 0.00 38.19 3.79
2377 2400 5.159209 GTGGCTTTGCATATCATTAGCATC 58.841 41.667 0.00 0.00 38.19 3.91
2378 2401 4.828387 TGGCTTTGCATATCATTAGCATCA 59.172 37.500 0.00 0.00 38.19 3.07
2379 2402 5.479027 TGGCTTTGCATATCATTAGCATCAT 59.521 36.000 0.00 0.00 38.19 2.45
2380 2403 5.805486 GGCTTTGCATATCATTAGCATCATG 59.195 40.000 0.00 0.00 38.19 3.07
2381 2404 5.805486 GCTTTGCATATCATTAGCATCATGG 59.195 40.000 0.00 0.00 38.19 3.66
2382 2405 5.907866 TTGCATATCATTAGCATCATGGG 57.092 39.130 0.00 0.00 38.19 4.00
2383 2406 4.925836 TGCATATCATTAGCATCATGGGT 58.074 39.130 0.00 0.00 32.55 4.51
2384 2407 6.064735 TGCATATCATTAGCATCATGGGTA 57.935 37.500 0.00 0.00 32.55 3.69
2385 2408 6.665695 TGCATATCATTAGCATCATGGGTAT 58.334 36.000 0.00 0.00 32.55 2.73
2386 2409 7.120716 TGCATATCATTAGCATCATGGGTATT 58.879 34.615 0.00 0.00 32.55 1.89
2387 2410 7.283807 TGCATATCATTAGCATCATGGGTATTC 59.716 37.037 0.00 0.00 32.55 1.75
2388 2411 7.283807 GCATATCATTAGCATCATGGGTATTCA 59.716 37.037 0.00 0.00 0.00 2.57
2389 2412 9.350951 CATATCATTAGCATCATGGGTATTCAT 57.649 33.333 0.00 0.00 0.00 2.57
2391 2414 8.743085 ATCATTAGCATCATGGGTATTCATAC 57.257 34.615 0.00 0.00 0.00 2.39
2392 2415 7.921304 TCATTAGCATCATGGGTATTCATACT 58.079 34.615 0.00 0.00 33.81 2.12
2393 2416 9.045745 TCATTAGCATCATGGGTATTCATACTA 57.954 33.333 0.00 0.00 33.81 1.82
2394 2417 9.671279 CATTAGCATCATGGGTATTCATACTAA 57.329 33.333 0.00 0.00 33.81 2.24
2395 2418 9.672673 ATTAGCATCATGGGTATTCATACTAAC 57.327 33.333 0.00 0.00 33.81 2.34
2396 2419 7.078249 AGCATCATGGGTATTCATACTAACA 57.922 36.000 0.00 0.00 33.81 2.41
2397 2420 7.517320 AGCATCATGGGTATTCATACTAACAA 58.483 34.615 0.00 0.00 33.81 2.83
2398 2421 8.166061 AGCATCATGGGTATTCATACTAACAAT 58.834 33.333 0.00 0.00 33.81 2.71
2399 2422 9.448438 GCATCATGGGTATTCATACTAACAATA 57.552 33.333 0.00 0.00 33.81 1.90
2404 2427 9.806448 ATGGGTATTCATACTAACAATATTGCA 57.194 29.630 15.48 2.93 33.81 4.08
2405 2428 9.634021 TGGGTATTCATACTAACAATATTGCAA 57.366 29.630 15.48 0.00 33.81 4.08
2429 2452 9.476202 CAATCATGCTCATCATTCACATATTTT 57.524 29.630 0.00 0.00 31.79 1.82
2433 2456 8.860128 CATGCTCATCATTCACATATTTTATGC 58.140 33.333 0.00 0.00 31.79 3.14
2434 2457 7.372714 TGCTCATCATTCACATATTTTATGCC 58.627 34.615 0.00 0.00 0.00 4.40
2435 2458 7.014422 TGCTCATCATTCACATATTTTATGCCA 59.986 33.333 0.00 0.00 0.00 4.92
2436 2459 7.868922 GCTCATCATTCACATATTTTATGCCAA 59.131 33.333 0.00 0.00 0.00 4.52
2437 2460 9.406828 CTCATCATTCACATATTTTATGCCAAG 57.593 33.333 0.00 0.00 0.00 3.61
2438 2461 7.868922 TCATCATTCACATATTTTATGCCAAGC 59.131 33.333 0.00 0.00 0.00 4.01
2439 2462 7.110043 TCATTCACATATTTTATGCCAAGCA 57.890 32.000 0.00 0.00 44.86 3.91
2453 2476 5.102953 TGCCAAGCATTCTATGTAACTCT 57.897 39.130 0.00 0.00 31.71 3.24
2454 2477 5.500234 TGCCAAGCATTCTATGTAACTCTT 58.500 37.500 0.00 0.00 31.71 2.85
2455 2478 5.586243 TGCCAAGCATTCTATGTAACTCTTC 59.414 40.000 0.00 0.00 31.71 2.87
2456 2479 5.819901 GCCAAGCATTCTATGTAACTCTTCT 59.180 40.000 0.00 0.00 0.00 2.85
2457 2480 6.317391 GCCAAGCATTCTATGTAACTCTTCTT 59.683 38.462 0.00 0.00 0.00 2.52
2458 2481 7.466590 GCCAAGCATTCTATGTAACTCTTCTTC 60.467 40.741 0.00 0.00 0.00 2.87
2459 2482 7.768120 CCAAGCATTCTATGTAACTCTTCTTCT 59.232 37.037 0.00 0.00 0.00 2.85
2460 2483 9.809096 CAAGCATTCTATGTAACTCTTCTTCTA 57.191 33.333 0.00 0.00 0.00 2.10
2462 2485 9.196139 AGCATTCTATGTAACTCTTCTTCTAGT 57.804 33.333 0.00 0.00 0.00 2.57
2470 2493 7.818642 TGTAACTCTTCTTCTAGTACTTGAGC 58.181 38.462 0.00 0.00 0.00 4.26
2471 2494 5.907866 ACTCTTCTTCTAGTACTTGAGCC 57.092 43.478 0.00 0.00 0.00 4.70
2472 2495 4.707934 ACTCTTCTTCTAGTACTTGAGCCC 59.292 45.833 0.00 0.00 0.00 5.19
2473 2496 4.673968 TCTTCTTCTAGTACTTGAGCCCA 58.326 43.478 0.00 0.00 0.00 5.36
2474 2497 5.084519 TCTTCTTCTAGTACTTGAGCCCAA 58.915 41.667 0.00 0.00 0.00 4.12
2475 2498 5.721960 TCTTCTTCTAGTACTTGAGCCCAAT 59.278 40.000 0.00 0.00 0.00 3.16
2476 2499 6.213600 TCTTCTTCTAGTACTTGAGCCCAATT 59.786 38.462 0.00 0.00 0.00 2.32
2477 2500 6.374417 TCTTCTAGTACTTGAGCCCAATTT 57.626 37.500 0.00 0.00 0.00 1.82
2478 2501 6.779860 TCTTCTAGTACTTGAGCCCAATTTT 58.220 36.000 0.00 0.00 0.00 1.82
2479 2502 7.231467 TCTTCTAGTACTTGAGCCCAATTTTT 58.769 34.615 0.00 0.00 0.00 1.94
2480 2503 7.390718 TCTTCTAGTACTTGAGCCCAATTTTTC 59.609 37.037 0.00 0.00 0.00 2.29
2481 2504 6.779860 TCTAGTACTTGAGCCCAATTTTTCT 58.220 36.000 0.00 0.00 0.00 2.52
2482 2505 7.231467 TCTAGTACTTGAGCCCAATTTTTCTT 58.769 34.615 0.00 0.00 0.00 2.52
2483 2506 6.332735 AGTACTTGAGCCCAATTTTTCTTC 57.667 37.500 0.00 0.00 0.00 2.87
2484 2507 4.607293 ACTTGAGCCCAATTTTTCTTCC 57.393 40.909 0.00 0.00 0.00 3.46
2485 2508 3.324846 ACTTGAGCCCAATTTTTCTTCCC 59.675 43.478 0.00 0.00 0.00 3.97
2486 2509 2.969628 TGAGCCCAATTTTTCTTCCCA 58.030 42.857 0.00 0.00 0.00 4.37
2487 2510 3.519667 TGAGCCCAATTTTTCTTCCCAT 58.480 40.909 0.00 0.00 0.00 4.00
2488 2511 3.515104 TGAGCCCAATTTTTCTTCCCATC 59.485 43.478 0.00 0.00 0.00 3.51
2489 2512 3.515104 GAGCCCAATTTTTCTTCCCATCA 59.485 43.478 0.00 0.00 0.00 3.07
2490 2513 4.106324 AGCCCAATTTTTCTTCCCATCAT 58.894 39.130 0.00 0.00 0.00 2.45
2491 2514 4.537288 AGCCCAATTTTTCTTCCCATCATT 59.463 37.500 0.00 0.00 0.00 2.57
2492 2515 5.014438 AGCCCAATTTTTCTTCCCATCATTT 59.986 36.000 0.00 0.00 0.00 2.32
2493 2516 5.711506 GCCCAATTTTTCTTCCCATCATTTT 59.288 36.000 0.00 0.00 0.00 1.82
2494 2517 6.127925 GCCCAATTTTTCTTCCCATCATTTTC 60.128 38.462 0.00 0.00 0.00 2.29
2495 2518 6.941436 CCCAATTTTTCTTCCCATCATTTTCA 59.059 34.615 0.00 0.00 0.00 2.69
2496 2519 7.094677 CCCAATTTTTCTTCCCATCATTTTCAC 60.095 37.037 0.00 0.00 0.00 3.18
2497 2520 7.360269 CCAATTTTTCTTCCCATCATTTTCACG 60.360 37.037 0.00 0.00 0.00 4.35
2498 2521 6.398234 TTTTTCTTCCCATCATTTTCACGA 57.602 33.333 0.00 0.00 0.00 4.35
2499 2522 6.398234 TTTTCTTCCCATCATTTTCACGAA 57.602 33.333 0.00 0.00 0.00 3.85
2500 2523 6.398234 TTTCTTCCCATCATTTTCACGAAA 57.602 33.333 0.00 0.00 0.00 3.46
2501 2524 5.627499 TCTTCCCATCATTTTCACGAAAG 57.373 39.130 0.00 0.00 0.00 2.62
2502 2525 5.312895 TCTTCCCATCATTTTCACGAAAGA 58.687 37.500 0.00 0.00 0.00 2.52
2503 2526 5.181245 TCTTCCCATCATTTTCACGAAAGAC 59.819 40.000 0.00 0.00 0.00 3.01
2504 2527 4.393834 TCCCATCATTTTCACGAAAGACA 58.606 39.130 0.00 0.00 0.00 3.41
2505 2528 5.009631 TCCCATCATTTTCACGAAAGACAT 58.990 37.500 0.00 0.00 0.00 3.06
2506 2529 5.476599 TCCCATCATTTTCACGAAAGACATT 59.523 36.000 0.00 0.00 0.00 2.71
2507 2530 6.657117 TCCCATCATTTTCACGAAAGACATTA 59.343 34.615 0.00 0.00 0.00 1.90
2508 2531 7.175816 TCCCATCATTTTCACGAAAGACATTAA 59.824 33.333 0.00 0.00 0.00 1.40
2509 2532 7.812191 CCCATCATTTTCACGAAAGACATTAAA 59.188 33.333 0.00 0.00 0.00 1.52
2510 2533 9.190858 CCATCATTTTCACGAAAGACATTAAAA 57.809 29.630 0.00 0.00 0.00 1.52
2518 2541 9.663904 TTCACGAAAGACATTAAAAAGATGAAG 57.336 29.630 0.00 0.00 0.00 3.02
2519 2542 7.803189 TCACGAAAGACATTAAAAAGATGAAGC 59.197 33.333 0.00 0.00 0.00 3.86
2520 2543 7.591057 CACGAAAGACATTAAAAAGATGAAGCA 59.409 33.333 0.00 0.00 0.00 3.91
2521 2544 8.299570 ACGAAAGACATTAAAAAGATGAAGCAT 58.700 29.630 0.00 0.00 0.00 3.79
2522 2545 9.773328 CGAAAGACATTAAAAAGATGAAGCATA 57.227 29.630 0.00 0.00 0.00 3.14
2527 2550 9.674824 GACATTAAAAAGATGAAGCATATGAGG 57.325 33.333 6.97 0.00 0.00 3.86
2528 2551 8.139989 ACATTAAAAAGATGAAGCATATGAGGC 58.860 33.333 6.97 0.00 0.00 4.70
2529 2552 7.643569 TTAAAAAGATGAAGCATATGAGGCA 57.356 32.000 6.97 0.48 0.00 4.75
2530 2553 6.534475 AAAAAGATGAAGCATATGAGGCAA 57.466 33.333 6.97 0.00 0.00 4.52
2531 2554 5.511234 AAAGATGAAGCATATGAGGCAAC 57.489 39.130 6.97 0.00 0.00 4.17
2532 2555 3.484407 AGATGAAGCATATGAGGCAACC 58.516 45.455 6.97 0.00 37.17 3.77
2533 2556 3.137913 AGATGAAGCATATGAGGCAACCT 59.862 43.478 6.97 0.00 36.03 3.50
2534 2557 3.370840 TGAAGCATATGAGGCAACCTT 57.629 42.857 6.97 0.00 31.76 3.50
2535 2558 4.502105 TGAAGCATATGAGGCAACCTTA 57.498 40.909 6.97 0.00 31.76 2.69
2536 2559 4.854173 TGAAGCATATGAGGCAACCTTAA 58.146 39.130 6.97 0.00 31.76 1.85
2537 2560 5.448654 TGAAGCATATGAGGCAACCTTAAT 58.551 37.500 6.97 0.00 31.76 1.40
2538 2561 5.893255 TGAAGCATATGAGGCAACCTTAATT 59.107 36.000 6.97 0.00 31.76 1.40
2539 2562 6.039717 TGAAGCATATGAGGCAACCTTAATTC 59.960 38.462 6.97 0.00 31.76 2.17
2540 2563 4.829492 AGCATATGAGGCAACCTTAATTCC 59.171 41.667 6.97 0.00 31.76 3.01
2541 2564 4.584325 GCATATGAGGCAACCTTAATTCCA 59.416 41.667 6.97 0.00 31.76 3.53
2542 2565 5.244626 GCATATGAGGCAACCTTAATTCCAT 59.755 40.000 6.97 0.00 31.76 3.41
2543 2566 6.239402 GCATATGAGGCAACCTTAATTCCATT 60.239 38.462 6.97 0.00 31.76 3.16
2544 2567 7.687592 GCATATGAGGCAACCTTAATTCCATTT 60.688 37.037 6.97 0.00 31.76 2.32
2545 2568 6.625532 ATGAGGCAACCTTAATTCCATTTT 57.374 33.333 0.00 0.00 31.76 1.82
2546 2569 6.432403 TGAGGCAACCTTAATTCCATTTTT 57.568 33.333 0.00 0.00 31.76 1.94
2607 2630 9.884465 AAAACAAGAAACTAGAAGATTCGATTG 57.116 29.630 0.00 0.98 32.96 2.67
2608 2631 7.066374 ACAAGAAACTAGAAGATTCGATTGC 57.934 36.000 0.00 0.00 32.96 3.56
2609 2632 6.650807 ACAAGAAACTAGAAGATTCGATTGCA 59.349 34.615 0.00 0.00 32.96 4.08
2610 2633 7.173218 ACAAGAAACTAGAAGATTCGATTGCAA 59.827 33.333 0.00 0.00 32.96 4.08
2611 2634 7.301068 AGAAACTAGAAGATTCGATTGCAAG 57.699 36.000 4.94 0.00 32.96 4.01
2612 2635 7.099764 AGAAACTAGAAGATTCGATTGCAAGA 58.900 34.615 4.94 0.00 32.96 3.02
2613 2636 7.768120 AGAAACTAGAAGATTCGATTGCAAGAT 59.232 33.333 4.94 0.00 32.96 2.40
2614 2637 7.475771 AACTAGAAGATTCGATTGCAAGATC 57.524 36.000 4.94 6.09 0.00 2.75
2615 2638 6.815089 ACTAGAAGATTCGATTGCAAGATCT 58.185 36.000 4.94 8.24 0.00 2.75
2616 2639 7.946207 ACTAGAAGATTCGATTGCAAGATCTA 58.054 34.615 4.94 1.63 0.00 1.98
2617 2640 8.417106 ACTAGAAGATTCGATTGCAAGATCTAA 58.583 33.333 4.94 0.00 0.00 2.10
2618 2641 9.254133 CTAGAAGATTCGATTGCAAGATCTAAA 57.746 33.333 4.94 0.00 0.00 1.85
2619 2642 8.140677 AGAAGATTCGATTGCAAGATCTAAAG 57.859 34.615 4.94 0.00 0.00 1.85
2620 2643 7.984050 AGAAGATTCGATTGCAAGATCTAAAGA 59.016 33.333 4.94 0.00 0.00 2.52
2621 2644 8.674263 AAGATTCGATTGCAAGATCTAAAGAT 57.326 30.769 4.94 0.00 37.51 2.40
2622 2645 9.770097 AAGATTCGATTGCAAGATCTAAAGATA 57.230 29.630 4.94 0.00 34.37 1.98
2623 2646 9.941325 AGATTCGATTGCAAGATCTAAAGATAT 57.059 29.630 4.94 0.00 34.37 1.63
2626 2649 8.988064 TCGATTGCAAGATCTAAAGATATACC 57.012 34.615 4.94 0.00 34.37 2.73
2627 2650 8.807118 TCGATTGCAAGATCTAAAGATATACCT 58.193 33.333 4.94 0.00 34.37 3.08
2628 2651 9.429359 CGATTGCAAGATCTAAAGATATACCTT 57.571 33.333 4.94 0.00 34.37 3.50
2632 2655 9.770097 TGCAAGATCTAAAGATATACCTTCAAG 57.230 33.333 0.00 0.00 34.37 3.02
2633 2656 8.716909 GCAAGATCTAAAGATATACCTTCAAGC 58.283 37.037 0.00 0.00 34.37 4.01
2634 2657 9.770097 CAAGATCTAAAGATATACCTTCAAGCA 57.230 33.333 0.00 0.00 34.37 3.91
2635 2658 9.771534 AAGATCTAAAGATATACCTTCAAGCAC 57.228 33.333 0.00 0.00 34.37 4.40
2636 2659 9.153479 AGATCTAAAGATATACCTTCAAGCACT 57.847 33.333 0.00 0.00 34.37 4.40
2637 2660 9.418045 GATCTAAAGATATACCTTCAAGCACTC 57.582 37.037 0.00 0.00 34.37 3.51
2638 2661 8.306313 TCTAAAGATATACCTTCAAGCACTCA 57.694 34.615 0.00 0.00 0.00 3.41
2639 2662 8.198109 TCTAAAGATATACCTTCAAGCACTCAC 58.802 37.037 0.00 0.00 0.00 3.51
2640 2663 5.283457 AGATATACCTTCAAGCACTCACC 57.717 43.478 0.00 0.00 0.00 4.02
2641 2664 4.965532 AGATATACCTTCAAGCACTCACCT 59.034 41.667 0.00 0.00 0.00 4.00
2642 2665 3.618690 ATACCTTCAAGCACTCACCTC 57.381 47.619 0.00 0.00 0.00 3.85
2643 2666 0.398318 ACCTTCAAGCACTCACCTCC 59.602 55.000 0.00 0.00 0.00 4.30
2644 2667 0.322008 CCTTCAAGCACTCACCTCCC 60.322 60.000 0.00 0.00 0.00 4.30
2645 2668 0.322008 CTTCAAGCACTCACCTCCCC 60.322 60.000 0.00 0.00 0.00 4.81
2646 2669 2.046892 CAAGCACTCACCTCCCCG 60.047 66.667 0.00 0.00 0.00 5.73
2647 2670 3.322466 AAGCACTCACCTCCCCGG 61.322 66.667 0.00 0.00 39.35 5.73
2650 2673 3.636231 CACTCACCTCCCCGGCAA 61.636 66.667 0.00 0.00 35.61 4.52
2651 2674 3.637273 ACTCACCTCCCCGGCAAC 61.637 66.667 0.00 0.00 35.61 4.17
2664 2687 2.429069 GCAACGGCGCCAGAAAAG 60.429 61.111 28.98 11.60 0.00 2.27
2665 2688 2.903547 GCAACGGCGCCAGAAAAGA 61.904 57.895 28.98 0.00 0.00 2.52
2666 2689 1.207593 CAACGGCGCCAGAAAAGAG 59.792 57.895 28.98 9.93 0.00 2.85
2667 2690 2.617274 AACGGCGCCAGAAAAGAGC 61.617 57.895 28.98 0.00 0.00 4.09
2668 2691 2.743928 CGGCGCCAGAAAAGAGCT 60.744 61.111 28.98 0.00 0.00 4.09
2669 2692 2.328099 CGGCGCCAGAAAAGAGCTT 61.328 57.895 28.98 0.00 0.00 3.74
2670 2693 1.211190 GGCGCCAGAAAAGAGCTTG 59.789 57.895 24.80 0.00 0.00 4.01
2671 2694 1.237285 GGCGCCAGAAAAGAGCTTGA 61.237 55.000 24.80 0.00 0.00 3.02
2672 2695 0.807496 GCGCCAGAAAAGAGCTTGAT 59.193 50.000 0.00 0.00 0.00 2.57
2673 2696 1.467035 GCGCCAGAAAAGAGCTTGATG 60.467 52.381 0.00 0.00 0.00 3.07
2674 2697 1.808945 CGCCAGAAAAGAGCTTGATGT 59.191 47.619 0.00 0.00 0.00 3.06
2675 2698 2.159599 CGCCAGAAAAGAGCTTGATGTC 60.160 50.000 0.00 0.00 0.00 3.06
2676 2699 3.080319 GCCAGAAAAGAGCTTGATGTCT 58.920 45.455 0.00 0.00 0.00 3.41
2677 2700 4.256920 GCCAGAAAAGAGCTTGATGTCTA 58.743 43.478 0.00 0.00 0.00 2.59
2678 2701 4.094146 GCCAGAAAAGAGCTTGATGTCTAC 59.906 45.833 0.00 0.00 0.00 2.59
2679 2702 5.486526 CCAGAAAAGAGCTTGATGTCTACT 58.513 41.667 0.00 0.00 0.00 2.57
2680 2703 6.634805 CCAGAAAAGAGCTTGATGTCTACTA 58.365 40.000 0.00 0.00 0.00 1.82
2681 2704 7.271511 CCAGAAAAGAGCTTGATGTCTACTAT 58.728 38.462 0.00 0.00 0.00 2.12
2682 2705 7.224362 CCAGAAAAGAGCTTGATGTCTACTATG 59.776 40.741 0.00 0.00 0.00 2.23
2683 2706 6.760770 AGAAAAGAGCTTGATGTCTACTATGC 59.239 38.462 0.00 0.00 0.00 3.14
2684 2707 5.604758 AAGAGCTTGATGTCTACTATGCA 57.395 39.130 0.00 0.00 0.00 3.96
2685 2708 5.604758 AGAGCTTGATGTCTACTATGCAA 57.395 39.130 0.00 0.00 0.00 4.08
2686 2709 5.355596 AGAGCTTGATGTCTACTATGCAAC 58.644 41.667 0.00 0.00 0.00 4.17
2687 2710 4.446371 AGCTTGATGTCTACTATGCAACC 58.554 43.478 0.00 0.00 0.00 3.77
2688 2711 4.163078 AGCTTGATGTCTACTATGCAACCT 59.837 41.667 0.00 0.00 0.00 3.50
2689 2712 4.878397 GCTTGATGTCTACTATGCAACCTT 59.122 41.667 0.00 0.00 0.00 3.50
2690 2713 5.007136 GCTTGATGTCTACTATGCAACCTTC 59.993 44.000 0.00 0.00 0.00 3.46
2691 2714 5.939764 TGATGTCTACTATGCAACCTTCT 57.060 39.130 0.00 0.00 0.00 2.85
2692 2715 6.299805 TGATGTCTACTATGCAACCTTCTT 57.700 37.500 0.00 0.00 0.00 2.52
2693 2716 6.341316 TGATGTCTACTATGCAACCTTCTTC 58.659 40.000 0.00 0.00 0.00 2.87
2694 2717 6.155221 TGATGTCTACTATGCAACCTTCTTCT 59.845 38.462 0.00 0.00 0.00 2.85
2695 2718 6.360370 TGTCTACTATGCAACCTTCTTCTT 57.640 37.500 0.00 0.00 0.00 2.52
2696 2719 6.166279 TGTCTACTATGCAACCTTCTTCTTG 58.834 40.000 0.00 0.00 0.00 3.02
2697 2720 6.166982 GTCTACTATGCAACCTTCTTCTTGT 58.833 40.000 0.00 0.00 0.00 3.16
2698 2721 7.039293 TGTCTACTATGCAACCTTCTTCTTGTA 60.039 37.037 0.00 0.00 0.00 2.41
2699 2722 7.489757 GTCTACTATGCAACCTTCTTCTTGTAG 59.510 40.741 0.00 0.00 0.00 2.74
2700 2723 6.360370 ACTATGCAACCTTCTTCTTGTAGA 57.640 37.500 0.00 0.00 0.00 2.59
2701 2724 6.166982 ACTATGCAACCTTCTTCTTGTAGAC 58.833 40.000 0.00 0.00 0.00 2.59
2702 2725 3.390135 TGCAACCTTCTTCTTGTAGACG 58.610 45.455 0.00 0.00 0.00 4.18
2703 2726 3.181469 TGCAACCTTCTTCTTGTAGACGT 60.181 43.478 0.00 0.00 0.00 4.34
2704 2727 3.808174 GCAACCTTCTTCTTGTAGACGTT 59.192 43.478 0.00 0.00 0.00 3.99
2705 2728 4.318831 GCAACCTTCTTCTTGTAGACGTTG 60.319 45.833 0.00 0.00 37.53 4.10
2706 2729 4.667519 ACCTTCTTCTTGTAGACGTTGT 57.332 40.909 0.00 0.00 0.00 3.32
2707 2730 5.019785 ACCTTCTTCTTGTAGACGTTGTT 57.980 39.130 0.00 0.00 0.00 2.83
2708 2731 4.809426 ACCTTCTTCTTGTAGACGTTGTTG 59.191 41.667 0.00 0.00 0.00 3.33
2709 2732 4.211374 CCTTCTTCTTGTAGACGTTGTTGG 59.789 45.833 0.00 0.00 0.00 3.77
2710 2733 3.724374 TCTTCTTGTAGACGTTGTTGGG 58.276 45.455 0.00 0.00 0.00 4.12
2711 2734 1.873698 TCTTGTAGACGTTGTTGGGC 58.126 50.000 0.00 0.00 0.00 5.36
2712 2735 0.872388 CTTGTAGACGTTGTTGGGCC 59.128 55.000 0.00 0.00 0.00 5.80
2713 2736 0.470766 TTGTAGACGTTGTTGGGCCT 59.529 50.000 4.53 0.00 0.00 5.19
2714 2737 0.034337 TGTAGACGTTGTTGGGCCTC 59.966 55.000 4.53 0.00 0.00 4.70
2715 2738 0.672711 GTAGACGTTGTTGGGCCTCC 60.673 60.000 4.53 0.00 0.00 4.30
2716 2739 1.122632 TAGACGTTGTTGGGCCTCCA 61.123 55.000 4.53 0.00 42.25 3.86
2724 2747 2.853542 TGGGCCTCCAAGTGCAGA 60.854 61.111 4.53 0.00 40.73 4.26
2725 2748 2.045536 GGGCCTCCAAGTGCAGAG 60.046 66.667 0.84 0.00 0.00 3.35
2729 2752 3.733709 CCTCCAAGTGCAGAGGTTT 57.266 52.632 10.81 0.00 44.01 3.27
2730 2753 1.242076 CCTCCAAGTGCAGAGGTTTG 58.758 55.000 10.81 0.88 44.01 2.93
2731 2754 1.477558 CCTCCAAGTGCAGAGGTTTGT 60.478 52.381 10.81 0.00 44.01 2.83
2732 2755 2.224523 CCTCCAAGTGCAGAGGTTTGTA 60.225 50.000 10.81 0.00 44.01 2.41
2733 2756 3.070018 CTCCAAGTGCAGAGGTTTGTAG 58.930 50.000 0.00 0.00 0.00 2.74
2734 2757 2.154462 CCAAGTGCAGAGGTTTGTAGG 58.846 52.381 0.00 0.00 0.00 3.18
2735 2758 2.224523 CCAAGTGCAGAGGTTTGTAGGA 60.225 50.000 0.00 0.00 0.00 2.94
2736 2759 2.808543 CAAGTGCAGAGGTTTGTAGGAC 59.191 50.000 0.00 0.00 0.00 3.85
2737 2760 2.047061 AGTGCAGAGGTTTGTAGGACA 58.953 47.619 0.00 0.00 0.00 4.02
2738 2761 2.037772 AGTGCAGAGGTTTGTAGGACAG 59.962 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 47 2.111043 ACCAACCAGCAGTGTCCG 59.889 61.111 0.00 0.00 0.00 4.79
127 129 5.258841 TCAGTTACTCTCTCCGTTCCAATA 58.741 41.667 0.00 0.00 0.00 1.90
757 768 4.065088 TGTAGAGACTGGCACATTGAAAC 58.935 43.478 0.00 0.00 38.20 2.78
861 872 7.346471 AGGCTGAAAAATGGTTAGAGCTAATA 58.654 34.615 0.00 0.00 0.00 0.98
878 890 3.825328 AGAGCAGAAAAGAAGGCTGAAA 58.175 40.909 0.00 0.00 36.59 2.69
879 891 3.498774 AGAGCAGAAAAGAAGGCTGAA 57.501 42.857 0.00 0.00 36.59 3.02
1065 1079 5.411781 CAGACAGTTACCAGAACTATGACC 58.588 45.833 0.00 0.00 0.00 4.02
1208 1223 7.560991 TCATGAGGGTAATTCAGCAATTTATGT 59.439 33.333 0.00 0.00 33.95 2.29
1272 1287 3.485877 GGAACAGTGCAAGCGACATAATC 60.486 47.826 0.00 0.00 0.00 1.75
1316 1331 9.423061 GTACCTACTTAGTTGACGGATTAAAAA 57.577 33.333 0.00 0.00 0.00 1.94
1392 1407 4.957296 ACAAACATAAACAGACTCGGAGT 58.043 39.130 11.09 11.09 0.00 3.85
1710 1730 4.059511 CTGAGAACAGCCATCATCATCTC 58.940 47.826 0.00 0.00 37.33 2.75
1714 1734 3.708403 AACTGAGAACAGCCATCATCA 57.292 42.857 0.00 0.00 46.95 3.07
2104 2127 7.052873 CCAGGAATTCAAATCTCATCTACAGT 58.947 38.462 7.93 0.00 0.00 3.55
2145 2168 9.444600 AAACCGACTTTTACAACACTCATATAT 57.555 29.630 0.00 0.00 0.00 0.86
2354 2377 4.572985 TGCTAATGATATGCAAAGCCAC 57.427 40.909 0.00 0.00 38.26 5.01
2355 2378 4.828387 TGATGCTAATGATATGCAAAGCCA 59.172 37.500 0.00 0.00 40.24 4.75
2356 2379 5.381174 TGATGCTAATGATATGCAAAGCC 57.619 39.130 0.00 0.00 40.24 4.35
2357 2380 5.805486 CCATGATGCTAATGATATGCAAAGC 59.195 40.000 0.00 0.00 40.24 3.51
2358 2381 6.071560 ACCCATGATGCTAATGATATGCAAAG 60.072 38.462 0.00 0.00 40.24 2.77
2359 2382 5.776208 ACCCATGATGCTAATGATATGCAAA 59.224 36.000 0.00 0.00 40.24 3.68
2360 2383 5.326900 ACCCATGATGCTAATGATATGCAA 58.673 37.500 0.00 0.00 40.24 4.08
2361 2384 4.925836 ACCCATGATGCTAATGATATGCA 58.074 39.130 0.00 0.00 41.13 3.96
2362 2385 7.283807 TGAATACCCATGATGCTAATGATATGC 59.716 37.037 0.00 0.00 0.00 3.14
2363 2386 8.741603 TGAATACCCATGATGCTAATGATATG 57.258 34.615 0.00 0.00 0.00 1.78
2365 2388 9.836864 GTATGAATACCCATGATGCTAATGATA 57.163 33.333 0.00 0.00 0.00 2.15
2366 2389 8.554870 AGTATGAATACCCATGATGCTAATGAT 58.445 33.333 0.00 0.00 33.79 2.45
2367 2390 7.921304 AGTATGAATACCCATGATGCTAATGA 58.079 34.615 0.00 0.00 33.79 2.57
2368 2391 9.671279 TTAGTATGAATACCCATGATGCTAATG 57.329 33.333 0.00 0.00 33.79 1.90
2369 2392 9.672673 GTTAGTATGAATACCCATGATGCTAAT 57.327 33.333 0.00 0.00 33.79 1.73
2370 2393 8.655901 TGTTAGTATGAATACCCATGATGCTAA 58.344 33.333 0.00 0.00 33.79 3.09
2371 2394 8.201242 TGTTAGTATGAATACCCATGATGCTA 57.799 34.615 0.00 0.00 33.79 3.49
2372 2395 7.078249 TGTTAGTATGAATACCCATGATGCT 57.922 36.000 0.00 0.00 33.79 3.79
2373 2396 7.744087 TTGTTAGTATGAATACCCATGATGC 57.256 36.000 0.00 0.00 33.79 3.91
2378 2401 9.806448 TGCAATATTGTTAGTATGAATACCCAT 57.194 29.630 16.61 0.00 33.79 4.00
2379 2402 9.634021 TTGCAATATTGTTAGTATGAATACCCA 57.366 29.630 16.61 0.00 33.79 4.51
2403 2426 9.476202 AAAATATGTGAATGATGAGCATGATTG 57.524 29.630 0.00 0.00 37.28 2.67
2407 2430 8.860128 GCATAAAATATGTGAATGATGAGCATG 58.140 33.333 0.00 0.00 37.28 4.06
2408 2431 8.033038 GGCATAAAATATGTGAATGATGAGCAT 58.967 33.333 0.00 0.00 39.43 3.79
2409 2432 7.014422 TGGCATAAAATATGTGAATGATGAGCA 59.986 33.333 0.00 0.00 0.00 4.26
2410 2433 7.372714 TGGCATAAAATATGTGAATGATGAGC 58.627 34.615 0.00 0.00 0.00 4.26
2411 2434 9.406828 CTTGGCATAAAATATGTGAATGATGAG 57.593 33.333 0.00 0.00 0.00 2.90
2412 2435 7.868922 GCTTGGCATAAAATATGTGAATGATGA 59.131 33.333 0.00 0.00 0.00 2.92
2413 2436 7.654116 TGCTTGGCATAAAATATGTGAATGATG 59.346 33.333 0.00 0.00 31.71 3.07
2414 2437 7.728148 TGCTTGGCATAAAATATGTGAATGAT 58.272 30.769 0.00 0.00 31.71 2.45
2415 2438 7.110043 TGCTTGGCATAAAATATGTGAATGA 57.890 32.000 0.00 0.00 31.71 2.57
2431 2454 5.102953 AGAGTTACATAGAATGCTTGGCA 57.897 39.130 0.00 0.00 44.86 4.92
2432 2455 5.819901 AGAAGAGTTACATAGAATGCTTGGC 59.180 40.000 0.00 0.00 0.00 4.52
2433 2456 7.768120 AGAAGAAGAGTTACATAGAATGCTTGG 59.232 37.037 0.00 0.00 0.00 3.61
2434 2457 8.715191 AGAAGAAGAGTTACATAGAATGCTTG 57.285 34.615 0.00 0.00 0.00 4.01
2436 2459 9.196139 ACTAGAAGAAGAGTTACATAGAATGCT 57.804 33.333 0.00 0.00 0.00 3.79
2444 2467 8.463607 GCTCAAGTACTAGAAGAAGAGTTACAT 58.536 37.037 0.00 0.00 0.00 2.29
2445 2468 7.094291 GGCTCAAGTACTAGAAGAAGAGTTACA 60.094 40.741 0.00 0.00 0.00 2.41
2446 2469 7.252708 GGCTCAAGTACTAGAAGAAGAGTTAC 58.747 42.308 0.00 0.00 0.00 2.50
2447 2470 6.377712 GGGCTCAAGTACTAGAAGAAGAGTTA 59.622 42.308 0.00 0.00 0.00 2.24
2448 2471 5.186215 GGGCTCAAGTACTAGAAGAAGAGTT 59.814 44.000 0.00 0.00 0.00 3.01
2449 2472 4.707934 GGGCTCAAGTACTAGAAGAAGAGT 59.292 45.833 0.00 0.00 0.00 3.24
2450 2473 4.707448 TGGGCTCAAGTACTAGAAGAAGAG 59.293 45.833 0.00 0.00 0.00 2.85
2451 2474 4.673968 TGGGCTCAAGTACTAGAAGAAGA 58.326 43.478 0.00 0.00 0.00 2.87
2452 2475 5.407407 TTGGGCTCAAGTACTAGAAGAAG 57.593 43.478 0.00 0.00 0.00 2.85
2453 2476 6.374417 AATTGGGCTCAAGTACTAGAAGAA 57.626 37.500 4.75 0.00 36.19 2.52
2454 2477 6.374417 AAATTGGGCTCAAGTACTAGAAGA 57.626 37.500 4.75 0.00 36.19 2.87
2455 2478 7.391833 AGAAAAATTGGGCTCAAGTACTAGAAG 59.608 37.037 4.75 0.00 36.19 2.85
2456 2479 7.231467 AGAAAAATTGGGCTCAAGTACTAGAA 58.769 34.615 4.75 0.00 36.19 2.10
2457 2480 6.779860 AGAAAAATTGGGCTCAAGTACTAGA 58.220 36.000 4.75 0.00 36.19 2.43
2458 2481 7.362142 GGAAGAAAAATTGGGCTCAAGTACTAG 60.362 40.741 4.75 0.00 36.19 2.57
2459 2482 6.433093 GGAAGAAAAATTGGGCTCAAGTACTA 59.567 38.462 4.75 0.00 36.19 1.82
2460 2483 5.243954 GGAAGAAAAATTGGGCTCAAGTACT 59.756 40.000 4.75 0.10 36.19 2.73
2461 2484 5.470368 GGAAGAAAAATTGGGCTCAAGTAC 58.530 41.667 4.75 0.00 36.19 2.73
2462 2485 4.526650 GGGAAGAAAAATTGGGCTCAAGTA 59.473 41.667 4.75 0.00 36.19 2.24
2463 2486 3.324846 GGGAAGAAAAATTGGGCTCAAGT 59.675 43.478 4.75 0.00 36.19 3.16
2464 2487 3.324556 TGGGAAGAAAAATTGGGCTCAAG 59.675 43.478 4.75 0.00 36.19 3.02
2465 2488 3.312890 TGGGAAGAAAAATTGGGCTCAA 58.687 40.909 0.00 0.00 37.28 3.02
2466 2489 2.969628 TGGGAAGAAAAATTGGGCTCA 58.030 42.857 0.00 0.00 0.00 4.26
2467 2490 3.515104 TGATGGGAAGAAAAATTGGGCTC 59.485 43.478 0.00 0.00 0.00 4.70
2468 2491 3.519667 TGATGGGAAGAAAAATTGGGCT 58.480 40.909 0.00 0.00 0.00 5.19
2469 2492 3.979101 TGATGGGAAGAAAAATTGGGC 57.021 42.857 0.00 0.00 0.00 5.36
2470 2493 6.941436 TGAAAATGATGGGAAGAAAAATTGGG 59.059 34.615 0.00 0.00 0.00 4.12
2471 2494 7.360269 CGTGAAAATGATGGGAAGAAAAATTGG 60.360 37.037 0.00 0.00 0.00 3.16
2472 2495 7.384660 TCGTGAAAATGATGGGAAGAAAAATTG 59.615 33.333 0.00 0.00 0.00 2.32
2473 2496 7.441017 TCGTGAAAATGATGGGAAGAAAAATT 58.559 30.769 0.00 0.00 0.00 1.82
2474 2497 6.991938 TCGTGAAAATGATGGGAAGAAAAAT 58.008 32.000 0.00 0.00 0.00 1.82
2475 2498 6.398234 TCGTGAAAATGATGGGAAGAAAAA 57.602 33.333 0.00 0.00 0.00 1.94
2476 2499 6.398234 TTCGTGAAAATGATGGGAAGAAAA 57.602 33.333 0.00 0.00 0.00 2.29
2477 2500 6.264292 TCTTTCGTGAAAATGATGGGAAGAAA 59.736 34.615 0.00 0.00 0.00 2.52
2478 2501 5.767665 TCTTTCGTGAAAATGATGGGAAGAA 59.232 36.000 0.00 0.00 0.00 2.52
2479 2502 5.181245 GTCTTTCGTGAAAATGATGGGAAGA 59.819 40.000 0.00 0.00 0.00 2.87
2480 2503 5.048782 TGTCTTTCGTGAAAATGATGGGAAG 60.049 40.000 0.00 0.00 0.00 3.46
2481 2504 4.824537 TGTCTTTCGTGAAAATGATGGGAA 59.175 37.500 0.00 0.00 0.00 3.97
2482 2505 4.393834 TGTCTTTCGTGAAAATGATGGGA 58.606 39.130 0.00 0.00 0.00 4.37
2483 2506 4.764679 TGTCTTTCGTGAAAATGATGGG 57.235 40.909 0.00 0.00 0.00 4.00
2484 2507 8.741101 TTTAATGTCTTTCGTGAAAATGATGG 57.259 30.769 0.00 0.00 0.00 3.51
2492 2515 9.663904 CTTCATCTTTTTAATGTCTTTCGTGAA 57.336 29.630 0.00 0.00 0.00 3.18
2493 2516 7.803189 GCTTCATCTTTTTAATGTCTTTCGTGA 59.197 33.333 0.00 0.00 0.00 4.35
2494 2517 7.591057 TGCTTCATCTTTTTAATGTCTTTCGTG 59.409 33.333 0.00 0.00 0.00 4.35
2495 2518 7.648142 TGCTTCATCTTTTTAATGTCTTTCGT 58.352 30.769 0.00 0.00 0.00 3.85
2496 2519 8.679288 ATGCTTCATCTTTTTAATGTCTTTCG 57.321 30.769 0.00 0.00 0.00 3.46
2501 2524 9.674824 CCTCATATGCTTCATCTTTTTAATGTC 57.325 33.333 0.00 0.00 0.00 3.06
2502 2525 8.139989 GCCTCATATGCTTCATCTTTTTAATGT 58.860 33.333 0.00 0.00 0.00 2.71
2503 2526 8.139350 TGCCTCATATGCTTCATCTTTTTAATG 58.861 33.333 0.00 0.00 0.00 1.90
2504 2527 8.241497 TGCCTCATATGCTTCATCTTTTTAAT 57.759 30.769 0.00 0.00 0.00 1.40
2505 2528 7.643569 TGCCTCATATGCTTCATCTTTTTAA 57.356 32.000 0.00 0.00 0.00 1.52
2506 2529 7.416664 GGTTGCCTCATATGCTTCATCTTTTTA 60.417 37.037 0.00 0.00 0.00 1.52
2507 2530 6.335777 GTTGCCTCATATGCTTCATCTTTTT 58.664 36.000 0.00 0.00 0.00 1.94
2508 2531 5.163478 GGTTGCCTCATATGCTTCATCTTTT 60.163 40.000 0.00 0.00 0.00 2.27
2509 2532 4.340381 GGTTGCCTCATATGCTTCATCTTT 59.660 41.667 0.00 0.00 0.00 2.52
2510 2533 3.887716 GGTTGCCTCATATGCTTCATCTT 59.112 43.478 0.00 0.00 0.00 2.40
2511 2534 3.137913 AGGTTGCCTCATATGCTTCATCT 59.862 43.478 0.00 0.00 0.00 2.90
2512 2535 3.484407 AGGTTGCCTCATATGCTTCATC 58.516 45.455 0.00 0.00 0.00 2.92
2513 2536 3.589951 AGGTTGCCTCATATGCTTCAT 57.410 42.857 0.00 0.00 0.00 2.57
2514 2537 3.370840 AAGGTTGCCTCATATGCTTCA 57.629 42.857 0.00 0.00 30.89 3.02
2515 2538 6.396829 AATTAAGGTTGCCTCATATGCTTC 57.603 37.500 0.00 0.00 30.89 3.86
2516 2539 5.302823 GGAATTAAGGTTGCCTCATATGCTT 59.697 40.000 0.00 0.00 30.89 3.91
2517 2540 4.829492 GGAATTAAGGTTGCCTCATATGCT 59.171 41.667 0.00 0.00 30.89 3.79
2518 2541 4.584325 TGGAATTAAGGTTGCCTCATATGC 59.416 41.667 0.00 0.00 30.89 3.14
2519 2542 6.906157 ATGGAATTAAGGTTGCCTCATATG 57.094 37.500 0.00 0.00 30.89 1.78
2520 2543 7.919385 AAATGGAATTAAGGTTGCCTCATAT 57.081 32.000 0.00 0.00 33.67 1.78
2521 2544 7.732222 AAAATGGAATTAAGGTTGCCTCATA 57.268 32.000 0.00 0.00 33.67 2.15
2522 2545 6.625532 AAAATGGAATTAAGGTTGCCTCAT 57.374 33.333 0.00 0.00 33.67 2.90
2523 2546 6.432403 AAAAATGGAATTAAGGTTGCCTCA 57.568 33.333 0.00 0.00 33.67 3.86
2581 2604 9.884465 CAATCGAATCTTCTAGTTTCTTGTTTT 57.116 29.630 0.00 0.00 0.00 2.43
2582 2605 8.017946 GCAATCGAATCTTCTAGTTTCTTGTTT 58.982 33.333 0.00 0.00 0.00 2.83
2583 2606 7.173218 TGCAATCGAATCTTCTAGTTTCTTGTT 59.827 33.333 0.00 0.00 0.00 2.83
2584 2607 6.650807 TGCAATCGAATCTTCTAGTTTCTTGT 59.349 34.615 0.00 0.00 0.00 3.16
2585 2608 7.065216 TGCAATCGAATCTTCTAGTTTCTTG 57.935 36.000 0.00 0.00 0.00 3.02
2586 2609 7.604164 TCTTGCAATCGAATCTTCTAGTTTCTT 59.396 33.333 0.00 0.00 0.00 2.52
2587 2610 7.099764 TCTTGCAATCGAATCTTCTAGTTTCT 58.900 34.615 0.00 0.00 0.00 2.52
2588 2611 7.295952 TCTTGCAATCGAATCTTCTAGTTTC 57.704 36.000 0.00 0.00 0.00 2.78
2589 2612 7.768120 AGATCTTGCAATCGAATCTTCTAGTTT 59.232 33.333 0.00 0.00 0.00 2.66
2590 2613 7.271511 AGATCTTGCAATCGAATCTTCTAGTT 58.728 34.615 0.00 0.00 0.00 2.24
2591 2614 6.815089 AGATCTTGCAATCGAATCTTCTAGT 58.185 36.000 0.00 0.00 0.00 2.57
2592 2615 8.809159 TTAGATCTTGCAATCGAATCTTCTAG 57.191 34.615 14.90 0.00 0.00 2.43
2593 2616 9.254133 CTTTAGATCTTGCAATCGAATCTTCTA 57.746 33.333 14.90 6.10 0.00 2.10
2594 2617 7.984050 TCTTTAGATCTTGCAATCGAATCTTCT 59.016 33.333 14.90 6.83 0.00 2.85
2595 2618 8.136057 TCTTTAGATCTTGCAATCGAATCTTC 57.864 34.615 14.90 0.88 0.00 2.87
2596 2619 8.674263 ATCTTTAGATCTTGCAATCGAATCTT 57.326 30.769 14.90 4.84 0.00 2.40
2597 2620 9.941325 ATATCTTTAGATCTTGCAATCGAATCT 57.059 29.630 0.00 8.99 36.05 2.40
2600 2623 9.424319 GGTATATCTTTAGATCTTGCAATCGAA 57.576 33.333 0.00 0.00 36.05 3.71
2601 2624 8.807118 AGGTATATCTTTAGATCTTGCAATCGA 58.193 33.333 0.00 0.00 36.05 3.59
2602 2625 8.994429 AGGTATATCTTTAGATCTTGCAATCG 57.006 34.615 0.00 0.00 36.05 3.34
2606 2629 9.770097 CTTGAAGGTATATCTTTAGATCTTGCA 57.230 33.333 0.00 0.00 36.05 4.08
2607 2630 8.716909 GCTTGAAGGTATATCTTTAGATCTTGC 58.283 37.037 0.00 0.00 36.05 4.01
2608 2631 9.770097 TGCTTGAAGGTATATCTTTAGATCTTG 57.230 33.333 0.00 0.00 36.05 3.02
2609 2632 9.771534 GTGCTTGAAGGTATATCTTTAGATCTT 57.228 33.333 0.00 0.00 36.05 2.40
2610 2633 9.153479 AGTGCTTGAAGGTATATCTTTAGATCT 57.847 33.333 0.00 0.00 36.05 2.75
2611 2634 9.418045 GAGTGCTTGAAGGTATATCTTTAGATC 57.582 37.037 0.00 0.00 36.05 2.75
2612 2635 8.928448 TGAGTGCTTGAAGGTATATCTTTAGAT 58.072 33.333 0.00 0.00 38.51 1.98
2613 2636 8.198109 GTGAGTGCTTGAAGGTATATCTTTAGA 58.802 37.037 0.00 0.00 0.00 2.10
2614 2637 7.439655 GGTGAGTGCTTGAAGGTATATCTTTAG 59.560 40.741 0.00 2.53 0.00 1.85
2615 2638 7.125811 AGGTGAGTGCTTGAAGGTATATCTTTA 59.874 37.037 0.00 0.00 0.00 1.85
2616 2639 6.069963 AGGTGAGTGCTTGAAGGTATATCTTT 60.070 38.462 0.00 0.00 0.00 2.52
2617 2640 5.426833 AGGTGAGTGCTTGAAGGTATATCTT 59.573 40.000 0.00 0.00 0.00 2.40
2618 2641 4.965532 AGGTGAGTGCTTGAAGGTATATCT 59.034 41.667 0.00 0.00 0.00 1.98
2619 2642 5.283457 AGGTGAGTGCTTGAAGGTATATC 57.717 43.478 0.00 0.00 0.00 1.63
2620 2643 4.101741 GGAGGTGAGTGCTTGAAGGTATAT 59.898 45.833 0.00 0.00 0.00 0.86
2621 2644 3.451178 GGAGGTGAGTGCTTGAAGGTATA 59.549 47.826 0.00 0.00 0.00 1.47
2622 2645 2.237392 GGAGGTGAGTGCTTGAAGGTAT 59.763 50.000 0.00 0.00 0.00 2.73
2623 2646 1.623811 GGAGGTGAGTGCTTGAAGGTA 59.376 52.381 0.00 0.00 0.00 3.08
2624 2647 0.398318 GGAGGTGAGTGCTTGAAGGT 59.602 55.000 0.00 0.00 0.00 3.50
2625 2648 0.322008 GGGAGGTGAGTGCTTGAAGG 60.322 60.000 0.00 0.00 0.00 3.46
2626 2649 0.322008 GGGGAGGTGAGTGCTTGAAG 60.322 60.000 0.00 0.00 0.00 3.02
2627 2650 1.761174 GGGGAGGTGAGTGCTTGAA 59.239 57.895 0.00 0.00 0.00 2.69
2628 2651 2.583441 CGGGGAGGTGAGTGCTTGA 61.583 63.158 0.00 0.00 0.00 3.02
2629 2652 2.046892 CGGGGAGGTGAGTGCTTG 60.047 66.667 0.00 0.00 0.00 4.01
2630 2653 3.322466 CCGGGGAGGTGAGTGCTT 61.322 66.667 0.00 0.00 34.51 3.91
2633 2656 3.636231 TTGCCGGGGAGGTGAGTG 61.636 66.667 2.18 0.00 43.70 3.51
2634 2657 3.637273 GTTGCCGGGGAGGTGAGT 61.637 66.667 2.18 0.00 43.70 3.41
2635 2658 4.760047 CGTTGCCGGGGAGGTGAG 62.760 72.222 2.18 0.00 43.70 3.51
2647 2670 2.429069 CTTTTCTGGCGCCGTTGC 60.429 61.111 23.90 0.00 0.00 4.17
2648 2671 1.207593 CTCTTTTCTGGCGCCGTTG 59.792 57.895 23.90 14.75 0.00 4.10
2649 2672 2.617274 GCTCTTTTCTGGCGCCGTT 61.617 57.895 23.90 0.00 0.00 4.44
2650 2673 3.050275 GCTCTTTTCTGGCGCCGT 61.050 61.111 23.90 0.00 0.00 5.68
2651 2674 2.328099 AAGCTCTTTTCTGGCGCCG 61.328 57.895 23.90 16.91 0.00 6.46
2652 2675 1.211190 CAAGCTCTTTTCTGGCGCC 59.789 57.895 22.73 22.73 0.00 6.53
2653 2676 0.807496 ATCAAGCTCTTTTCTGGCGC 59.193 50.000 0.00 0.00 0.00 6.53
2654 2677 1.808945 ACATCAAGCTCTTTTCTGGCG 59.191 47.619 0.00 0.00 0.00 5.69
2655 2678 3.080319 AGACATCAAGCTCTTTTCTGGC 58.920 45.455 0.00 0.00 0.00 4.85
2656 2679 5.486526 AGTAGACATCAAGCTCTTTTCTGG 58.513 41.667 0.00 0.00 0.00 3.86
2657 2680 7.254387 GCATAGTAGACATCAAGCTCTTTTCTG 60.254 40.741 0.00 0.00 0.00 3.02
2658 2681 6.760770 GCATAGTAGACATCAAGCTCTTTTCT 59.239 38.462 0.00 0.00 0.00 2.52
2659 2682 6.536582 TGCATAGTAGACATCAAGCTCTTTTC 59.463 38.462 0.00 0.00 0.00 2.29
2660 2683 6.409704 TGCATAGTAGACATCAAGCTCTTTT 58.590 36.000 0.00 0.00 0.00 2.27
2661 2684 5.982356 TGCATAGTAGACATCAAGCTCTTT 58.018 37.500 0.00 0.00 0.00 2.52
2662 2685 5.604758 TGCATAGTAGACATCAAGCTCTT 57.395 39.130 0.00 0.00 0.00 2.85
2663 2686 5.355596 GTTGCATAGTAGACATCAAGCTCT 58.644 41.667 0.00 0.00 0.00 4.09
2664 2687 4.509600 GGTTGCATAGTAGACATCAAGCTC 59.490 45.833 0.00 0.00 0.00 4.09
2665 2688 4.163078 AGGTTGCATAGTAGACATCAAGCT 59.837 41.667 0.00 0.00 37.42 3.74
2666 2689 4.446371 AGGTTGCATAGTAGACATCAAGC 58.554 43.478 0.00 0.00 33.64 4.01
2667 2690 6.344500 AGAAGGTTGCATAGTAGACATCAAG 58.656 40.000 0.00 0.00 0.00 3.02
2668 2691 6.299805 AGAAGGTTGCATAGTAGACATCAA 57.700 37.500 0.00 0.00 0.00 2.57
2669 2692 5.939764 AGAAGGTTGCATAGTAGACATCA 57.060 39.130 0.00 0.00 0.00 3.07
2670 2693 6.578023 AGAAGAAGGTTGCATAGTAGACATC 58.422 40.000 0.00 0.00 0.00 3.06
2671 2694 6.552445 AGAAGAAGGTTGCATAGTAGACAT 57.448 37.500 0.00 0.00 0.00 3.06
2672 2695 6.166279 CAAGAAGAAGGTTGCATAGTAGACA 58.834 40.000 0.00 0.00 0.00 3.41
2673 2696 6.166982 ACAAGAAGAAGGTTGCATAGTAGAC 58.833 40.000 0.00 0.00 0.00 2.59
2674 2697 6.360370 ACAAGAAGAAGGTTGCATAGTAGA 57.640 37.500 0.00 0.00 0.00 2.59
2675 2698 7.489757 GTCTACAAGAAGAAGGTTGCATAGTAG 59.510 40.741 0.00 0.00 0.00 2.57
2676 2699 7.321153 GTCTACAAGAAGAAGGTTGCATAGTA 58.679 38.462 0.00 0.00 0.00 1.82
2677 2700 6.166982 GTCTACAAGAAGAAGGTTGCATAGT 58.833 40.000 0.00 0.00 0.00 2.12
2678 2701 5.289675 CGTCTACAAGAAGAAGGTTGCATAG 59.710 44.000 0.00 0.00 0.00 2.23
2679 2702 5.168569 CGTCTACAAGAAGAAGGTTGCATA 58.831 41.667 0.00 0.00 0.00 3.14
2680 2703 3.997021 CGTCTACAAGAAGAAGGTTGCAT 59.003 43.478 0.00 0.00 0.00 3.96
2681 2704 3.181469 ACGTCTACAAGAAGAAGGTTGCA 60.181 43.478 0.00 0.00 30.29 4.08
2682 2705 3.391049 ACGTCTACAAGAAGAAGGTTGC 58.609 45.455 0.00 0.00 30.29 4.17
2683 2706 4.809426 ACAACGTCTACAAGAAGAAGGTTG 59.191 41.667 13.28 13.28 42.32 3.77
2684 2707 5.019785 ACAACGTCTACAAGAAGAAGGTT 57.980 39.130 0.00 0.00 30.29 3.50
2685 2708 4.667519 ACAACGTCTACAAGAAGAAGGT 57.332 40.909 0.00 0.00 30.29 3.50
2686 2709 4.211374 CCAACAACGTCTACAAGAAGAAGG 59.789 45.833 0.00 0.00 30.29 3.46
2687 2710 4.211374 CCCAACAACGTCTACAAGAAGAAG 59.789 45.833 0.00 0.00 0.00 2.85
2688 2711 4.124238 CCCAACAACGTCTACAAGAAGAA 58.876 43.478 0.00 0.00 0.00 2.52
2689 2712 3.724374 CCCAACAACGTCTACAAGAAGA 58.276 45.455 0.00 0.00 0.00 2.87
2690 2713 2.223377 GCCCAACAACGTCTACAAGAAG 59.777 50.000 0.00 0.00 0.00 2.85
2691 2714 2.215196 GCCCAACAACGTCTACAAGAA 58.785 47.619 0.00 0.00 0.00 2.52
2692 2715 1.541670 GGCCCAACAACGTCTACAAGA 60.542 52.381 0.00 0.00 0.00 3.02
2693 2716 0.872388 GGCCCAACAACGTCTACAAG 59.128 55.000 0.00 0.00 0.00 3.16
2694 2717 0.470766 AGGCCCAACAACGTCTACAA 59.529 50.000 0.00 0.00 0.00 2.41
2695 2718 0.034337 GAGGCCCAACAACGTCTACA 59.966 55.000 0.00 0.00 0.00 2.74
2696 2719 0.672711 GGAGGCCCAACAACGTCTAC 60.673 60.000 0.00 0.00 0.00 2.59
2697 2720 1.122632 TGGAGGCCCAACAACGTCTA 61.123 55.000 0.00 0.00 40.09 2.59
2698 2721 1.990160 TTGGAGGCCCAACAACGTCT 61.990 55.000 0.00 0.00 46.94 4.18
2699 2722 1.515521 CTTGGAGGCCCAACAACGTC 61.516 60.000 0.00 0.00 46.94 4.34
2700 2723 1.528309 CTTGGAGGCCCAACAACGT 60.528 57.895 0.00 0.00 46.94 3.99
2701 2724 1.528309 ACTTGGAGGCCCAACAACG 60.528 57.895 0.00 0.00 46.94 4.10
2702 2725 2.041153 CACTTGGAGGCCCAACAAC 58.959 57.895 0.00 0.00 46.94 3.32
2703 2726 1.832167 GCACTTGGAGGCCCAACAA 60.832 57.895 0.00 1.03 46.94 2.83
2704 2727 2.203480 GCACTTGGAGGCCCAACA 60.203 61.111 0.00 0.00 46.94 3.33
2705 2728 2.203480 TGCACTTGGAGGCCCAAC 60.203 61.111 0.00 0.00 46.94 3.77
2707 2730 2.853542 TCTGCACTTGGAGGCCCA 60.854 61.111 0.00 0.00 41.64 5.36
2708 2731 2.045536 CTCTGCACTTGGAGGCCC 60.046 66.667 0.00 0.00 34.00 5.80
2709 2732 2.045536 CCTCTGCACTTGGAGGCC 60.046 66.667 6.78 0.00 41.92 5.19
2712 2735 1.972872 ACAAACCTCTGCACTTGGAG 58.027 50.000 2.33 0.00 34.56 3.86
2713 2736 2.224523 CCTACAAACCTCTGCACTTGGA 60.225 50.000 2.33 0.00 0.00 3.53
2714 2737 2.154462 CCTACAAACCTCTGCACTTGG 58.846 52.381 0.00 0.00 0.00 3.61
2715 2738 2.808543 GTCCTACAAACCTCTGCACTTG 59.191 50.000 0.00 0.00 0.00 3.16
2716 2739 2.438021 TGTCCTACAAACCTCTGCACTT 59.562 45.455 0.00 0.00 0.00 3.16
2717 2740 2.037772 CTGTCCTACAAACCTCTGCACT 59.962 50.000 0.00 0.00 0.00 4.40
2718 2741 2.417719 CTGTCCTACAAACCTCTGCAC 58.582 52.381 0.00 0.00 0.00 4.57
2719 2742 2.839486 CTGTCCTACAAACCTCTGCA 57.161 50.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.