Multiple sequence alignment - TraesCS1D01G388900

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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 TraesCS1D01G388900 chr1D 100.000 2591 0 0 1 2591 460866942 460864352 0.000000e+00 4785
1 TraesCS1D01G388900 chr1B 92.231 2008 113 27 439 2410 633137357 633135357 0.000000e+00 2804
2 TraesCS1D01G388900 chr1B 94.837 368 10 4 1 359 633137721 633137354 1.350000e-157 566
3 TraesCS1D01G388900 chr1A 95.719 1308 45 7 439 1745 551982224 551980927 0.000000e+00 2095
4 TraesCS1D01G388900 chr1A 95.822 359 14 1 1 359 551982578 551982221 1.730000e-161 579
5 TraesCS1D01G388900 chr1A 84.740 557 48 20 1783 2311 551980797 551980250 8.210000e-145 523
6 TraesCS1D01G388900 chr1A 95.960 99 4 0 346 444 575557261 575557359 7.420000e-36 161
7 TraesCS1D01G388900 chr4B 90.984 122 7 4 327 445 166003038 166003158 7.420000e-36 161
8 TraesCS1D01G388900 chr7D 96.000 100 1 3 348 446 94261219 94261316 2.670000e-35 159
9 TraesCS1D01G388900 chr7D 97.802 91 2 0 353 443 104453475 104453565 9.600000e-35 158
10 TraesCS1D01G388900 chr6A 91.379 116 7 3 341 455 172113280 172113167 3.450000e-34 156
11 TraesCS1D01G388900 chr3B 94.118 102 3 3 352 450 101314949 101315050 4.470000e-33 152
12 TraesCS1D01G388900 chr3B 88.430 121 8 5 354 472 55098859 55098975 9.670000e-30 141
13 TraesCS1D01G388900 chr5D 93.269 104 4 3 347 448 223231462 223231360 1.610000e-32 150
14 TraesCS1D01G388900 chr5A 91.150 113 5 5 332 440 428189464 428189353 5.780000e-32 148
15 TraesCS1D01G388900 chr2D 78.689 183 35 4 1360 1540 111336769 111336949 4.530000e-23 119
16 TraesCS1D01G388900 chr2B 78.142 183 36 4 1360 1540 161419823 161420003 2.110000e-21 113
17 TraesCS1D01G388900 chr2A 77.596 183 37 4 1360 1540 111426138 111426318 9.800000e-20 108


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 TraesCS1D01G388900 chr1D 460864352 460866942 2590 True 4785.000000 4785 100.000000 1 2591 1 chr1D.!!$R1 2590
1 TraesCS1D01G388900 chr1B 633135357 633137721 2364 True 1685.000000 2804 93.534000 1 2410 2 chr1B.!!$R1 2409
2 TraesCS1D01G388900 chr1A 551980250 551982578 2328 True 1065.666667 2095 92.093667 1 2311 3 chr1A.!!$R1 2310

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
991 1003 1.623542 CCCCAGAACCCTAACCTCCG 61.624 65.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2135 0.322997 TAGTGGAACCCGGCATTTGG 60.323 55.0 0.0 0.0 37.8 3.28 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
197 200 3.833442 TGCGTATGATATCGTCCACATC 58.167 45.455 0.00 0.00 0.00 3.06
277 287 5.055812 GGAAGGAGCTAATGTCAGATGAAG 58.944 45.833 0.00 0.00 0.00 3.02
360 370 9.659830 CACATTTTTGTTGTTAGTTACTACTCC 57.340 33.333 0.00 0.00 35.78 3.85
361 371 8.843262 ACATTTTTGTTGTTAGTTACTACTCCC 58.157 33.333 0.00 0.00 35.78 4.30
362 372 9.063615 CATTTTTGTTGTTAGTTACTACTCCCT 57.936 33.333 0.00 0.00 35.78 4.20
363 373 8.667076 TTTTTGTTGTTAGTTACTACTCCCTC 57.333 34.615 0.00 0.00 35.78 4.30
364 374 5.990120 TGTTGTTAGTTACTACTCCCTCC 57.010 43.478 0.00 0.00 35.78 4.30
365 375 4.460382 TGTTGTTAGTTACTACTCCCTCCG 59.540 45.833 0.00 0.00 35.78 4.63
366 376 4.307032 TGTTAGTTACTACTCCCTCCGT 57.693 45.455 0.00 0.00 35.78 4.69
367 377 5.435686 TGTTAGTTACTACTCCCTCCGTA 57.564 43.478 0.00 0.00 35.78 4.02
368 378 5.815581 TGTTAGTTACTACTCCCTCCGTAA 58.184 41.667 0.00 0.00 35.78 3.18
369 379 6.245408 TGTTAGTTACTACTCCCTCCGTAAA 58.755 40.000 0.00 0.00 35.78 2.01
370 380 6.151144 TGTTAGTTACTACTCCCTCCGTAAAC 59.849 42.308 0.00 0.00 35.78 2.01
371 381 4.928263 AGTTACTACTCCCTCCGTAAACT 58.072 43.478 0.00 0.00 0.00 2.66
372 382 6.067217 AGTTACTACTCCCTCCGTAAACTA 57.933 41.667 0.00 0.00 0.00 2.24
373 383 6.485171 AGTTACTACTCCCTCCGTAAACTAA 58.515 40.000 0.00 0.00 0.00 2.24
374 384 7.122048 AGTTACTACTCCCTCCGTAAACTAAT 58.878 38.462 0.00 0.00 0.00 1.73
375 385 8.275040 AGTTACTACTCCCTCCGTAAACTAATA 58.725 37.037 0.00 0.00 0.00 0.98
376 386 9.072375 GTTACTACTCCCTCCGTAAACTAATAT 57.928 37.037 0.00 0.00 0.00 1.28
379 389 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
380 390 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
381 391 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
382 392 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
383 393 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
384 394 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
385 395 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
386 396 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
414 424 9.733219 GATAACTACTTTAGTGATCTAAACGCT 57.267 33.333 4.09 0.00 41.55 5.07
415 425 9.733219 ATAACTACTTTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
416 426 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
417 427 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
418 428 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
419 429 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
431 441 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
432 442 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
433 443 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
434 444 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
435 445 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
436 446 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
437 447 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
438 448 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
439 449 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
440 450 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
516 527 3.966665 TGGCCAGTGTATCAGATATCACA 59.033 43.478 0.00 0.00 33.84 3.58
518 529 4.562347 GGCCAGTGTATCAGATATCACAGG 60.562 50.000 19.43 19.43 39.38 4.00
519 530 4.039730 GCCAGTGTATCAGATATCACAGGT 59.960 45.833 21.89 0.00 38.88 4.00
520 531 5.536260 CCAGTGTATCAGATATCACAGGTG 58.464 45.833 17.99 11.34 34.38 4.00
521 532 5.069648 CCAGTGTATCAGATATCACAGGTGT 59.930 44.000 17.99 0.00 34.38 4.16
597 608 7.044771 CGAAACAATTACATCACATCATTTCCG 60.045 37.037 0.00 0.00 0.00 4.30
598 609 5.581605 ACAATTACATCACATCATTTCCGC 58.418 37.500 0.00 0.00 0.00 5.54
785 796 6.817641 TGTGTTTTTCAGCTGATTTTGATTGT 59.182 30.769 19.04 0.00 0.00 2.71
991 1003 1.623542 CCCCAGAACCCTAACCTCCG 61.624 65.000 0.00 0.00 0.00 4.63
1455 1467 1.141234 GGAGATCCGGACGTTCACC 59.859 63.158 6.12 5.10 0.00 4.02
1638 1650 2.028130 AGATCTCTCTCGCGGAATTGT 58.972 47.619 6.13 0.00 0.00 2.71
1639 1651 3.215151 AGATCTCTCTCGCGGAATTGTA 58.785 45.455 6.13 0.00 0.00 2.41
1687 1699 4.558226 TGGATGACTTGCTGTAGTGAAT 57.442 40.909 0.00 0.00 0.00 2.57
1692 1704 6.294176 GGATGACTTGCTGTAGTGAATTTGTT 60.294 38.462 0.00 0.00 0.00 2.83
1723 1735 0.535797 GGCCCTGTCGCCTATATACC 59.464 60.000 0.00 0.00 46.10 2.73
1724 1736 0.535797 GCCCTGTCGCCTATATACCC 59.464 60.000 0.00 0.00 0.00 3.69
1766 1824 4.764679 TTAGCACACACCAATCACATTC 57.235 40.909 0.00 0.00 0.00 2.67
1776 1834 7.124599 ACACACCAATCACATTCCATTATGATT 59.875 33.333 0.00 0.00 41.37 2.57
1779 1837 7.865889 CACCAATCACATTCCATTATGATTCAG 59.134 37.037 0.00 0.00 39.25 3.02
1781 1839 8.418662 CCAATCACATTCCATTATGATTCAGTT 58.581 33.333 0.00 0.00 39.25 3.16
1795 1853 9.844790 TTATGATTCAGTTTGTGACATTTGATC 57.155 29.630 0.00 0.00 33.71 2.92
1796 1854 7.274603 TGATTCAGTTTGTGACATTTGATCA 57.725 32.000 0.00 0.00 33.71 2.92
1933 2037 3.366374 GCAAATGTGGTCTACTTTCTGCC 60.366 47.826 9.06 0.00 31.81 4.85
1946 2071 2.776670 TTCTGCCGTGCTCTGCTCTG 62.777 60.000 3.86 0.00 0.00 3.35
1956 2081 1.678123 GCTCTGCTCTGCCTTGAATGA 60.678 52.381 0.00 0.00 0.00 2.57
1981 2106 2.687425 TGAATCCTTGTGTGTTGGTGTG 59.313 45.455 0.00 0.00 0.00 3.82
1982 2107 1.032014 ATCCTTGTGTGTTGGTGTGC 58.968 50.000 0.00 0.00 0.00 4.57
1996 2122 6.856426 GTGTTGGTGTGCTTAGTTTTCTTATC 59.144 38.462 0.00 0.00 0.00 1.75
1998 2124 5.626142 TGGTGTGCTTAGTTTTCTTATCCA 58.374 37.500 0.00 0.00 0.00 3.41
2000 2126 5.390567 GGTGTGCTTAGTTTTCTTATCCACG 60.391 44.000 0.00 0.00 0.00 4.94
2001 2127 4.693566 TGTGCTTAGTTTTCTTATCCACGG 59.306 41.667 0.00 0.00 0.00 4.94
2008 2135 2.325583 TTCTTATCCACGGCACATCC 57.674 50.000 0.00 0.00 0.00 3.51
2038 2165 4.377897 CGGGTTCCACTATTCCATAGAAC 58.622 47.826 0.00 0.00 36.68 3.01
2039 2166 4.141801 CGGGTTCCACTATTCCATAGAACA 60.142 45.833 0.00 0.00 36.68 3.18
2042 2169 6.833933 GGGTTCCACTATTCCATAGAACAAAT 59.166 38.462 0.00 0.00 36.68 2.32
2043 2170 7.996644 GGGTTCCACTATTCCATAGAACAAATA 59.003 37.037 0.00 0.00 36.68 1.40
2131 2259 6.658816 TGTATGAACCATATGATTACCATGGC 59.341 38.462 13.04 0.00 42.54 4.40
2135 2263 4.914983 ACCATATGATTACCATGGCTGAG 58.085 43.478 13.04 0.00 42.54 3.35
2174 2303 4.130118 GGACTGTCAGTGTCAATTGAACT 58.870 43.478 11.04 12.66 36.26 3.01
2185 2315 4.222114 GTCAATTGAACTTTTCAGGCTCG 58.778 43.478 10.35 0.00 41.38 5.03
2302 2436 8.510243 TCTAAAAATCAGATAAGAAGCATGCA 57.490 30.769 21.98 0.00 0.00 3.96
2314 2448 3.439476 AGAAGCATGCACTGAAATGACTC 59.561 43.478 21.98 0.00 0.00 3.36
2315 2449 1.736126 AGCATGCACTGAAATGACTCG 59.264 47.619 21.98 0.00 0.00 4.18
2320 2454 2.224042 TGCACTGAAATGACTCGTGACT 60.224 45.455 0.00 0.00 0.00 3.41
2330 2464 2.224042 TGACTCGTGACTGCAATTGAGT 60.224 45.455 10.34 9.77 36.53 3.41
2351 2485 6.043854 AGTTGCCTTTTGTTAGTTTTGGAA 57.956 33.333 0.00 0.00 0.00 3.53
2352 2486 6.468543 AGTTGCCTTTTGTTAGTTTTGGAAA 58.531 32.000 0.00 0.00 0.00 3.13
2353 2487 6.370442 AGTTGCCTTTTGTTAGTTTTGGAAAC 59.630 34.615 0.00 0.00 33.14 2.78
2354 2488 6.043854 TGCCTTTTGTTAGTTTTGGAAACT 57.956 33.333 10.51 10.51 0.00 2.66
2355 2489 6.103330 TGCCTTTTGTTAGTTTTGGAAACTC 58.897 36.000 9.15 0.00 0.00 3.01
2397 2531 5.782047 CATGCATTTGGTTCCTTGTTAGAA 58.218 37.500 0.00 0.00 0.00 2.10
2410 2544 3.021269 TGTTAGAAGTACTGTGGTGCG 57.979 47.619 0.00 0.00 33.30 5.34
2411 2545 1.725164 GTTAGAAGTACTGTGGTGCGC 59.275 52.381 0.00 0.00 33.30 6.09
2412 2546 1.254026 TAGAAGTACTGTGGTGCGCT 58.746 50.000 9.73 0.00 33.30 5.92
2413 2547 0.319900 AGAAGTACTGTGGTGCGCTG 60.320 55.000 9.73 0.00 33.30 5.18
2414 2548 1.291877 GAAGTACTGTGGTGCGCTGG 61.292 60.000 9.73 0.00 33.30 4.85
2415 2549 1.754380 AAGTACTGTGGTGCGCTGGA 61.754 55.000 9.73 0.00 33.30 3.86
2416 2550 1.738099 GTACTGTGGTGCGCTGGAG 60.738 63.158 9.73 0.00 0.00 3.86
2417 2551 3.589654 TACTGTGGTGCGCTGGAGC 62.590 63.158 9.73 0.00 37.78 4.70
2426 2560 2.282462 CGCTGGAGCCCAACCTTT 60.282 61.111 0.00 0.00 37.91 3.11
2427 2561 2.629656 CGCTGGAGCCCAACCTTTG 61.630 63.158 0.00 0.00 37.91 2.77
2428 2562 2.935740 GCTGGAGCCCAACCTTTGC 61.936 63.158 0.00 0.00 30.80 3.68
2429 2563 1.228675 CTGGAGCCCAACCTTTGCT 60.229 57.895 0.00 0.00 38.24 3.91
2431 2565 4.830573 GAGCCCAACCTTTGCTCT 57.169 55.556 3.61 0.00 46.19 4.09
2432 2566 2.261215 GAGCCCAACCTTTGCTCTG 58.739 57.895 3.61 0.00 46.19 3.35
2433 2567 0.538287 GAGCCCAACCTTTGCTCTGT 60.538 55.000 3.61 0.00 46.19 3.41
2434 2568 0.825010 AGCCCAACCTTTGCTCTGTG 60.825 55.000 0.00 0.00 0.00 3.66
2435 2569 0.823356 GCCCAACCTTTGCTCTGTGA 60.823 55.000 0.00 0.00 0.00 3.58
2436 2570 1.915141 CCCAACCTTTGCTCTGTGAT 58.085 50.000 0.00 0.00 0.00 3.06
2437 2571 1.815003 CCCAACCTTTGCTCTGTGATC 59.185 52.381 0.00 0.00 0.00 2.92
2438 2572 2.553904 CCCAACCTTTGCTCTGTGATCT 60.554 50.000 0.00 0.00 0.00 2.75
2439 2573 3.307691 CCCAACCTTTGCTCTGTGATCTA 60.308 47.826 0.00 0.00 0.00 1.98
2440 2574 3.686726 CCAACCTTTGCTCTGTGATCTAC 59.313 47.826 0.00 0.00 0.00 2.59
2441 2575 3.618690 ACCTTTGCTCTGTGATCTACC 57.381 47.619 0.00 0.00 0.00 3.18
2442 2576 3.177228 ACCTTTGCTCTGTGATCTACCT 58.823 45.455 0.00 0.00 0.00 3.08
2443 2577 3.055530 ACCTTTGCTCTGTGATCTACCTG 60.056 47.826 0.00 0.00 0.00 4.00
2444 2578 3.055530 CCTTTGCTCTGTGATCTACCTGT 60.056 47.826 0.00 0.00 0.00 4.00
2445 2579 3.599730 TTGCTCTGTGATCTACCTGTG 57.400 47.619 0.00 0.00 0.00 3.66
2446 2580 2.529632 TGCTCTGTGATCTACCTGTGT 58.470 47.619 0.00 0.00 0.00 3.72
2447 2581 2.899900 TGCTCTGTGATCTACCTGTGTT 59.100 45.455 0.00 0.00 0.00 3.32
2448 2582 3.257393 GCTCTGTGATCTACCTGTGTTG 58.743 50.000 0.00 0.00 0.00 3.33
2449 2583 3.306364 GCTCTGTGATCTACCTGTGTTGT 60.306 47.826 0.00 0.00 0.00 3.32
2450 2584 4.240888 CTCTGTGATCTACCTGTGTTGTG 58.759 47.826 0.00 0.00 0.00 3.33
2451 2585 3.006859 TCTGTGATCTACCTGTGTTGTGG 59.993 47.826 0.00 0.00 0.00 4.17
2452 2586 2.076863 GTGATCTACCTGTGTTGTGGC 58.923 52.381 0.00 0.00 0.00 5.01
2453 2587 1.696884 TGATCTACCTGTGTTGTGGCA 59.303 47.619 0.00 0.00 0.00 4.92
2454 2588 2.105649 TGATCTACCTGTGTTGTGGCAA 59.894 45.455 0.00 0.00 0.00 4.52
2455 2589 2.719531 TCTACCTGTGTTGTGGCAAA 57.280 45.000 0.00 0.00 0.00 3.68
2456 2590 2.294074 TCTACCTGTGTTGTGGCAAAC 58.706 47.619 0.00 0.00 0.00 2.93
2457 2591 2.020720 CTACCTGTGTTGTGGCAAACA 58.979 47.619 9.98 9.98 37.71 2.83
2458 2592 1.261480 ACCTGTGTTGTGGCAAACAA 58.739 45.000 14.00 0.38 46.66 2.83
2478 2612 8.663911 CAAACAAATTCAAGTTTGGTGTAATGT 58.336 29.630 16.95 0.00 46.57 2.71
2479 2613 7.769272 ACAAATTCAAGTTTGGTGTAATGTG 57.231 32.000 4.63 0.00 42.07 3.21
2480 2614 7.327214 ACAAATTCAAGTTTGGTGTAATGTGT 58.673 30.769 4.63 0.00 42.07 3.72
2481 2615 7.821846 ACAAATTCAAGTTTGGTGTAATGTGTT 59.178 29.630 4.63 0.00 42.07 3.32
2482 2616 7.769272 AATTCAAGTTTGGTGTAATGTGTTG 57.231 32.000 0.00 0.00 0.00 3.33
2483 2617 5.255710 TCAAGTTTGGTGTAATGTGTTGG 57.744 39.130 0.00 0.00 0.00 3.77
2484 2618 3.726291 AGTTTGGTGTAATGTGTTGGC 57.274 42.857 0.00 0.00 0.00 4.52
2485 2619 2.364002 AGTTTGGTGTAATGTGTTGGCC 59.636 45.455 0.00 0.00 0.00 5.36
2486 2620 2.073252 TTGGTGTAATGTGTTGGCCA 57.927 45.000 0.00 0.00 0.00 5.36
2487 2621 1.614996 TGGTGTAATGTGTTGGCCAG 58.385 50.000 5.11 0.00 0.00 4.85
2488 2622 1.133637 TGGTGTAATGTGTTGGCCAGT 60.134 47.619 5.11 0.00 0.00 4.00
2489 2623 1.960689 GGTGTAATGTGTTGGCCAGTT 59.039 47.619 5.11 0.04 0.00 3.16
2490 2624 3.150767 GGTGTAATGTGTTGGCCAGTTA 58.849 45.455 5.11 0.00 0.00 2.24
2491 2625 3.570550 GGTGTAATGTGTTGGCCAGTTAA 59.429 43.478 5.11 0.00 0.00 2.01
2492 2626 4.542735 GTGTAATGTGTTGGCCAGTTAAC 58.457 43.478 5.11 0.97 0.00 2.01
2493 2627 4.036971 GTGTAATGTGTTGGCCAGTTAACA 59.963 41.667 5.11 4.35 34.66 2.41
2494 2628 4.645136 TGTAATGTGTTGGCCAGTTAACAA 59.355 37.500 9.55 1.89 38.40 2.83
2495 2629 4.744795 AATGTGTTGGCCAGTTAACAAA 57.255 36.364 9.55 5.09 38.40 2.83
2496 2630 3.791973 TGTGTTGGCCAGTTAACAAAG 57.208 42.857 9.55 0.00 38.40 2.77
2497 2631 3.093057 TGTGTTGGCCAGTTAACAAAGT 58.907 40.909 9.55 0.00 38.40 2.66
2498 2632 4.270834 TGTGTTGGCCAGTTAACAAAGTA 58.729 39.130 9.55 0.00 38.40 2.24
2499 2633 4.096682 TGTGTTGGCCAGTTAACAAAGTAC 59.903 41.667 9.55 0.00 38.40 2.73
2500 2634 4.096682 GTGTTGGCCAGTTAACAAAGTACA 59.903 41.667 9.55 1.98 38.40 2.90
2501 2635 4.336993 TGTTGGCCAGTTAACAAAGTACAG 59.663 41.667 5.11 0.00 34.17 2.74
2502 2636 4.425180 TGGCCAGTTAACAAAGTACAGA 57.575 40.909 0.00 0.00 0.00 3.41
2503 2637 4.980573 TGGCCAGTTAACAAAGTACAGAT 58.019 39.130 0.00 0.00 0.00 2.90
2504 2638 5.381757 TGGCCAGTTAACAAAGTACAGATT 58.618 37.500 0.00 0.00 0.00 2.40
2505 2639 5.830991 TGGCCAGTTAACAAAGTACAGATTT 59.169 36.000 0.00 0.00 0.00 2.17
2506 2640 6.149633 GGCCAGTTAACAAAGTACAGATTTG 58.850 40.000 8.61 0.00 42.17 2.32
2523 2657 8.044060 ACAGATTTGTACACTGGATTGTTATG 57.956 34.615 14.44 0.00 35.25 1.90
2524 2658 6.968904 CAGATTTGTACACTGGATTGTTATGC 59.031 38.462 0.00 0.00 0.00 3.14
2525 2659 6.658816 AGATTTGTACACTGGATTGTTATGCA 59.341 34.615 0.00 0.00 0.00 3.96
2537 2671 9.289303 CTGGATTGTTATGCAGTTATAAAACAC 57.711 33.333 0.00 0.00 43.13 3.32
2538 2672 8.797438 TGGATTGTTATGCAGTTATAAAACACA 58.203 29.630 0.00 0.00 38.12 3.72
2539 2673 9.801873 GGATTGTTATGCAGTTATAAAACACAT 57.198 29.630 0.00 0.00 38.12 3.21
2541 2675 8.978564 TTGTTATGCAGTTATAAAACACATGG 57.021 30.769 0.00 0.00 38.12 3.66
2542 2676 8.116651 TGTTATGCAGTTATAAAACACATGGT 57.883 30.769 0.00 0.00 38.12 3.55
2543 2677 8.240682 TGTTATGCAGTTATAAAACACATGGTC 58.759 33.333 0.00 1.15 38.12 4.02
2544 2678 6.832520 ATGCAGTTATAAAACACATGGTCA 57.167 33.333 0.00 0.00 38.12 4.02
2545 2679 6.641169 TGCAGTTATAAAACACATGGTCAA 57.359 33.333 0.00 0.00 38.12 3.18
2546 2680 6.442952 TGCAGTTATAAAACACATGGTCAAC 58.557 36.000 0.00 0.00 38.12 3.18
2547 2681 6.039829 TGCAGTTATAAAACACATGGTCAACA 59.960 34.615 0.00 0.00 38.12 3.33
2548 2682 6.582295 GCAGTTATAAAACACATGGTCAACAG 59.418 38.462 0.00 0.00 38.12 3.16
2549 2683 7.521423 GCAGTTATAAAACACATGGTCAACAGA 60.521 37.037 0.00 0.00 38.12 3.41
2550 2684 8.514594 CAGTTATAAAACACATGGTCAACAGAT 58.485 33.333 0.00 0.00 38.12 2.90
2551 2685 9.077885 AGTTATAAAACACATGGTCAACAGATT 57.922 29.630 0.00 0.00 38.12 2.40
2552 2686 9.128107 GTTATAAAACACATGGTCAACAGATTG 57.872 33.333 0.00 0.00 35.56 2.67
2553 2687 5.596836 AAAACACATGGTCAACAGATTGT 57.403 34.783 0.00 0.00 37.11 2.71
2554 2688 5.596836 AAACACATGGTCAACAGATTGTT 57.403 34.783 0.00 0.00 42.08 2.83
2555 2689 6.707440 AAACACATGGTCAACAGATTGTTA 57.293 33.333 0.00 0.00 38.77 2.41
2556 2690 5.689383 ACACATGGTCAACAGATTGTTAC 57.311 39.130 0.00 0.00 38.77 2.50
2557 2691 4.518970 ACACATGGTCAACAGATTGTTACC 59.481 41.667 0.00 10.78 38.77 2.85
2558 2692 4.518590 CACATGGTCAACAGATTGTTACCA 59.481 41.667 17.41 17.41 42.40 3.25
2559 2693 4.518970 ACATGGTCAACAGATTGTTACCAC 59.481 41.667 17.43 7.10 41.76 4.16
2560 2694 4.157849 TGGTCAACAGATTGTTACCACA 57.842 40.909 13.98 3.20 38.77 4.17
2561 2695 3.880490 TGGTCAACAGATTGTTACCACAC 59.120 43.478 13.98 1.65 38.77 3.82
2562 2696 3.880490 GGTCAACAGATTGTTACCACACA 59.120 43.478 11.94 0.00 38.77 3.72
2563 2697 4.518970 GGTCAACAGATTGTTACCACACAT 59.481 41.667 11.94 0.00 38.77 3.21
2564 2698 5.009610 GGTCAACAGATTGTTACCACACATT 59.990 40.000 11.94 0.00 38.77 2.71
2565 2699 6.460953 GGTCAACAGATTGTTACCACACATTT 60.461 38.462 11.94 0.00 38.77 2.32
2566 2700 6.417635 GTCAACAGATTGTTACCACACATTTG 59.582 38.462 0.00 0.00 38.77 2.32
2567 2701 6.319911 TCAACAGATTGTTACCACACATTTGA 59.680 34.615 0.00 0.00 38.77 2.69
2568 2702 6.317789 ACAGATTGTTACCACACATTTGAG 57.682 37.500 0.00 0.00 30.32 3.02
2569 2703 5.827797 ACAGATTGTTACCACACATTTGAGT 59.172 36.000 0.00 0.00 30.32 3.41
2570 2704 6.321181 ACAGATTGTTACCACACATTTGAGTT 59.679 34.615 0.00 0.00 30.32 3.01
2571 2705 7.147915 ACAGATTGTTACCACACATTTGAGTTT 60.148 33.333 0.00 0.00 30.32 2.66
2572 2706 7.379529 CAGATTGTTACCACACATTTGAGTTTC 59.620 37.037 0.00 0.00 30.32 2.78
2573 2707 6.767524 TTGTTACCACACATTTGAGTTTCT 57.232 33.333 0.00 0.00 30.32 2.52
2574 2708 6.130298 TGTTACCACACATTTGAGTTTCTG 57.870 37.500 0.00 0.00 0.00 3.02
2575 2709 5.883115 TGTTACCACACATTTGAGTTTCTGA 59.117 36.000 0.00 0.00 0.00 3.27
2576 2710 6.545666 TGTTACCACACATTTGAGTTTCTGAT 59.454 34.615 0.00 0.00 0.00 2.90
2577 2711 7.717436 TGTTACCACACATTTGAGTTTCTGATA 59.283 33.333 0.00 0.00 0.00 2.15
2578 2712 8.730680 GTTACCACACATTTGAGTTTCTGATAT 58.269 33.333 0.00 0.00 0.00 1.63
2579 2713 7.383102 ACCACACATTTGAGTTTCTGATATC 57.617 36.000 0.00 0.00 0.00 1.63
2580 2714 6.942005 ACCACACATTTGAGTTTCTGATATCA 59.058 34.615 5.07 5.07 0.00 2.15
2581 2715 7.613022 ACCACACATTTGAGTTTCTGATATCAT 59.387 33.333 5.72 0.00 0.00 2.45
2582 2716 7.913821 CCACACATTTGAGTTTCTGATATCATG 59.086 37.037 5.72 0.06 0.00 3.07
2583 2717 7.431376 CACACATTTGAGTTTCTGATATCATGC 59.569 37.037 5.72 0.00 0.00 4.06
2584 2718 7.338703 ACACATTTGAGTTTCTGATATCATGCT 59.661 33.333 5.72 2.34 0.00 3.79
2585 2719 7.856398 CACATTTGAGTTTCTGATATCATGCTC 59.144 37.037 5.72 11.27 0.00 4.26
2586 2720 6.932356 TTTGAGTTTCTGATATCATGCTCC 57.068 37.500 5.72 0.00 0.00 4.70
2587 2721 5.883685 TGAGTTTCTGATATCATGCTCCT 57.116 39.130 5.72 0.00 0.00 3.69
2588 2722 5.608449 TGAGTTTCTGATATCATGCTCCTG 58.392 41.667 5.72 0.00 0.00 3.86
2589 2723 4.970711 AGTTTCTGATATCATGCTCCTGG 58.029 43.478 5.72 0.00 0.00 4.45
2590 2724 3.413846 TTCTGATATCATGCTCCTGGC 57.586 47.619 5.72 0.00 42.22 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 200 4.465660 TCTCCTTCCATCAGAACTCAGAAG 59.534 45.833 0.00 0.00 0.00 2.85
277 287 3.387397 GGGAAATCTTGCATATGCTTGC 58.613 45.455 27.13 17.31 42.66 4.01
358 368 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
359 369 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
360 370 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
387 397 9.733219 GCGTTTAGATCACTAAAGTAGTTATCT 57.267 33.333 13.75 13.75 46.18 1.98
388 398 9.733219 AGCGTTTAGATCACTAAAGTAGTTATC 57.267 33.333 0.00 2.65 45.42 1.75
389 399 9.733219 GAGCGTTTAGATCACTAAAGTAGTTAT 57.267 33.333 0.00 0.00 45.42 1.89
390 400 8.954350 AGAGCGTTTAGATCACTAAAGTAGTTA 58.046 33.333 0.00 0.00 45.42 2.24
391 401 7.828712 AGAGCGTTTAGATCACTAAAGTAGTT 58.171 34.615 0.00 0.00 45.42 2.24
392 402 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
393 403 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
405 415 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
406 416 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
407 417 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
408 418 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
409 419 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
410 420 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
411 421 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
412 422 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
413 423 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
414 424 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
415 425 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
418 428 9.819754 AATAGTACTCCCTCCGTAAACTAATAT 57.180 33.333 0.00 0.00 0.00 1.28
420 430 9.072375 GTAATAGTACTCCCTCCGTAAACTAAT 57.928 37.037 0.00 0.00 0.00 1.73
421 431 8.275040 AGTAATAGTACTCCCTCCGTAAACTAA 58.725 37.037 0.00 0.00 35.55 2.24
422 432 7.716998 CAGTAATAGTACTCCCTCCGTAAACTA 59.283 40.741 0.00 0.00 38.58 2.24
423 433 6.545298 CAGTAATAGTACTCCCTCCGTAAACT 59.455 42.308 0.00 0.00 38.58 2.66
424 434 6.319911 ACAGTAATAGTACTCCCTCCGTAAAC 59.680 42.308 0.00 0.00 38.58 2.01
425 435 6.426587 ACAGTAATAGTACTCCCTCCGTAAA 58.573 40.000 0.00 0.00 38.58 2.01
426 436 6.006275 ACAGTAATAGTACTCCCTCCGTAA 57.994 41.667 0.00 0.00 38.58 3.18
427 437 5.367937 AGACAGTAATAGTACTCCCTCCGTA 59.632 44.000 0.00 0.00 38.58 4.02
428 438 4.165758 AGACAGTAATAGTACTCCCTCCGT 59.834 45.833 0.00 0.00 38.58 4.69
429 439 4.716794 AGACAGTAATAGTACTCCCTCCG 58.283 47.826 0.00 0.00 38.58 4.63
430 440 6.840527 ACTAGACAGTAATAGTACTCCCTCC 58.159 44.000 0.00 0.00 38.58 4.30
431 441 8.623030 CAAACTAGACAGTAATAGTACTCCCTC 58.377 40.741 0.00 0.00 38.58 4.30
432 442 7.560626 CCAAACTAGACAGTAATAGTACTCCCT 59.439 40.741 0.00 3.45 38.58 4.20
433 443 7.341512 ACCAAACTAGACAGTAATAGTACTCCC 59.658 40.741 0.00 0.00 38.58 4.30
434 444 8.189460 CACCAAACTAGACAGTAATAGTACTCC 58.811 40.741 0.00 0.00 38.58 3.85
435 445 8.954350 TCACCAAACTAGACAGTAATAGTACTC 58.046 37.037 0.00 0.00 38.58 2.59
436 446 8.874744 TCACCAAACTAGACAGTAATAGTACT 57.125 34.615 0.00 0.00 41.49 2.73
437 447 9.351570 GTTCACCAAACTAGACAGTAATAGTAC 57.648 37.037 0.00 0.00 33.48 2.73
438 448 9.305555 AGTTCACCAAACTAGACAGTAATAGTA 57.694 33.333 0.00 0.00 46.55 1.82
439 449 8.088981 CAGTTCACCAAACTAGACAGTAATAGT 58.911 37.037 0.00 0.00 46.69 2.12
440 450 7.063544 GCAGTTCACCAAACTAGACAGTAATAG 59.936 40.741 0.00 0.00 46.69 1.73
518 529 7.958112 AACGAATTTAAGTGTTGTGTTACAC 57.042 32.000 8.76 8.76 46.86 2.90
519 530 9.488124 GTAAACGAATTTAAGTGTTGTGTTACA 57.512 29.630 0.00 0.00 32.04 2.41
520 531 8.946935 GGTAAACGAATTTAAGTGTTGTGTTAC 58.053 33.333 0.00 0.00 32.04 2.50
521 532 8.127954 GGGTAAACGAATTTAAGTGTTGTGTTA 58.872 33.333 0.00 0.00 32.04 2.41
540 551 3.681417 GGTGAACTACGACATGGGTAAAC 59.319 47.826 0.00 0.00 0.00 2.01
597 608 1.199789 TGATTCAACAGCATGAACGGC 59.800 47.619 0.00 0.00 41.78 5.68
598 609 2.485426 AGTGATTCAACAGCATGAACGG 59.515 45.455 0.00 0.00 41.78 4.44
756 767 6.090628 TCAAAATCAGCTGAAAAACACACAAC 59.909 34.615 22.50 0.00 0.00 3.32
758 769 5.718146 TCAAAATCAGCTGAAAAACACACA 58.282 33.333 22.50 0.00 0.00 3.72
759 770 6.833342 ATCAAAATCAGCTGAAAAACACAC 57.167 33.333 22.50 0.00 0.00 3.82
829 841 4.322567 AGGTCATGCTTCTCTCTCAAAAC 58.677 43.478 0.00 0.00 0.00 2.43
858 870 0.465460 GCCCAATGAGCCCATTACGA 60.465 55.000 0.00 0.00 40.81 3.43
860 872 1.035139 CAGCCCAATGAGCCCATTAC 58.965 55.000 0.00 0.00 40.81 1.89
991 1003 1.977293 GAGGAGGCCATGGTGGAGAC 61.977 65.000 14.67 0.00 40.96 3.36
1455 1467 3.068691 TCCTTGAGCCCGAGGTCG 61.069 66.667 0.73 0.00 43.71 4.79
1687 1699 2.627699 GGGCCATCAGTTTCTCAACAAA 59.372 45.455 4.39 0.00 35.05 2.83
1692 1704 1.003580 GACAGGGCCATCAGTTTCTCA 59.996 52.381 6.18 0.00 0.00 3.27
1724 1736 8.038944 TGCTAAAACATCCTAGGTAACAACTAG 58.961 37.037 9.08 4.68 38.09 2.57
1766 1824 8.865978 CAAATGTCACAAACTGAATCATAATGG 58.134 33.333 0.00 0.00 0.00 3.16
1795 1853 4.247267 AGGATCACAGCAAAACAATGTG 57.753 40.909 0.00 0.00 44.48 3.21
1796 1854 5.072741 ACTAGGATCACAGCAAAACAATGT 58.927 37.500 0.00 0.00 0.00 2.71
1805 1909 3.116096 AGGGTTACTAGGATCACAGCA 57.884 47.619 0.00 0.00 0.00 4.41
1933 2037 2.047465 AAGGCAGAGCAGAGCACG 60.047 61.111 0.00 0.00 0.00 5.34
1946 2071 5.166398 CAAGGATTCAGTTTCATTCAAGGC 58.834 41.667 0.00 0.00 0.00 4.35
1956 2081 4.023291 ACCAACACACAAGGATTCAGTTT 58.977 39.130 0.00 0.00 0.00 2.66
1981 2106 3.687698 TGCCGTGGATAAGAAAACTAAGC 59.312 43.478 0.00 0.00 0.00 3.09
1982 2107 4.693566 TGTGCCGTGGATAAGAAAACTAAG 59.306 41.667 0.00 0.00 0.00 2.18
1996 2122 1.512230 CATTTGGGATGTGCCGTGG 59.488 57.895 0.00 0.00 37.63 4.94
1998 2124 3.287445 GCATTTGGGATGTGCCGT 58.713 55.556 0.00 0.00 37.63 5.68
2001 2127 2.495866 CCGGCATTTGGGATGTGC 59.504 61.111 0.00 0.00 38.12 4.57
2008 2135 0.322997 TAGTGGAACCCGGCATTTGG 60.323 55.000 0.00 0.00 37.80 3.28
2150 2278 1.800586 CAATTGACACTGACAGTCCCG 59.199 52.381 4.74 0.00 35.15 5.14
2174 2303 3.283751 TGAAAACCTTCGAGCCTGAAAA 58.716 40.909 0.00 0.00 33.94 2.29
2185 2315 7.067981 AGAGAATCCAGCATTATGAAAACCTTC 59.932 37.037 0.00 0.00 33.66 3.46
2275 2408 9.230932 GCATGCTTCTTATCTGATTTTTAGAAC 57.769 33.333 11.37 0.00 0.00 3.01
2278 2411 8.404000 AGTGCATGCTTCTTATCTGATTTTTAG 58.596 33.333 20.33 0.00 0.00 1.85
2296 2430 1.466167 ACGAGTCATTTCAGTGCATGC 59.534 47.619 11.82 11.82 0.00 4.06
2302 2436 2.224042 TGCAGTCACGAGTCATTTCAGT 60.224 45.455 0.00 0.00 0.00 3.41
2330 2464 6.468543 AGTTTCCAAAACTAACAAAAGGCAA 58.531 32.000 3.34 0.00 0.00 4.52
2339 2473 8.610855 GTGTAACTTGAGTTTCCAAAACTAAC 57.389 34.615 5.13 0.00 39.31 2.34
2397 2531 2.159819 CTCCAGCGCACCACAGTACT 62.160 60.000 11.47 0.00 0.00 2.73
2410 2544 2.935740 GCAAAGGTTGGGCTCCAGC 61.936 63.158 0.36 0.36 33.81 4.85
2411 2545 1.228675 AGCAAAGGTTGGGCTCCAG 60.229 57.895 0.00 0.00 33.81 3.86
2412 2546 1.228552 GAGCAAAGGTTGGGCTCCA 60.229 57.895 0.00 0.00 46.35 3.86
2413 2547 3.686760 GAGCAAAGGTTGGGCTCC 58.313 61.111 0.00 0.00 46.35 4.70
2415 2549 0.825010 CACAGAGCAAAGGTTGGGCT 60.825 55.000 0.00 0.00 41.35 5.19
2416 2550 0.823356 TCACAGAGCAAAGGTTGGGC 60.823 55.000 0.00 0.00 0.00 5.36
2417 2551 1.815003 GATCACAGAGCAAAGGTTGGG 59.185 52.381 0.00 0.00 0.00 4.12
2418 2552 2.787994 AGATCACAGAGCAAAGGTTGG 58.212 47.619 0.00 0.00 0.00 3.77
2419 2553 3.686726 GGTAGATCACAGAGCAAAGGTTG 59.313 47.826 0.00 0.00 0.00 3.77
2420 2554 3.584848 AGGTAGATCACAGAGCAAAGGTT 59.415 43.478 0.00 0.00 0.00 3.50
2421 2555 3.055530 CAGGTAGATCACAGAGCAAAGGT 60.056 47.826 0.00 0.00 0.00 3.50
2422 2556 3.055530 ACAGGTAGATCACAGAGCAAAGG 60.056 47.826 0.00 0.00 0.00 3.11
2423 2557 3.931468 CACAGGTAGATCACAGAGCAAAG 59.069 47.826 0.00 0.00 0.00 2.77
2424 2558 3.324846 ACACAGGTAGATCACAGAGCAAA 59.675 43.478 0.00 0.00 0.00 3.68
2425 2559 2.899900 ACACAGGTAGATCACAGAGCAA 59.100 45.455 0.00 0.00 0.00 3.91
2426 2560 2.529632 ACACAGGTAGATCACAGAGCA 58.470 47.619 0.00 0.00 0.00 4.26
2427 2561 3.257393 CAACACAGGTAGATCACAGAGC 58.743 50.000 0.00 0.00 0.00 4.09
2428 2562 4.240888 CACAACACAGGTAGATCACAGAG 58.759 47.826 0.00 0.00 0.00 3.35
2429 2563 3.006859 CCACAACACAGGTAGATCACAGA 59.993 47.826 0.00 0.00 0.00 3.41
2430 2564 3.329386 CCACAACACAGGTAGATCACAG 58.671 50.000 0.00 0.00 0.00 3.66
2431 2565 2.549992 GCCACAACACAGGTAGATCACA 60.550 50.000 0.00 0.00 0.00 3.58
2432 2566 2.076863 GCCACAACACAGGTAGATCAC 58.923 52.381 0.00 0.00 0.00 3.06
2433 2567 1.696884 TGCCACAACACAGGTAGATCA 59.303 47.619 0.00 0.00 0.00 2.92
2434 2568 2.472695 TGCCACAACACAGGTAGATC 57.527 50.000 0.00 0.00 0.00 2.75
2435 2569 2.884639 GTTTGCCACAACACAGGTAGAT 59.115 45.455 0.00 0.00 0.00 1.98
2436 2570 2.294074 GTTTGCCACAACACAGGTAGA 58.706 47.619 0.00 0.00 0.00 2.59
2437 2571 2.020720 TGTTTGCCACAACACAGGTAG 58.979 47.619 0.00 0.00 29.87 3.18
2438 2572 2.130272 TGTTTGCCACAACACAGGTA 57.870 45.000 0.00 0.00 29.87 3.08
2439 2573 1.261480 TTGTTTGCCACAACACAGGT 58.739 45.000 0.00 0.00 40.71 4.00
2440 2574 2.376808 TTTGTTTGCCACAACACAGG 57.623 45.000 0.00 0.00 45.54 4.00
2441 2575 3.931468 TGAATTTGTTTGCCACAACACAG 59.069 39.130 0.00 0.00 45.54 3.66
2442 2576 3.930336 TGAATTTGTTTGCCACAACACA 58.070 36.364 0.00 0.00 45.54 3.72
2443 2577 4.391523 ACTTGAATTTGTTTGCCACAACAC 59.608 37.500 0.00 0.00 45.54 3.32
2444 2578 4.573900 ACTTGAATTTGTTTGCCACAACA 58.426 34.783 0.00 0.00 45.54 3.33
2445 2579 5.544136 AACTTGAATTTGTTTGCCACAAC 57.456 34.783 0.00 0.00 45.54 3.32
2446 2580 5.106396 CCAAACTTGAATTTGTTTGCCACAA 60.106 36.000 18.72 0.00 46.65 3.33
2447 2581 4.394300 CCAAACTTGAATTTGTTTGCCACA 59.606 37.500 18.72 0.00 46.65 4.17
2448 2582 4.394610 ACCAAACTTGAATTTGTTTGCCAC 59.605 37.500 18.72 0.00 46.65 5.01
2449 2583 4.394300 CACCAAACTTGAATTTGTTTGCCA 59.606 37.500 18.72 0.00 46.65 4.92
2450 2584 4.394610 ACACCAAACTTGAATTTGTTTGCC 59.605 37.500 18.72 0.00 46.65 4.52
2451 2585 5.544136 ACACCAAACTTGAATTTGTTTGC 57.456 34.783 18.72 0.00 46.65 3.68
2453 2587 8.663911 CACATTACACCAAACTTGAATTTGTTT 58.336 29.630 0.00 0.00 37.79 2.83
2454 2588 7.821846 ACACATTACACCAAACTTGAATTTGTT 59.178 29.630 0.00 0.00 37.79 2.83
2455 2589 7.327214 ACACATTACACCAAACTTGAATTTGT 58.673 30.769 0.00 0.00 37.79 2.83
2456 2590 7.769272 ACACATTACACCAAACTTGAATTTG 57.231 32.000 0.00 0.00 38.96 2.32
2457 2591 7.279758 CCAACACATTACACCAAACTTGAATTT 59.720 33.333 0.00 0.00 0.00 1.82
2458 2592 6.760770 CCAACACATTACACCAAACTTGAATT 59.239 34.615 0.00 0.00 0.00 2.17
2459 2593 6.279882 CCAACACATTACACCAAACTTGAAT 58.720 36.000 0.00 0.00 0.00 2.57
2460 2594 5.655488 CCAACACATTACACCAAACTTGAA 58.345 37.500 0.00 0.00 0.00 2.69
2461 2595 4.440802 GCCAACACATTACACCAAACTTGA 60.441 41.667 0.00 0.00 0.00 3.02
2462 2596 3.801594 GCCAACACATTACACCAAACTTG 59.198 43.478 0.00 0.00 0.00 3.16
2463 2597 3.181470 GGCCAACACATTACACCAAACTT 60.181 43.478 0.00 0.00 0.00 2.66
2464 2598 2.364002 GGCCAACACATTACACCAAACT 59.636 45.455 0.00 0.00 0.00 2.66
2465 2599 2.101582 TGGCCAACACATTACACCAAAC 59.898 45.455 0.61 0.00 0.00 2.93
2466 2600 2.363680 CTGGCCAACACATTACACCAAA 59.636 45.455 7.01 0.00 0.00 3.28
2467 2601 1.959985 CTGGCCAACACATTACACCAA 59.040 47.619 7.01 0.00 0.00 3.67
2468 2602 1.133637 ACTGGCCAACACATTACACCA 60.134 47.619 7.01 0.00 0.00 4.17
2469 2603 1.616159 ACTGGCCAACACATTACACC 58.384 50.000 7.01 0.00 0.00 4.16
2470 2604 4.036971 TGTTAACTGGCCAACACATTACAC 59.963 41.667 7.01 3.69 29.93 2.90
2471 2605 4.207955 TGTTAACTGGCCAACACATTACA 58.792 39.130 7.01 2.20 29.93 2.41
2472 2606 4.839668 TGTTAACTGGCCAACACATTAC 57.160 40.909 7.01 0.00 29.93 1.89
2473 2607 5.361285 ACTTTGTTAACTGGCCAACACATTA 59.639 36.000 7.01 0.00 34.52 1.90
2474 2608 4.161377 ACTTTGTTAACTGGCCAACACATT 59.839 37.500 7.01 0.00 34.52 2.71
2475 2609 3.704061 ACTTTGTTAACTGGCCAACACAT 59.296 39.130 7.01 0.00 34.52 3.21
2476 2610 3.093057 ACTTTGTTAACTGGCCAACACA 58.907 40.909 7.01 4.25 34.52 3.72
2477 2611 3.793797 ACTTTGTTAACTGGCCAACAC 57.206 42.857 7.01 1.26 34.52 3.32
2478 2612 4.270834 TGTACTTTGTTAACTGGCCAACA 58.729 39.130 7.01 5.16 32.98 3.33
2479 2613 4.577283 TCTGTACTTTGTTAACTGGCCAAC 59.423 41.667 7.01 1.81 0.00 3.77
2480 2614 4.783055 TCTGTACTTTGTTAACTGGCCAA 58.217 39.130 7.01 0.00 0.00 4.52
2481 2615 4.425180 TCTGTACTTTGTTAACTGGCCA 57.575 40.909 4.71 4.71 0.00 5.36
2482 2616 5.959618 AATCTGTACTTTGTTAACTGGCC 57.040 39.130 7.22 0.00 0.00 5.36
2483 2617 6.735130 ACAAATCTGTACTTTGTTAACTGGC 58.265 36.000 7.22 0.00 42.58 4.85
2497 2631 9.161629 CATAACAATCCAGTGTACAAATCTGTA 57.838 33.333 0.00 0.00 36.96 2.74
2498 2632 7.362056 GCATAACAATCCAGTGTACAAATCTGT 60.362 37.037 0.00 0.00 39.75 3.41
2499 2633 6.968904 GCATAACAATCCAGTGTACAAATCTG 59.031 38.462 0.00 0.53 0.00 2.90
2500 2634 6.658816 TGCATAACAATCCAGTGTACAAATCT 59.341 34.615 0.00 0.00 0.00 2.40
2501 2635 6.851609 TGCATAACAATCCAGTGTACAAATC 58.148 36.000 0.00 0.00 0.00 2.17
2502 2636 6.434028 ACTGCATAACAATCCAGTGTACAAAT 59.566 34.615 0.00 0.00 37.18 2.32
2503 2637 5.767665 ACTGCATAACAATCCAGTGTACAAA 59.232 36.000 0.00 0.00 37.18 2.83
2504 2638 5.312895 ACTGCATAACAATCCAGTGTACAA 58.687 37.500 0.00 0.00 37.18 2.41
2505 2639 4.905429 ACTGCATAACAATCCAGTGTACA 58.095 39.130 0.00 0.00 37.18 2.90
2506 2640 5.880054 AACTGCATAACAATCCAGTGTAC 57.120 39.130 0.00 0.00 38.45 2.90
2507 2641 9.674068 TTTATAACTGCATAACAATCCAGTGTA 57.326 29.630 0.00 0.00 38.45 2.90
2508 2642 8.574251 TTTATAACTGCATAACAATCCAGTGT 57.426 30.769 0.00 0.00 38.45 3.55
2509 2643 9.289303 GTTTTATAACTGCATAACAATCCAGTG 57.711 33.333 0.00 0.00 38.45 3.66
2510 2644 9.019656 TGTTTTATAACTGCATAACAATCCAGT 57.980 29.630 0.00 0.00 40.02 4.00
2511 2645 9.289303 GTGTTTTATAACTGCATAACAATCCAG 57.711 33.333 0.00 0.00 35.24 3.86
2512 2646 8.797438 TGTGTTTTATAACTGCATAACAATCCA 58.203 29.630 0.00 0.00 35.24 3.41
2513 2647 9.801873 ATGTGTTTTATAACTGCATAACAATCC 57.198 29.630 0.00 0.00 35.24 3.01
2515 2649 9.585099 CCATGTGTTTTATAACTGCATAACAAT 57.415 29.630 0.00 0.00 35.24 2.71
2516 2650 8.580720 ACCATGTGTTTTATAACTGCATAACAA 58.419 29.630 0.00 0.00 35.24 2.83
2517 2651 8.116651 ACCATGTGTTTTATAACTGCATAACA 57.883 30.769 0.00 0.00 35.24 2.41
2518 2652 8.240682 TGACCATGTGTTTTATAACTGCATAAC 58.759 33.333 0.00 0.00 35.24 1.89
2519 2653 8.341892 TGACCATGTGTTTTATAACTGCATAA 57.658 30.769 0.00 0.00 35.24 1.90
2520 2654 7.929941 TGACCATGTGTTTTATAACTGCATA 57.070 32.000 0.00 0.00 35.24 3.14
2521 2655 6.832520 TGACCATGTGTTTTATAACTGCAT 57.167 33.333 0.00 0.67 35.24 3.96
2522 2656 6.039829 TGTTGACCATGTGTTTTATAACTGCA 59.960 34.615 0.00 0.00 35.24 4.41
2523 2657 6.442952 TGTTGACCATGTGTTTTATAACTGC 58.557 36.000 0.00 0.00 35.24 4.40
2524 2658 7.870826 TCTGTTGACCATGTGTTTTATAACTG 58.129 34.615 0.00 0.00 35.24 3.16
2525 2659 8.635765 ATCTGTTGACCATGTGTTTTATAACT 57.364 30.769 0.00 0.00 35.24 2.24
2526 2660 9.128107 CAATCTGTTGACCATGTGTTTTATAAC 57.872 33.333 0.00 0.00 37.53 1.89
2527 2661 8.855110 ACAATCTGTTGACCATGTGTTTTATAA 58.145 29.630 0.00 0.00 38.71 0.98
2528 2662 8.402798 ACAATCTGTTGACCATGTGTTTTATA 57.597 30.769 0.00 0.00 38.71 0.98
2529 2663 7.288810 ACAATCTGTTGACCATGTGTTTTAT 57.711 32.000 0.00 0.00 38.71 1.40
2530 2664 6.707440 ACAATCTGTTGACCATGTGTTTTA 57.293 33.333 0.00 0.00 38.71 1.52
2531 2665 5.596836 ACAATCTGTTGACCATGTGTTTT 57.403 34.783 0.00 0.00 38.71 2.43
2532 2666 5.596836 AACAATCTGTTGACCATGTGTTT 57.403 34.783 0.00 0.00 39.45 2.83
2533 2667 5.009610 GGTAACAATCTGTTGACCATGTGTT 59.990 40.000 2.30 0.00 41.30 3.32
2534 2668 4.518970 GGTAACAATCTGTTGACCATGTGT 59.481 41.667 2.30 0.00 41.30 3.72
2535 2669 5.046910 GGTAACAATCTGTTGACCATGTG 57.953 43.478 2.30 0.00 41.30 3.21
2552 2686 6.371809 TCAGAAACTCAAATGTGTGGTAAC 57.628 37.500 0.00 0.00 0.00 2.50
2553 2687 8.862325 ATATCAGAAACTCAAATGTGTGGTAA 57.138 30.769 0.00 0.00 0.00 2.85
2554 2688 8.100164 TGATATCAGAAACTCAAATGTGTGGTA 58.900 33.333 0.00 0.00 0.00 3.25
2555 2689 6.942005 TGATATCAGAAACTCAAATGTGTGGT 59.058 34.615 0.00 0.00 0.00 4.16
2556 2690 7.381766 TGATATCAGAAACTCAAATGTGTGG 57.618 36.000 0.00 0.00 0.00 4.17
2557 2691 7.431376 GCATGATATCAGAAACTCAAATGTGTG 59.569 37.037 11.78 0.00 0.00 3.82
2558 2692 7.338703 AGCATGATATCAGAAACTCAAATGTGT 59.661 33.333 11.78 0.00 0.00 3.72
2559 2693 7.704271 AGCATGATATCAGAAACTCAAATGTG 58.296 34.615 11.78 1.00 0.00 3.21
2560 2694 7.013083 GGAGCATGATATCAGAAACTCAAATGT 59.987 37.037 20.00 0.00 0.00 2.71
2561 2695 7.228906 AGGAGCATGATATCAGAAACTCAAATG 59.771 37.037 20.00 9.21 0.00 2.32
2562 2696 7.228906 CAGGAGCATGATATCAGAAACTCAAAT 59.771 37.037 20.00 9.30 0.00 2.32
2563 2697 6.541278 CAGGAGCATGATATCAGAAACTCAAA 59.459 38.462 20.00 0.00 0.00 2.69
2564 2698 6.053650 CAGGAGCATGATATCAGAAACTCAA 58.946 40.000 20.00 0.00 0.00 3.02
2565 2699 5.454329 CCAGGAGCATGATATCAGAAACTCA 60.454 44.000 20.00 0.00 0.00 3.41
2566 2700 4.996122 CCAGGAGCATGATATCAGAAACTC 59.004 45.833 11.78 13.30 0.00 3.01
2567 2701 4.746089 GCCAGGAGCATGATATCAGAAACT 60.746 45.833 11.78 5.52 42.97 2.66
2568 2702 3.501445 GCCAGGAGCATGATATCAGAAAC 59.499 47.826 11.78 3.32 42.97 2.78
2569 2703 3.748083 GCCAGGAGCATGATATCAGAAA 58.252 45.455 11.78 0.00 42.97 2.52
2570 2704 3.413846 GCCAGGAGCATGATATCAGAA 57.586 47.619 11.78 0.00 42.97 3.02


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

AutoCloner maintained by Alex Coulton.