Multiple sequence alignment - TraesCS5B01G290200

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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 TraesCS5B01G290200 chr5B 100.000 2771 0 0 1 2771 476169022 476171792 0.000000e+00 5118.0
1 TraesCS5B01G290200 chr5B 97.143 35 1 0 1480 1514 535700294 535700328 2.980000e-05 60.2
2 TraesCS5B01G290200 chr5D 92.252 2504 86 43 1 2459 396369028 396371468 0.000000e+00 3450.0
3 TraesCS5B01G290200 chr5A 89.918 2083 103 41 459 2468 502071168 502073216 0.000000e+00 2584.0
4 TraesCS5B01G290200 chr5A 87.500 320 17 7 1 311 502070705 502071010 5.680000e-92 348.0
5 TraesCS5B01G290200 chr5A 85.333 150 10 6 354 491 502071007 502071156 8.000000e-31 145.0
6 TraesCS5B01G290200 chr5A 92.683 41 3 0 1477 1517 680843356 680843316 2.980000e-05 60.2
7 TraesCS5B01G290200 chr3B 97.712 306 5 2 2466 2771 134598502 134598805 2.440000e-145 525.0
8 TraesCS5B01G290200 chr3B 97.059 306 7 2 2466 2771 135390136 135389833 5.290000e-142 514.0
9 TraesCS5B01G290200 chr2B 96.026 302 10 2 2470 2771 49595863 49595564 8.920000e-135 490.0
10 TraesCS5B01G290200 chr2B 91.429 315 11 3 2470 2771 677976819 677977130 4.270000e-113 418.0
11 TraesCS5B01G290200 chr2B 92.500 40 3 0 1045 1084 82361338 82361377 1.070000e-04 58.4
12 TraesCS5B01G290200 chr2B 92.500 40 3 0 1045 1084 82713832 82713871 1.070000e-04 58.4
13 TraesCS5B01G290200 chr2B 90.698 43 3 1 1042 1084 82851730 82851771 3.860000e-04 56.5
14 TraesCS5B01G290200 chr7B 90.794 315 13 9 2470 2771 470294602 470294291 9.240000e-110 407.0
15 TraesCS5B01G290200 chr7B 90.159 315 15 3 2470 2771 470243615 470243304 2.000000e-106 396.0
16 TraesCS5B01G290200 chrUn 90.476 315 14 3 2470 2771 201220578 201220889 4.300000e-108 401.0
17 TraesCS5B01G290200 chr1B 90.159 315 15 3 2470 2771 408111446 408111135 2.000000e-106 396.0
18 TraesCS5B01G290200 chr6B 89.028 319 18 5 2467 2771 229143731 229144046 2.010000e-101 379.0
19 TraesCS5B01G290200 chr6B 95.349 43 1 1 1484 1525 51580035 51579993 1.780000e-07 67.6
20 TraesCS5B01G290200 chr6D 93.478 46 2 1 1484 1528 27819924 27819879 1.780000e-07 67.6
21 TraesCS5B01G290200 chr6A 95.122 41 2 0 1484 1524 30190853 30190813 6.410000e-07 65.8
22 TraesCS5B01G290200 chr4B 92.683 41 3 0 1477 1517 643311116 643311076 2.980000e-05 60.2
23 TraesCS5B01G290200 chr4D 94.595 37 2 0 1481 1517 500023785 500023749 1.070000e-04 58.4
24 TraesCS5B01G290200 chr2A 92.500 40 3 0 1045 1084 54111938 54111977 1.070000e-04 58.4


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 TraesCS5B01G290200 chr5B 476169022 476171792 2770 False 5118.000000 5118 100.000000 1 2771 1 chr5B.!!$F1 2770
1 TraesCS5B01G290200 chr5D 396369028 396371468 2440 False 3450.000000 3450 92.252000 1 2459 1 chr5D.!!$F1 2458
2 TraesCS5B01G290200 chr5A 502070705 502073216 2511 False 1025.666667 2584 87.583667 1 2468 3 chr5A.!!$F1 2467

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
322 338 0.320771 GCATGGCCCACGTATAGGAG 60.321 60.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1784 1925 0.461516 ATGATCGCACTGCAGGTCTG 60.462 55.0 19.93 8.64 0.0 3.51 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
182 195 2.097954 TGTGGTAGCTTGTATCGTACGG 59.902 50.000 16.52 0.00 0.00 4.02
183 196 2.355756 GTGGTAGCTTGTATCGTACGGA 59.644 50.000 16.52 2.44 0.00 4.69
184 197 2.615447 TGGTAGCTTGTATCGTACGGAG 59.385 50.000 16.52 7.21 0.00 4.63
297 313 3.723764 CGAAACAACGTCCAGTCAAAATG 59.276 43.478 0.00 0.00 0.00 2.32
318 334 4.868026 GTGCATGGCCCACGTATA 57.132 55.556 0.00 0.00 0.00 1.47
320 336 0.884704 GTGCATGGCCCACGTATAGG 60.885 60.000 0.00 0.00 0.00 2.57
321 337 1.051556 TGCATGGCCCACGTATAGGA 61.052 55.000 0.00 0.00 0.00 2.94
322 338 0.320771 GCATGGCCCACGTATAGGAG 60.321 60.000 0.00 0.00 0.00 3.69
323 339 0.321671 CATGGCCCACGTATAGGAGG 59.678 60.000 0.00 0.43 0.00 4.30
326 342 1.186267 GGCCCACGTATAGGAGGGAG 61.186 65.000 26.34 6.49 40.50 4.30
327 343 1.817911 GCCCACGTATAGGAGGGAGC 61.818 65.000 26.34 11.81 40.50 4.70
328 344 0.469331 CCCACGTATAGGAGGGAGCA 60.469 60.000 19.80 0.00 40.50 4.26
329 345 0.962489 CCACGTATAGGAGGGAGCAG 59.038 60.000 0.00 0.00 0.00 4.24
330 346 0.962489 CACGTATAGGAGGGAGCAGG 59.038 60.000 0.00 0.00 0.00 4.85
331 347 0.851469 ACGTATAGGAGGGAGCAGGA 59.149 55.000 0.00 0.00 0.00 3.86
332 348 1.249407 CGTATAGGAGGGAGCAGGAC 58.751 60.000 0.00 0.00 0.00 3.85
333 349 1.634960 GTATAGGAGGGAGCAGGACC 58.365 60.000 0.00 0.00 0.00 4.46
339 355 3.827752 GGGAGCAGGACCCTTCTT 58.172 61.111 0.00 0.00 43.65 2.52
340 356 1.604915 GGGAGCAGGACCCTTCTTC 59.395 63.158 0.00 0.00 43.65 2.87
341 357 1.201429 GGGAGCAGGACCCTTCTTCA 61.201 60.000 0.00 0.00 43.65 3.02
342 358 0.915364 GGAGCAGGACCCTTCTTCAT 59.085 55.000 0.00 0.00 0.00 2.57
343 359 1.407989 GGAGCAGGACCCTTCTTCATG 60.408 57.143 0.00 0.00 0.00 3.07
344 360 1.556911 GAGCAGGACCCTTCTTCATGA 59.443 52.381 0.00 0.00 0.00 3.07
345 361 1.988107 AGCAGGACCCTTCTTCATGAA 59.012 47.619 8.12 8.12 0.00 2.57
346 362 2.376518 AGCAGGACCCTTCTTCATGAAA 59.623 45.455 9.88 0.00 33.79 2.69
347 363 3.011032 AGCAGGACCCTTCTTCATGAAAT 59.989 43.478 9.88 0.00 33.79 2.17
348 364 3.766051 GCAGGACCCTTCTTCATGAAATT 59.234 43.478 9.88 0.00 33.79 1.82
349 365 4.949856 GCAGGACCCTTCTTCATGAAATTA 59.050 41.667 9.88 0.00 33.79 1.40
350 366 5.595952 GCAGGACCCTTCTTCATGAAATTAT 59.404 40.000 9.88 0.00 33.79 1.28
351 367 6.097412 GCAGGACCCTTCTTCATGAAATTATT 59.903 38.462 9.88 0.00 33.79 1.40
355 371 8.633561 GGACCCTTCTTCATGAAATTATTAAGG 58.366 37.037 9.88 13.60 33.79 2.69
366 382 5.066893 TGAAATTATTAAGGCTGCTCTGCTG 59.933 40.000 0.00 0.00 0.00 4.41
414 438 1.191535 ACGGTATCAGTAGCTGCCAA 58.808 50.000 0.00 0.00 0.00 4.52
456 496 1.526887 CGATCACAATCACATACGCCC 59.473 52.381 0.00 0.00 31.76 6.13
478 518 4.022068 CCGGCCATTACGTACTTAGGATTA 60.022 45.833 2.24 0.00 0.00 1.75
589 670 7.834068 ACATGACAGTGTCAAATACATAGAC 57.166 36.000 28.70 0.00 45.96 2.59
590 671 7.386059 ACATGACAGTGTCAAATACATAGACA 58.614 34.615 28.70 2.46 45.96 3.41
591 672 7.877612 ACATGACAGTGTCAAATACATAGACAA 59.122 33.333 28.70 1.31 45.96 3.18
612 706 0.384309 TGTACGTGAGATCGATGGCC 59.616 55.000 0.54 0.00 34.70 5.36
632 726 3.217626 CCTTATCACATCCCTTTCAGCC 58.782 50.000 0.00 0.00 0.00 4.85
713 807 2.014068 GCTCGAATGGAAGAGTTGGGG 61.014 57.143 0.00 0.00 36.88 4.96
723 818 3.646162 GGAAGAGTTGGGGGAACAATTTT 59.354 43.478 0.00 0.00 36.98 1.82
993 1102 4.941873 GCACCTTAAACCTGCAACTATACT 59.058 41.667 0.00 0.00 0.00 2.12
994 1103 6.110707 GCACCTTAAACCTGCAACTATACTA 58.889 40.000 0.00 0.00 0.00 1.82
995 1104 6.036844 GCACCTTAAACCTGCAACTATACTAC 59.963 42.308 0.00 0.00 0.00 2.73
997 1106 5.233689 CCTTAAACCTGCAACTATACTACGC 59.766 44.000 0.00 0.00 0.00 4.42
998 1107 4.467198 AAACCTGCAACTATACTACGCT 57.533 40.909 0.00 0.00 0.00 5.07
999 1108 5.587388 AAACCTGCAACTATACTACGCTA 57.413 39.130 0.00 0.00 0.00 4.26
1547 1683 0.387622 CAGAACAAGCGTGCCAATGG 60.388 55.000 0.00 0.00 0.00 3.16
1588 1724 2.598099 TCGTGTGCCGGGTGTCTA 60.598 61.111 2.18 0.00 37.11 2.59
1609 1745 1.143684 TGAAAAGCAGAGCAAGGAGGT 59.856 47.619 0.00 0.00 0.00 3.85
1710 1846 2.251642 GGACCACACTTGTCACGCC 61.252 63.158 0.00 0.00 34.36 5.68
1788 1929 3.126225 GCTCCAGCTGCTGCAGAC 61.126 66.667 32.30 22.02 42.74 3.51
1855 2006 7.633553 GCATTTAAATTCCAGCCTTCCTTGTAT 60.634 37.037 0.00 0.00 0.00 2.29
1856 2007 8.912988 CATTTAAATTCCAGCCTTCCTTGTATA 58.087 33.333 0.00 0.00 0.00 1.47
1937 2095 7.279758 AGAGAAGAAGAAATCTCCATTAAAGCG 59.720 37.037 0.00 0.00 42.45 4.68
1998 2160 3.187227 CCAAGACACTCATCAACGAAAGG 59.813 47.826 0.00 0.00 0.00 3.11
2107 2277 0.620700 ACCGGTCCCTTTGGCTCTAT 60.621 55.000 0.00 0.00 0.00 1.98
2347 2523 2.733945 GCTCCGAGATCTCTGCCC 59.266 66.667 20.26 4.90 0.00 5.36
2468 2644 3.056458 CGTGTAGGGTGACAGGCA 58.944 61.111 0.00 0.00 0.00 4.75
2469 2645 1.374252 CGTGTAGGGTGACAGGCAC 60.374 63.158 0.00 0.00 46.98 5.01
2476 2652 3.420943 GTGACAGGCACGCAAACT 58.579 55.556 0.00 0.00 37.83 2.66
2477 2653 1.279840 GTGACAGGCACGCAAACTC 59.720 57.895 0.00 0.00 37.83 3.01
2478 2654 1.891919 TGACAGGCACGCAAACTCC 60.892 57.895 0.00 0.00 0.00 3.85
2479 2655 1.598130 GACAGGCACGCAAACTCCT 60.598 57.895 0.00 0.00 0.00 3.69
2480 2656 1.152963 ACAGGCACGCAAACTCCTT 60.153 52.632 0.00 0.00 0.00 3.36
2481 2657 0.751643 ACAGGCACGCAAACTCCTTT 60.752 50.000 0.00 0.00 0.00 3.11
2482 2658 0.385390 CAGGCACGCAAACTCCTTTT 59.615 50.000 0.00 0.00 0.00 2.27
2483 2659 1.111277 AGGCACGCAAACTCCTTTTT 58.889 45.000 0.00 0.00 0.00 1.94
2484 2660 2.034053 CAGGCACGCAAACTCCTTTTTA 59.966 45.455 0.00 0.00 0.00 1.52
2485 2661 2.034179 AGGCACGCAAACTCCTTTTTAC 59.966 45.455 0.00 0.00 0.00 2.01
2486 2662 2.390938 GCACGCAAACTCCTTTTTACC 58.609 47.619 0.00 0.00 0.00 2.85
2487 2663 2.646250 CACGCAAACTCCTTTTTACCG 58.354 47.619 0.00 0.00 0.00 4.02
2488 2664 1.605232 ACGCAAACTCCTTTTTACCGG 59.395 47.619 0.00 0.00 0.00 5.28
2489 2665 1.874872 CGCAAACTCCTTTTTACCGGA 59.125 47.619 9.46 0.00 0.00 5.14
2505 2681 3.202548 GGAGACGGGATGTACAGGA 57.797 57.895 0.33 0.00 0.00 3.86
2506 2682 1.033574 GGAGACGGGATGTACAGGAG 58.966 60.000 0.33 0.00 0.00 3.69
2507 2683 0.386113 GAGACGGGATGTACAGGAGC 59.614 60.000 0.33 0.00 0.00 4.70
2508 2684 1.043673 AGACGGGATGTACAGGAGCC 61.044 60.000 0.33 0.00 0.00 4.70
2509 2685 2.351336 GACGGGATGTACAGGAGCCG 62.351 65.000 0.33 0.00 0.00 5.52
2510 2686 2.125326 CGGGATGTACAGGAGCCGA 61.125 63.158 0.33 0.00 0.00 5.54
2511 2687 1.672854 CGGGATGTACAGGAGCCGAA 61.673 60.000 0.33 0.00 0.00 4.30
2512 2688 0.759346 GGGATGTACAGGAGCCGAAT 59.241 55.000 0.33 0.00 0.00 3.34
2513 2689 1.270358 GGGATGTACAGGAGCCGAATC 60.270 57.143 0.33 0.00 0.00 2.52
2514 2690 1.270358 GGATGTACAGGAGCCGAATCC 60.270 57.143 0.33 0.00 39.89 3.01
2515 2691 1.412710 GATGTACAGGAGCCGAATCCA 59.587 52.381 0.33 0.00 42.26 3.41
2516 2692 0.535335 TGTACAGGAGCCGAATCCAC 59.465 55.000 8.36 0.00 42.26 4.02
2517 2693 0.179081 GTACAGGAGCCGAATCCACC 60.179 60.000 8.36 0.00 42.26 4.61
2518 2694 1.335132 TACAGGAGCCGAATCCACCC 61.335 60.000 8.36 0.00 42.26 4.61
2519 2695 2.041265 AGGAGCCGAATCCACCCT 59.959 61.111 8.36 0.00 42.26 4.34
2520 2696 1.616628 AGGAGCCGAATCCACCCTT 60.617 57.895 8.36 0.00 42.26 3.95
2521 2697 1.153147 GGAGCCGAATCCACCCTTC 60.153 63.158 1.38 0.00 39.34 3.46
2522 2698 1.602237 GAGCCGAATCCACCCTTCA 59.398 57.895 0.00 0.00 0.00 3.02
2523 2699 0.744771 GAGCCGAATCCACCCTTCAC 60.745 60.000 0.00 0.00 0.00 3.18
2524 2700 1.201429 AGCCGAATCCACCCTTCACT 61.201 55.000 0.00 0.00 0.00 3.41
2525 2701 0.322546 GCCGAATCCACCCTTCACTT 60.323 55.000 0.00 0.00 0.00 3.16
2526 2702 1.453155 CCGAATCCACCCTTCACTTG 58.547 55.000 0.00 0.00 0.00 3.16
2527 2703 0.804989 CGAATCCACCCTTCACTTGC 59.195 55.000 0.00 0.00 0.00 4.01
2528 2704 1.611673 CGAATCCACCCTTCACTTGCT 60.612 52.381 0.00 0.00 0.00 3.91
2529 2705 2.519013 GAATCCACCCTTCACTTGCTT 58.481 47.619 0.00 0.00 0.00 3.91
2530 2706 2.683211 ATCCACCCTTCACTTGCTTT 57.317 45.000 0.00 0.00 0.00 3.51
2531 2707 3.806949 ATCCACCCTTCACTTGCTTTA 57.193 42.857 0.00 0.00 0.00 1.85
2532 2708 3.806949 TCCACCCTTCACTTGCTTTAT 57.193 42.857 0.00 0.00 0.00 1.40
2533 2709 3.420893 TCCACCCTTCACTTGCTTTATG 58.579 45.455 0.00 0.00 0.00 1.90
2534 2710 3.073798 TCCACCCTTCACTTGCTTTATGA 59.926 43.478 0.00 0.00 0.00 2.15
2535 2711 4.019174 CCACCCTTCACTTGCTTTATGAT 58.981 43.478 0.00 0.00 0.00 2.45
2536 2712 4.096984 CCACCCTTCACTTGCTTTATGATC 59.903 45.833 0.00 0.00 0.00 2.92
2537 2713 4.946157 CACCCTTCACTTGCTTTATGATCT 59.054 41.667 0.00 0.00 0.00 2.75
2538 2714 4.946157 ACCCTTCACTTGCTTTATGATCTG 59.054 41.667 0.00 0.00 0.00 2.90
2539 2715 4.946157 CCCTTCACTTGCTTTATGATCTGT 59.054 41.667 0.00 0.00 0.00 3.41
2540 2716 5.163683 CCCTTCACTTGCTTTATGATCTGTG 60.164 44.000 0.00 0.00 0.00 3.66
2541 2717 4.952262 TCACTTGCTTTATGATCTGTGC 57.048 40.909 0.00 0.00 0.00 4.57
2542 2718 3.691118 TCACTTGCTTTATGATCTGTGCC 59.309 43.478 0.00 0.00 0.00 5.01
2543 2719 3.693085 CACTTGCTTTATGATCTGTGCCT 59.307 43.478 0.00 0.00 0.00 4.75
2544 2720 4.877823 CACTTGCTTTATGATCTGTGCCTA 59.122 41.667 0.00 0.00 0.00 3.93
2545 2721 5.355071 CACTTGCTTTATGATCTGTGCCTAA 59.645 40.000 0.00 0.00 0.00 2.69
2546 2722 5.587844 ACTTGCTTTATGATCTGTGCCTAAG 59.412 40.000 0.00 0.00 0.00 2.18
2547 2723 5.102953 TGCTTTATGATCTGTGCCTAAGT 57.897 39.130 0.00 0.00 0.00 2.24
2548 2724 6.233905 TGCTTTATGATCTGTGCCTAAGTA 57.766 37.500 0.00 0.00 0.00 2.24
2549 2725 6.283694 TGCTTTATGATCTGTGCCTAAGTAG 58.716 40.000 0.00 0.00 0.00 2.57
2550 2726 5.698545 GCTTTATGATCTGTGCCTAAGTAGG 59.301 44.000 0.00 0.00 46.42 3.18
2551 2727 5.808366 TTATGATCTGTGCCTAAGTAGGG 57.192 43.478 6.51 0.00 43.82 3.53
2559 2735 1.424638 GCCTAAGTAGGGCTCATCCA 58.575 55.000 6.51 0.00 45.57 3.41
2560 2736 1.981495 GCCTAAGTAGGGCTCATCCAT 59.019 52.381 6.51 0.00 45.57 3.41
2561 2737 3.173965 GCCTAAGTAGGGCTCATCCATA 58.826 50.000 6.51 0.00 45.57 2.74
2562 2738 3.777522 GCCTAAGTAGGGCTCATCCATAT 59.222 47.826 6.51 0.00 45.57 1.78
2563 2739 4.383552 GCCTAAGTAGGGCTCATCCATATG 60.384 50.000 6.51 0.00 45.57 1.78
2564 2740 4.780021 CCTAAGTAGGGCTCATCCATATGT 59.220 45.833 1.24 0.00 39.86 2.29
2565 2741 5.958380 CCTAAGTAGGGCTCATCCATATGTA 59.042 44.000 1.24 0.00 39.86 2.29
2566 2742 6.613271 CCTAAGTAGGGCTCATCCATATGTAT 59.387 42.308 1.24 0.00 39.86 2.29
2567 2743 7.785028 CCTAAGTAGGGCTCATCCATATGTATA 59.215 40.741 1.24 0.00 39.86 1.47
2568 2744 9.201989 CTAAGTAGGGCTCATCCATATGTATAA 57.798 37.037 1.24 0.00 33.15 0.98
2569 2745 8.629821 AAGTAGGGCTCATCCATATGTATAAT 57.370 34.615 1.24 0.00 33.15 1.28
2570 2746 8.256356 AGTAGGGCTCATCCATATGTATAATC 57.744 38.462 1.24 0.00 33.15 1.75
2571 2747 7.846311 AGTAGGGCTCATCCATATGTATAATCA 59.154 37.037 1.24 0.00 33.15 2.57
2572 2748 7.702807 AGGGCTCATCCATATGTATAATCAT 57.297 36.000 1.24 0.00 36.21 2.45
2573 2749 7.515586 AGGGCTCATCCATATGTATAATCATG 58.484 38.462 1.24 0.00 36.21 3.07
2574 2750 7.128418 AGGGCTCATCCATATGTATAATCATGT 59.872 37.037 1.24 0.00 36.21 3.21
2575 2751 8.432013 GGGCTCATCCATATGTATAATCATGTA 58.568 37.037 1.24 0.00 36.21 2.29
2590 2766 8.743085 ATAATCATGTATTGAGACATATGCCC 57.257 34.615 1.58 0.00 37.99 5.36
2591 2767 5.830799 TCATGTATTGAGACATATGCCCT 57.169 39.130 1.58 0.00 37.99 5.19
2592 2768 6.191657 TCATGTATTGAGACATATGCCCTT 57.808 37.500 1.58 0.00 37.99 3.95
2593 2769 6.604171 TCATGTATTGAGACATATGCCCTTT 58.396 36.000 1.58 0.00 37.99 3.11
2594 2770 7.062322 TCATGTATTGAGACATATGCCCTTTT 58.938 34.615 1.58 0.00 37.99 2.27
2595 2771 6.698008 TGTATTGAGACATATGCCCTTTTG 57.302 37.500 1.58 0.00 0.00 2.44
2596 2772 6.186957 TGTATTGAGACATATGCCCTTTTGT 58.813 36.000 1.58 0.00 0.00 2.83
2597 2773 7.342581 TGTATTGAGACATATGCCCTTTTGTA 58.657 34.615 1.58 0.00 0.00 2.41
2598 2774 7.998383 TGTATTGAGACATATGCCCTTTTGTAT 59.002 33.333 1.58 0.00 0.00 2.29
2599 2775 9.502091 GTATTGAGACATATGCCCTTTTGTATA 57.498 33.333 1.58 0.00 0.00 1.47
2602 2778 9.725019 TTGAGACATATGCCCTTTTGTATATAG 57.275 33.333 1.58 0.00 0.00 1.31
2603 2779 8.880244 TGAGACATATGCCCTTTTGTATATAGT 58.120 33.333 1.58 0.00 0.00 2.12
2604 2780 9.372369 GAGACATATGCCCTTTTGTATATAGTC 57.628 37.037 1.58 0.00 0.00 2.59
2605 2781 8.880244 AGACATATGCCCTTTTGTATATAGTCA 58.120 33.333 1.58 0.00 0.00 3.41
2606 2782 9.502091 GACATATGCCCTTTTGTATATAGTCAA 57.498 33.333 1.58 0.00 0.00 3.18
2607 2783 9.860650 ACATATGCCCTTTTGTATATAGTCAAA 57.139 29.630 1.58 2.35 32.75 2.69
2610 2786 8.995027 ATGCCCTTTTGTATATAGTCAAATCA 57.005 30.769 6.12 4.26 34.30 2.57
2611 2787 8.815565 TGCCCTTTTGTATATAGTCAAATCAA 57.184 30.769 6.12 0.00 34.30 2.57
2612 2788 9.420118 TGCCCTTTTGTATATAGTCAAATCAAT 57.580 29.630 6.12 0.00 34.30 2.57
2613 2789 9.683069 GCCCTTTTGTATATAGTCAAATCAATG 57.317 33.333 6.12 0.00 34.30 2.82
2624 2800 6.738832 AGTCAAATCAATGTCAGATGTCAG 57.261 37.500 0.00 0.00 0.00 3.51
2625 2801 5.646793 AGTCAAATCAATGTCAGATGTCAGG 59.353 40.000 0.00 0.00 0.00 3.86
2626 2802 4.945543 TCAAATCAATGTCAGATGTCAGGG 59.054 41.667 0.00 0.00 0.00 4.45
2627 2803 4.849813 AATCAATGTCAGATGTCAGGGA 57.150 40.909 0.00 0.00 0.00 4.20
2628 2804 3.900966 TCAATGTCAGATGTCAGGGAG 57.099 47.619 0.00 0.00 0.00 4.30
2629 2805 3.444029 TCAATGTCAGATGTCAGGGAGA 58.556 45.455 0.00 0.00 0.00 3.71
2630 2806 3.450096 TCAATGTCAGATGTCAGGGAGAG 59.550 47.826 0.00 0.00 0.00 3.20
2631 2807 1.857965 TGTCAGATGTCAGGGAGAGG 58.142 55.000 0.00 0.00 0.00 3.69
2632 2808 0.463620 GTCAGATGTCAGGGAGAGGC 59.536 60.000 0.00 0.00 0.00 4.70
2633 2809 0.041684 TCAGATGTCAGGGAGAGGCA 59.958 55.000 0.00 0.00 0.00 4.75
2634 2810 0.464870 CAGATGTCAGGGAGAGGCAG 59.535 60.000 0.00 0.00 0.00 4.85
2635 2811 0.042431 AGATGTCAGGGAGAGGCAGT 59.958 55.000 0.00 0.00 0.00 4.40
2636 2812 1.289231 AGATGTCAGGGAGAGGCAGTA 59.711 52.381 0.00 0.00 0.00 2.74
2637 2813 1.410882 GATGTCAGGGAGAGGCAGTAC 59.589 57.143 0.00 0.00 0.00 2.73
2638 2814 0.409876 TGTCAGGGAGAGGCAGTACT 59.590 55.000 0.00 0.00 0.00 2.73
2639 2815 1.203187 TGTCAGGGAGAGGCAGTACTT 60.203 52.381 0.00 0.00 0.00 2.24
2640 2816 1.903183 GTCAGGGAGAGGCAGTACTTT 59.097 52.381 0.00 0.00 0.00 2.66
2641 2817 2.303311 GTCAGGGAGAGGCAGTACTTTT 59.697 50.000 0.00 0.00 0.00 2.27
2642 2818 2.979678 TCAGGGAGAGGCAGTACTTTTT 59.020 45.455 0.00 0.00 0.00 1.94
2661 2837 5.574891 TTTTTGCAGTGGATTATACGCAT 57.425 34.783 0.00 0.00 31.50 4.73
2662 2838 4.550577 TTTGCAGTGGATTATACGCATG 57.449 40.909 0.00 0.00 31.50 4.06
2663 2839 1.872952 TGCAGTGGATTATACGCATGC 59.127 47.619 7.91 7.91 0.00 4.06
2664 2840 1.872952 GCAGTGGATTATACGCATGCA 59.127 47.619 19.57 0.00 32.79 3.96
2665 2841 2.485426 GCAGTGGATTATACGCATGCAT 59.515 45.455 19.57 4.54 32.79 3.96
2666 2842 3.668757 GCAGTGGATTATACGCATGCATG 60.669 47.826 22.70 22.70 32.79 4.06
2680 2856 2.619362 GCATGCAGCATCTCTCTCC 58.381 57.895 14.21 0.00 44.79 3.71
2681 2857 0.107081 GCATGCAGCATCTCTCTCCT 59.893 55.000 14.21 0.00 44.79 3.69
2682 2858 1.874739 GCATGCAGCATCTCTCTCCTC 60.875 57.143 14.21 0.00 44.79 3.71
2683 2859 1.689813 CATGCAGCATCTCTCTCCTCT 59.310 52.381 4.38 0.00 0.00 3.69
2684 2860 1.401761 TGCAGCATCTCTCTCCTCTC 58.598 55.000 0.00 0.00 0.00 3.20
2685 2861 1.063792 TGCAGCATCTCTCTCCTCTCT 60.064 52.381 0.00 0.00 0.00 3.10
2686 2862 1.610522 GCAGCATCTCTCTCCTCTCTC 59.389 57.143 0.00 0.00 0.00 3.20
2687 2863 2.750807 GCAGCATCTCTCTCCTCTCTCT 60.751 54.545 0.00 0.00 0.00 3.10
2688 2864 3.144506 CAGCATCTCTCTCCTCTCTCTC 58.855 54.545 0.00 0.00 0.00 3.20
2689 2865 2.779430 AGCATCTCTCTCCTCTCTCTCA 59.221 50.000 0.00 0.00 0.00 3.27
2690 2866 3.202818 AGCATCTCTCTCCTCTCTCTCAA 59.797 47.826 0.00 0.00 0.00 3.02
2691 2867 3.953612 GCATCTCTCTCCTCTCTCTCAAA 59.046 47.826 0.00 0.00 0.00 2.69
2692 2868 4.202050 GCATCTCTCTCCTCTCTCTCAAAC 60.202 50.000 0.00 0.00 0.00 2.93
2693 2869 4.649267 TCTCTCTCCTCTCTCTCAAACA 57.351 45.455 0.00 0.00 0.00 2.83
2694 2870 4.991776 TCTCTCTCCTCTCTCTCAAACAA 58.008 43.478 0.00 0.00 0.00 2.83
2695 2871 5.389520 TCTCTCTCCTCTCTCTCAAACAAA 58.610 41.667 0.00 0.00 0.00 2.83
2696 2872 6.015918 TCTCTCTCCTCTCTCTCAAACAAAT 58.984 40.000 0.00 0.00 0.00 2.32
2697 2873 6.152661 TCTCTCTCCTCTCTCTCAAACAAATC 59.847 42.308 0.00 0.00 0.00 2.17
2698 2874 5.186797 TCTCTCCTCTCTCTCAAACAAATCC 59.813 44.000 0.00 0.00 0.00 3.01
2699 2875 4.840680 TCTCCTCTCTCTCAAACAAATCCA 59.159 41.667 0.00 0.00 0.00 3.41
2700 2876 5.486775 TCTCCTCTCTCTCAAACAAATCCAT 59.513 40.000 0.00 0.00 0.00 3.41
2701 2877 5.494724 TCCTCTCTCTCAAACAAATCCATG 58.505 41.667 0.00 0.00 0.00 3.66
2702 2878 4.096081 CCTCTCTCTCAAACAAATCCATGC 59.904 45.833 0.00 0.00 0.00 4.06
2703 2879 4.654915 TCTCTCTCAAACAAATCCATGCA 58.345 39.130 0.00 0.00 0.00 3.96
2704 2880 5.258841 TCTCTCTCAAACAAATCCATGCAT 58.741 37.500 0.00 0.00 0.00 3.96
2705 2881 5.713389 TCTCTCTCAAACAAATCCATGCATT 59.287 36.000 0.00 0.00 0.00 3.56
2706 2882 6.209986 TCTCTCTCAAACAAATCCATGCATTT 59.790 34.615 0.00 0.00 0.00 2.32
2707 2883 6.761312 TCTCTCAAACAAATCCATGCATTTT 58.239 32.000 0.00 0.00 0.00 1.82
2708 2884 7.894708 TCTCTCAAACAAATCCATGCATTTTA 58.105 30.769 0.00 0.00 0.00 1.52
2709 2885 8.533657 TCTCTCAAACAAATCCATGCATTTTAT 58.466 29.630 0.00 0.00 0.00 1.40
2710 2886 9.158233 CTCTCAAACAAATCCATGCATTTTATT 57.842 29.630 0.00 0.00 0.00 1.40
2711 2887 9.504708 TCTCAAACAAATCCATGCATTTTATTT 57.495 25.926 0.00 0.54 0.00 1.40
2715 2891 9.694137 AAACAAATCCATGCATTTTATTTTTGG 57.306 25.926 0.00 0.00 0.00 3.28
2716 2892 8.406730 ACAAATCCATGCATTTTATTTTTGGT 57.593 26.923 0.00 0.00 0.00 3.67
2717 2893 8.858094 ACAAATCCATGCATTTTATTTTTGGTT 58.142 25.926 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 8.576442 CCACCATTATATTAGCAACCCTTAAAG 58.424 37.037 0.00 0.00 0.00 1.85
55 56 1.456331 GCAGGCAGCCCACCATTAT 60.456 57.895 8.22 0.00 37.23 1.28
133 134 0.740149 GGGAACGAATCATGCATGCA 59.260 50.000 25.04 25.04 0.00 3.96
134 135 0.740149 TGGGAACGAATCATGCATGC 59.260 50.000 22.25 11.82 0.00 4.06
196 209 9.745880 GCTCTGCATGTTAATTACTAGTACTAA 57.254 33.333 0.91 1.09 0.00 2.24
315 331 0.487772 GGGTCCTGCTCCCTCCTATA 59.512 60.000 0.00 0.00 41.58 1.31
316 332 1.237458 GGGTCCTGCTCCCTCCTAT 59.763 63.158 0.00 0.00 41.58 2.57
317 333 2.696893 GGGTCCTGCTCCCTCCTA 59.303 66.667 0.00 0.00 41.58 2.94
322 338 1.201429 TGAAGAAGGGTCCTGCTCCC 61.201 60.000 0.00 0.00 44.90 4.30
323 339 0.915364 ATGAAGAAGGGTCCTGCTCC 59.085 55.000 0.00 0.00 28.66 4.70
326 342 2.496899 TTCATGAAGAAGGGTCCTGC 57.503 50.000 3.38 0.00 0.00 4.85
327 343 7.651027 AATAATTTCATGAAGAAGGGTCCTG 57.349 36.000 8.41 0.00 37.57 3.86
328 344 9.413734 CTTAATAATTTCATGAAGAAGGGTCCT 57.586 33.333 8.41 0.00 37.57 3.85
329 345 8.633561 CCTTAATAATTTCATGAAGAAGGGTCC 58.366 37.037 8.41 0.00 37.57 4.46
330 346 8.138074 GCCTTAATAATTTCATGAAGAAGGGTC 58.862 37.037 20.72 10.26 37.57 4.46
331 347 7.841222 AGCCTTAATAATTTCATGAAGAAGGGT 59.159 33.333 19.36 19.36 37.57 4.34
332 348 8.139989 CAGCCTTAATAATTTCATGAAGAAGGG 58.860 37.037 20.72 13.33 37.57 3.95
333 349 7.650903 GCAGCCTTAATAATTTCATGAAGAAGG 59.349 37.037 8.41 14.70 37.57 3.46
334 350 8.411683 AGCAGCCTTAATAATTTCATGAAGAAG 58.588 33.333 8.41 6.74 37.57 2.85
335 351 8.297470 AGCAGCCTTAATAATTTCATGAAGAA 57.703 30.769 8.41 0.00 0.00 2.52
336 352 7.776969 AGAGCAGCCTTAATAATTTCATGAAGA 59.223 33.333 8.41 0.72 0.00 2.87
337 353 7.861372 CAGAGCAGCCTTAATAATTTCATGAAG 59.139 37.037 8.41 0.00 0.00 3.02
338 354 7.682741 GCAGAGCAGCCTTAATAATTTCATGAA 60.683 37.037 3.38 3.38 0.00 2.57
339 355 6.238842 GCAGAGCAGCCTTAATAATTTCATGA 60.239 38.462 0.00 0.00 0.00 3.07
340 356 5.919141 GCAGAGCAGCCTTAATAATTTCATG 59.081 40.000 0.00 0.00 0.00 3.07
341 357 5.832060 AGCAGAGCAGCCTTAATAATTTCAT 59.168 36.000 0.00 0.00 34.23 2.57
342 358 5.066893 CAGCAGAGCAGCCTTAATAATTTCA 59.933 40.000 0.00 0.00 34.23 2.69
343 359 5.506982 CCAGCAGAGCAGCCTTAATAATTTC 60.507 44.000 0.00 0.00 34.23 2.17
344 360 4.340381 CCAGCAGAGCAGCCTTAATAATTT 59.660 41.667 0.00 0.00 34.23 1.82
345 361 3.887716 CCAGCAGAGCAGCCTTAATAATT 59.112 43.478 0.00 0.00 34.23 1.40
346 362 3.137176 TCCAGCAGAGCAGCCTTAATAAT 59.863 43.478 0.00 0.00 34.23 1.28
347 363 2.505407 TCCAGCAGAGCAGCCTTAATAA 59.495 45.455 0.00 0.00 34.23 1.40
348 364 2.103771 CTCCAGCAGAGCAGCCTTAATA 59.896 50.000 0.00 0.00 35.31 0.98
349 365 0.914644 TCCAGCAGAGCAGCCTTAAT 59.085 50.000 0.00 0.00 34.23 1.40
350 366 0.251354 CTCCAGCAGAGCAGCCTTAA 59.749 55.000 0.00 0.00 35.31 1.85
351 367 1.903294 CTCCAGCAGAGCAGCCTTA 59.097 57.895 0.00 0.00 35.31 2.69
366 382 5.078411 TCTTGCTTGAGAGATGTTACTCC 57.922 43.478 0.00 0.00 37.60 3.85
456 496 3.655276 ATCCTAAGTACGTAATGGCCG 57.345 47.619 0.00 0.00 0.00 6.13
509 549 9.163899 ACGATGTCATGTATTCGTATAGAGTAT 57.836 33.333 14.60 0.00 42.48 2.12
512 587 7.478978 GTGACGATGTCATGTATTCGTATAGAG 59.521 40.741 15.65 0.00 44.63 2.43
514 589 7.075741 TGTGACGATGTCATGTATTCGTATAG 58.924 38.462 15.65 0.00 44.63 1.31
586 667 4.696899 TCGATCTCACGTACATTTGTCT 57.303 40.909 0.00 0.00 34.70 3.41
587 668 4.207224 CCATCGATCTCACGTACATTTGTC 59.793 45.833 0.00 0.00 34.70 3.18
588 669 4.112634 CCATCGATCTCACGTACATTTGT 58.887 43.478 0.00 0.00 34.70 2.83
589 670 3.060272 GCCATCGATCTCACGTACATTTG 60.060 47.826 0.00 0.00 34.70 2.32
590 671 3.123804 GCCATCGATCTCACGTACATTT 58.876 45.455 0.00 0.00 34.70 2.32
591 672 2.545952 GGCCATCGATCTCACGTACATT 60.546 50.000 0.00 0.00 34.70 2.71
612 706 4.162040 AGGCTGAAAGGGATGTGATAAG 57.838 45.455 0.00 0.00 0.00 1.73
632 726 1.926511 AATTCAGGCGCCGCTTCAAG 61.927 55.000 23.20 6.35 0.00 3.02
699 793 1.455822 TGTTCCCCCAACTCTTCCAT 58.544 50.000 0.00 0.00 35.79 3.41
713 807 4.403734 TCCCTCACCACTAAAATTGTTCC 58.596 43.478 0.00 0.00 0.00 3.62
723 818 1.000019 CCCGTCTCCCTCACCACTA 60.000 63.158 0.00 0.00 0.00 2.74
925 1034 1.025041 CGATCACCGATCAGTCTGGA 58.975 55.000 0.00 0.00 38.84 3.86
928 1037 1.736586 GGCGATCACCGATCAGTCT 59.263 57.895 4.95 0.00 38.84 3.24
993 1102 2.288213 CCGCATCTTCTCCATTAGCGTA 60.288 50.000 0.00 0.00 41.87 4.42
994 1103 1.539065 CCGCATCTTCTCCATTAGCGT 60.539 52.381 0.00 0.00 41.87 5.07
995 1104 1.143305 CCGCATCTTCTCCATTAGCG 58.857 55.000 0.00 0.00 42.93 4.26
997 1106 1.202687 TGCCCGCATCTTCTCCATTAG 60.203 52.381 0.00 0.00 0.00 1.73
998 1107 0.836606 TGCCCGCATCTTCTCCATTA 59.163 50.000 0.00 0.00 0.00 1.90
999 1108 0.465097 CTGCCCGCATCTTCTCCATT 60.465 55.000 0.00 0.00 0.00 3.16
1368 1504 2.291043 CGTGGCCTTCCAGTACCCT 61.291 63.158 3.32 0.00 44.48 4.34
1588 1724 2.224967 ACCTCCTTGCTCTGCTTTTCAT 60.225 45.455 0.00 0.00 0.00 2.57
1784 1925 0.461516 ATGATCGCACTGCAGGTCTG 60.462 55.000 19.93 8.64 0.00 3.51
1785 1926 0.461516 CATGATCGCACTGCAGGTCT 60.462 55.000 19.93 0.00 0.00 3.85
1786 1927 2.012237 CATGATCGCACTGCAGGTC 58.988 57.895 19.93 8.05 0.00 3.85
1787 1928 2.110967 GCATGATCGCACTGCAGGT 61.111 57.895 19.93 0.24 35.96 4.00
1788 1929 2.713770 GCATGATCGCACTGCAGG 59.286 61.111 19.93 8.27 35.96 4.85
1855 2006 2.083774 CCGTACGTACAAGGACAGGTA 58.916 52.381 24.50 0.00 0.00 3.08
1856 2007 0.883833 CCGTACGTACAAGGACAGGT 59.116 55.000 24.50 0.00 0.00 4.00
1998 2160 4.037565 CGGGCTTAATTAATCCTGGTTTCC 59.962 45.833 16.20 0.28 0.00 3.13
2029 2191 2.469826 CGGCAGCGACTGATGTTATAA 58.530 47.619 10.46 0.00 32.92 0.98
2123 2293 7.868415 CCGTTACCAATTTTAGGTCATTTTTCA 59.132 33.333 0.00 0.00 40.54 2.69
2132 2302 3.349927 GCCTCCGTTACCAATTTTAGGT 58.650 45.455 0.00 0.00 43.14 3.08
2142 2312 1.035385 CCCATTTGGCCTCCGTTACC 61.035 60.000 3.32 0.00 0.00 2.85
2238 2408 4.609018 ACGTGCAGAGCTTGGCGT 62.609 61.111 6.14 2.29 0.00 5.68
2277 2453 4.147449 CATGCCGGCCACTCTCGA 62.147 66.667 26.77 1.65 0.00 4.04
2347 2523 3.470888 CCTACCCCCTGCGTCCAG 61.471 72.222 0.00 0.00 38.85 3.86
2468 2644 1.605232 CCGGTAAAAAGGAGTTTGCGT 59.395 47.619 0.00 0.00 0.00 5.24
2469 2645 1.874872 TCCGGTAAAAAGGAGTTTGCG 59.125 47.619 0.00 0.00 31.95 4.85
2470 2646 3.554259 CTCCGGTAAAAAGGAGTTTGC 57.446 47.619 0.00 0.00 46.68 3.68
2486 2662 0.750546 TCCTGTACATCCCGTCTCCG 60.751 60.000 0.00 0.00 0.00 4.63
2487 2663 1.033574 CTCCTGTACATCCCGTCTCC 58.966 60.000 0.00 0.00 0.00 3.71
2488 2664 0.386113 GCTCCTGTACATCCCGTCTC 59.614 60.000 0.00 0.00 0.00 3.36
2489 2665 1.043673 GGCTCCTGTACATCCCGTCT 61.044 60.000 0.00 0.00 0.00 4.18
2490 2666 1.442148 GGCTCCTGTACATCCCGTC 59.558 63.158 0.00 0.00 0.00 4.79
2491 2667 2.423898 CGGCTCCTGTACATCCCGT 61.424 63.158 12.64 0.00 0.00 5.28
2492 2668 1.672854 TTCGGCTCCTGTACATCCCG 61.673 60.000 13.97 13.97 37.21 5.14
2493 2669 0.759346 ATTCGGCTCCTGTACATCCC 59.241 55.000 0.00 0.00 0.00 3.85
2494 2670 1.270358 GGATTCGGCTCCTGTACATCC 60.270 57.143 0.00 0.00 32.18 3.51
2495 2671 1.412710 TGGATTCGGCTCCTGTACATC 59.587 52.381 0.00 0.00 36.20 3.06
2496 2672 1.139058 GTGGATTCGGCTCCTGTACAT 59.861 52.381 0.00 0.00 36.20 2.29
2497 2673 0.535335 GTGGATTCGGCTCCTGTACA 59.465 55.000 0.00 0.00 36.20 2.90
2498 2674 0.179081 GGTGGATTCGGCTCCTGTAC 60.179 60.000 5.88 0.00 36.20 2.90
2499 2675 1.335132 GGGTGGATTCGGCTCCTGTA 61.335 60.000 5.88 0.00 36.20 2.74
2500 2676 2.670148 GGGTGGATTCGGCTCCTGT 61.670 63.158 5.88 0.00 36.20 4.00
2501 2677 1.915078 AAGGGTGGATTCGGCTCCTG 61.915 60.000 5.88 0.00 36.20 3.86
2502 2678 1.616628 AAGGGTGGATTCGGCTCCT 60.617 57.895 5.88 0.00 36.20 3.69
2503 2679 1.153147 GAAGGGTGGATTCGGCTCC 60.153 63.158 0.00 0.00 35.74 4.70
2504 2680 0.744771 GTGAAGGGTGGATTCGGCTC 60.745 60.000 0.00 0.00 0.00 4.70
2505 2681 1.201429 AGTGAAGGGTGGATTCGGCT 61.201 55.000 0.00 0.00 0.00 5.52
2506 2682 0.322546 AAGTGAAGGGTGGATTCGGC 60.323 55.000 0.00 0.00 0.00 5.54
2507 2683 1.453155 CAAGTGAAGGGTGGATTCGG 58.547 55.000 0.00 0.00 0.00 4.30
2508 2684 0.804989 GCAAGTGAAGGGTGGATTCG 59.195 55.000 0.00 0.00 0.00 3.34
2509 2685 2.206576 AGCAAGTGAAGGGTGGATTC 57.793 50.000 0.00 0.00 0.00 2.52
2510 2686 2.683211 AAGCAAGTGAAGGGTGGATT 57.317 45.000 0.00 0.00 0.00 3.01
2511 2687 2.683211 AAAGCAAGTGAAGGGTGGAT 57.317 45.000 0.00 0.00 0.00 3.41
2512 2688 3.073798 TCATAAAGCAAGTGAAGGGTGGA 59.926 43.478 0.00 0.00 0.00 4.02
2513 2689 3.420893 TCATAAAGCAAGTGAAGGGTGG 58.579 45.455 0.00 0.00 0.00 4.61
2514 2690 4.946157 AGATCATAAAGCAAGTGAAGGGTG 59.054 41.667 0.00 0.00 0.00 4.61
2515 2691 4.946157 CAGATCATAAAGCAAGTGAAGGGT 59.054 41.667 0.00 0.00 0.00 4.34
2516 2692 4.946157 ACAGATCATAAAGCAAGTGAAGGG 59.054 41.667 0.00 0.00 0.00 3.95
2517 2693 5.675575 GCACAGATCATAAAGCAAGTGAAGG 60.676 44.000 0.00 0.00 0.00 3.46
2518 2694 5.330295 GCACAGATCATAAAGCAAGTGAAG 58.670 41.667 0.00 0.00 0.00 3.02
2519 2695 4.156556 GGCACAGATCATAAAGCAAGTGAA 59.843 41.667 0.00 0.00 0.00 3.18
2520 2696 3.691118 GGCACAGATCATAAAGCAAGTGA 59.309 43.478 0.00 0.00 0.00 3.41
2521 2697 3.693085 AGGCACAGATCATAAAGCAAGTG 59.307 43.478 0.00 0.00 0.00 3.16
2522 2698 3.960571 AGGCACAGATCATAAAGCAAGT 58.039 40.909 0.00 0.00 0.00 3.16
2523 2699 5.587844 ACTTAGGCACAGATCATAAAGCAAG 59.412 40.000 0.00 0.00 0.00 4.01
2524 2700 5.500234 ACTTAGGCACAGATCATAAAGCAA 58.500 37.500 0.00 0.00 0.00 3.91
2525 2701 5.102953 ACTTAGGCACAGATCATAAAGCA 57.897 39.130 0.00 0.00 0.00 3.91
2526 2702 5.698545 CCTACTTAGGCACAGATCATAAAGC 59.301 44.000 0.00 0.00 36.53 3.51
2527 2703 6.226787 CCCTACTTAGGCACAGATCATAAAG 58.773 44.000 0.00 0.00 42.26 1.85
2528 2704 6.174720 CCCTACTTAGGCACAGATCATAAA 57.825 41.667 0.00 0.00 42.26 1.40
2529 2705 5.808366 CCCTACTTAGGCACAGATCATAA 57.192 43.478 0.00 0.00 42.26 1.90
2539 2715 9.841349 TACATATGGATGAGCCCTACTTAGGCA 62.841 44.444 7.80 0.00 43.63 4.75
2540 2716 6.806874 ACATATGGATGAGCCCTACTTAGGC 61.807 48.000 7.80 0.00 42.54 3.93
2541 2717 4.780021 ACATATGGATGAGCCCTACTTAGG 59.220 45.833 7.80 0.00 38.59 2.69
2542 2718 7.667575 ATACATATGGATGAGCCCTACTTAG 57.332 40.000 7.80 0.00 36.48 2.18
2543 2719 9.729550 ATTATACATATGGATGAGCCCTACTTA 57.270 33.333 10.95 0.00 36.48 2.24
2544 2720 8.629821 ATTATACATATGGATGAGCCCTACTT 57.370 34.615 10.95 0.00 36.48 2.24
2545 2721 7.846311 TGATTATACATATGGATGAGCCCTACT 59.154 37.037 10.95 0.00 36.48 2.57
2546 2722 8.023021 TGATTATACATATGGATGAGCCCTAC 57.977 38.462 10.95 0.00 36.48 3.18
2547 2723 8.654094 CATGATTATACATATGGATGAGCCCTA 58.346 37.037 10.95 0.00 36.48 3.53
2548 2724 7.128418 ACATGATTATACATATGGATGAGCCCT 59.872 37.037 10.95 0.00 36.48 5.19
2549 2725 7.285566 ACATGATTATACATATGGATGAGCCC 58.714 38.462 10.95 0.00 36.48 5.19
2564 2740 9.836864 GGGCATATGTCTCAATACATGATTATA 57.163 33.333 7.36 0.00 40.29 0.98
2565 2741 8.554870 AGGGCATATGTCTCAATACATGATTAT 58.445 33.333 7.36 0.00 40.29 1.28
2566 2742 7.921304 AGGGCATATGTCTCAATACATGATTA 58.079 34.615 7.36 0.00 40.29 1.75
2567 2743 6.787170 AGGGCATATGTCTCAATACATGATT 58.213 36.000 7.36 0.00 40.29 2.57
2568 2744 6.384342 AGGGCATATGTCTCAATACATGAT 57.616 37.500 7.36 0.00 40.29 2.45
2569 2745 5.830799 AGGGCATATGTCTCAATACATGA 57.169 39.130 7.36 0.00 40.29 3.07
2570 2746 6.889301 AAAGGGCATATGTCTCAATACATG 57.111 37.500 7.36 0.00 40.29 3.21
2571 2747 6.835488 ACAAAAGGGCATATGTCTCAATACAT 59.165 34.615 7.36 0.00 42.62 2.29
2572 2748 6.186957 ACAAAAGGGCATATGTCTCAATACA 58.813 36.000 7.36 0.00 0.00 2.29
2573 2749 6.699575 ACAAAAGGGCATATGTCTCAATAC 57.300 37.500 7.36 0.00 0.00 1.89
2576 2752 9.725019 CTATATACAAAAGGGCATATGTCTCAA 57.275 33.333 7.36 0.00 0.00 3.02
2577 2753 8.880244 ACTATATACAAAAGGGCATATGTCTCA 58.120 33.333 7.36 0.00 0.00 3.27
2578 2754 9.372369 GACTATATACAAAAGGGCATATGTCTC 57.628 37.037 7.36 0.00 0.00 3.36
2579 2755 8.880244 TGACTATATACAAAAGGGCATATGTCT 58.120 33.333 7.36 1.17 0.00 3.41
2580 2756 9.502091 TTGACTATATACAAAAGGGCATATGTC 57.498 33.333 4.29 0.58 0.00 3.06
2581 2757 9.860650 TTTGACTATATACAAAAGGGCATATGT 57.139 29.630 4.29 0.00 33.90 2.29
2585 2761 8.995027 TGATTTGACTATATACAAAAGGGCAT 57.005 30.769 0.00 0.00 39.01 4.40
2586 2762 8.815565 TTGATTTGACTATATACAAAAGGGCA 57.184 30.769 0.00 0.00 39.01 5.36
2587 2763 9.683069 CATTGATTTGACTATATACAAAAGGGC 57.317 33.333 0.00 0.00 39.01 5.19
2598 2774 9.538508 CTGACATCTGACATTGATTTGACTATA 57.461 33.333 0.00 0.00 0.00 1.31
2599 2775 7.498239 CCTGACATCTGACATTGATTTGACTAT 59.502 37.037 0.00 0.00 0.00 2.12
2600 2776 6.820152 CCTGACATCTGACATTGATTTGACTA 59.180 38.462 0.00 0.00 0.00 2.59
2601 2777 5.646793 CCTGACATCTGACATTGATTTGACT 59.353 40.000 0.00 0.00 0.00 3.41
2602 2778 5.163683 CCCTGACATCTGACATTGATTTGAC 60.164 44.000 0.00 0.00 0.00 3.18
2603 2779 4.945543 CCCTGACATCTGACATTGATTTGA 59.054 41.667 0.00 0.00 0.00 2.69
2604 2780 4.945543 TCCCTGACATCTGACATTGATTTG 59.054 41.667 0.00 0.00 0.00 2.32
2605 2781 5.045359 TCTCCCTGACATCTGACATTGATTT 60.045 40.000 0.00 0.00 0.00 2.17
2606 2782 4.472470 TCTCCCTGACATCTGACATTGATT 59.528 41.667 0.00 0.00 0.00 2.57
2607 2783 4.035814 TCTCCCTGACATCTGACATTGAT 58.964 43.478 0.00 0.00 0.00 2.57
2608 2784 3.444029 TCTCCCTGACATCTGACATTGA 58.556 45.455 0.00 0.00 0.00 2.57
2609 2785 3.431905 CCTCTCCCTGACATCTGACATTG 60.432 52.174 0.00 0.00 0.00 2.82
2610 2786 2.770802 CCTCTCCCTGACATCTGACATT 59.229 50.000 0.00 0.00 0.00 2.71
2611 2787 2.396608 CCTCTCCCTGACATCTGACAT 58.603 52.381 0.00 0.00 0.00 3.06
2612 2788 1.857965 CCTCTCCCTGACATCTGACA 58.142 55.000 0.00 0.00 0.00 3.58
2613 2789 0.463620 GCCTCTCCCTGACATCTGAC 59.536 60.000 0.00 0.00 0.00 3.51
2614 2790 0.041684 TGCCTCTCCCTGACATCTGA 59.958 55.000 0.00 0.00 0.00 3.27
2615 2791 0.464870 CTGCCTCTCCCTGACATCTG 59.535 60.000 0.00 0.00 0.00 2.90
2616 2792 0.042431 ACTGCCTCTCCCTGACATCT 59.958 55.000 0.00 0.00 0.00 2.90
2617 2793 1.410882 GTACTGCCTCTCCCTGACATC 59.589 57.143 0.00 0.00 0.00 3.06
2618 2794 1.007721 AGTACTGCCTCTCCCTGACAT 59.992 52.381 0.00 0.00 0.00 3.06
2619 2795 0.409876 AGTACTGCCTCTCCCTGACA 59.590 55.000 0.00 0.00 0.00 3.58
2620 2796 1.562783 AAGTACTGCCTCTCCCTGAC 58.437 55.000 0.00 0.00 0.00 3.51
2621 2797 2.327325 AAAGTACTGCCTCTCCCTGA 57.673 50.000 0.00 0.00 0.00 3.86
2622 2798 3.425162 AAAAAGTACTGCCTCTCCCTG 57.575 47.619 0.00 0.00 0.00 4.45
2639 2815 5.339177 CATGCGTATAATCCACTGCAAAAA 58.661 37.500 0.00 0.00 35.78 1.94
2640 2816 4.733230 GCATGCGTATAATCCACTGCAAAA 60.733 41.667 0.00 0.00 35.78 2.44
2641 2817 3.243035 GCATGCGTATAATCCACTGCAAA 60.243 43.478 0.00 0.00 35.78 3.68
2642 2818 2.290367 GCATGCGTATAATCCACTGCAA 59.710 45.455 0.00 0.00 35.78 4.08
2643 2819 1.872952 GCATGCGTATAATCCACTGCA 59.127 47.619 0.00 0.00 36.69 4.41
2644 2820 1.872952 TGCATGCGTATAATCCACTGC 59.127 47.619 14.09 0.00 0.00 4.40
2645 2821 3.668757 GCATGCATGCGTATAATCCACTG 60.669 47.826 33.99 1.91 44.67 3.66
2646 2822 2.485426 GCATGCATGCGTATAATCCACT 59.515 45.455 33.99 0.00 44.67 4.00
2647 2823 2.855180 GCATGCATGCGTATAATCCAC 58.145 47.619 33.99 6.35 44.67 4.02
2662 2838 0.107081 AGGAGAGAGATGCTGCATGC 59.893 55.000 21.53 11.82 43.25 4.06
2663 2839 1.689813 AGAGGAGAGAGATGCTGCATG 59.310 52.381 21.53 0.00 0.00 4.06
2664 2840 1.965643 GAGAGGAGAGAGATGCTGCAT 59.034 52.381 16.20 16.20 0.00 3.96
2665 2841 1.063792 AGAGAGGAGAGAGATGCTGCA 60.064 52.381 4.13 4.13 0.00 4.41
2666 2842 1.610522 GAGAGAGGAGAGAGATGCTGC 59.389 57.143 0.00 0.00 0.00 5.25
2667 2843 3.144506 GAGAGAGAGGAGAGAGATGCTG 58.855 54.545 0.00 0.00 0.00 4.41
2668 2844 2.779430 TGAGAGAGAGGAGAGAGATGCT 59.221 50.000 0.00 0.00 0.00 3.79
2669 2845 3.213206 TGAGAGAGAGGAGAGAGATGC 57.787 52.381 0.00 0.00 0.00 3.91
2670 2846 4.949238 TGTTTGAGAGAGAGGAGAGAGATG 59.051 45.833 0.00 0.00 0.00 2.90
2671 2847 5.191727 TGTTTGAGAGAGAGGAGAGAGAT 57.808 43.478 0.00 0.00 0.00 2.75
2672 2848 4.649267 TGTTTGAGAGAGAGGAGAGAGA 57.351 45.455 0.00 0.00 0.00 3.10
2673 2849 5.720371 TTTGTTTGAGAGAGAGGAGAGAG 57.280 43.478 0.00 0.00 0.00 3.20
2674 2850 5.186797 GGATTTGTTTGAGAGAGAGGAGAGA 59.813 44.000 0.00 0.00 0.00 3.10
2675 2851 5.046735 TGGATTTGTTTGAGAGAGAGGAGAG 60.047 44.000 0.00 0.00 0.00 3.20
2676 2852 4.840680 TGGATTTGTTTGAGAGAGAGGAGA 59.159 41.667 0.00 0.00 0.00 3.71
2677 2853 5.157940 TGGATTTGTTTGAGAGAGAGGAG 57.842 43.478 0.00 0.00 0.00 3.69
2678 2854 5.494724 CATGGATTTGTTTGAGAGAGAGGA 58.505 41.667 0.00 0.00 0.00 3.71
2679 2855 4.096081 GCATGGATTTGTTTGAGAGAGAGG 59.904 45.833 0.00 0.00 0.00 3.69
2680 2856 4.698780 TGCATGGATTTGTTTGAGAGAGAG 59.301 41.667 0.00 0.00 0.00 3.20
2681 2857 4.654915 TGCATGGATTTGTTTGAGAGAGA 58.345 39.130 0.00 0.00 0.00 3.10
2682 2858 5.578005 ATGCATGGATTTGTTTGAGAGAG 57.422 39.130 0.00 0.00 0.00 3.20
2683 2859 5.988310 AATGCATGGATTTGTTTGAGAGA 57.012 34.783 6.63 0.00 0.00 3.10
2684 2860 8.712285 ATAAAATGCATGGATTTGTTTGAGAG 57.288 30.769 23.72 0.00 0.00 3.20
2685 2861 9.504708 AAATAAAATGCATGGATTTGTTTGAGA 57.495 25.926 23.72 6.23 0.00 3.27
2689 2865 9.694137 CCAAAAATAAAATGCATGGATTTGTTT 57.306 25.926 23.72 21.89 0.00 2.83
2690 2866 8.858094 ACCAAAAATAAAATGCATGGATTTGTT 58.142 25.926 23.72 18.17 0.00 2.83
2691 2867 8.406730 ACCAAAAATAAAATGCATGGATTTGT 57.593 26.923 23.72 16.05 0.00 2.83


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

AutoCloner maintained by Alex Coulton.